cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1254974.v2
title: Effects of Data Sparsity and Spatiotemporal Variability on Hazard Maps of Workplace Noise

description: Personal sampling, considered a state-of-the-art technique to assess worker exposures to occupational hazards, is often conducted for the duration of a work shift so that time-weighted average (TWA) exposures may be evaluated relative to published occupational exposure limits (OELs). Such cross-shift measurements, however, provide little information on the spatial variability of exposures, except after a very large number of samples. Hazard maps, contour plots (or similar depiction) of hazard intensity throughout the workplace, have gained popularity as a way to locate sources and to visualize spatial variability of physical and chemical hazards within a facility. However, these maps are often generated from short duration measures and have little ability to assess temporal variability. To assess the potential bias that results from the use of short-duration measurements to represent the TWA in a hazard map, noise intensity measurements were collected at high spatial and temporal resolution in two facilities. Static monitors were distributed throughout the facility and used to capture the temporal variability at these locations. Roving monitors (typical of the hazard mapping process) captured spatial variability over multiple traverses through the facility. The differences in hazards maps generated with different sampling techniques were evaluated. Hazard maps produced from sparse, roving monitor data were in good agreement with the TWA hazard maps at the facility with low temporal variability. Estimated values were within 5 dB of the TWA over approximately 90% of the facility. However, at the facility with higher temporal variability, large differences between hazard maps were observed for different traverses through the facility. On the second day of sampling, estimates were at least 5 dB different than the TWA for more than half of the locations within the facility. The temporal variability of noise was found to have a greater influence on map accuracy than the spatial sampling resolution.
DOI: 10.6084/m9.figshare.1258895
title: Data from: Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy

description: The data file of describles the clinicopathological features, genotypes and prognosis of all the patients analyzed in the paper "Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy".
DOI: 10.6084/m9.figshare.1258895.v2
title: Data from: Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy

description: The data file of describles the clinicopathological features, genotypes and prognosis of all the patients analyzed in the paper "Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy".
DOI: 10.6084/m9.figshare.1258895.v1
title: patients and SNPs

description: The data file of describles the clinicopathological features, genotypes and prognosis of all the patients analyzed in the paper "Oxidative stress-related genetic polymorphisms are associated with the prognosis of metastatic gastric cancer patients treated with epirubicin, oxaliplatin and 5-fluorouracil combination chemotherapy".
DOI: 10.6084/m9.figshare.1263505
title: A subduction-related metasomatically enriched mantle origin for the Luoboling and Zhongliao Cretaceous granitoids from South China: implications for magma evolution and Cu–Mo mineralization

description: The Luoboling granodiorite porphyry and Zhongliao porphyritic biotite-granodiorite occur within the Zijinshan ore field in Fujian Province, southeast China. LA–ICP–MS zircon U–Pb dating yields ages of 103.1 ± 1.1 Ma (2σ, MSWD = 3.1) and 95.9 ± 0.6 Ma (2σ, MSWD = 1.2) for the Luoboling and Zhongliao intrusions, respectively. All rocks show high SiO<sub>2</sub>, K<sub>2</sub>O, and light rare earth element levels, variable CaO and Fe<sub>2</sub>O<sub>3</sub><sup>T</sup>, but low heavy rare earth element and high field strength element (Nb, Ta, Ti) concentrations. They also exhibit uniform initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7064–0.7068) and ε<sub>Nd</sub>(t) values (−4.0 to −2.6), falling within the compositional field of Cretaceous basalts and mafic dikes in the Cathaysia Block. Together with their relatively high Hf isotopic ratios (ε<sub>Hf</sub>(t) = −5.8 to +0.7), these data suggest that the Luoboling and Zhongliao intrusions were derived from a subduction-enriched mantle source. We infer fractional crystallization processes involving early fractionation of clinopyroxene and olivine, and subsequent fractionation of garnet forming the Luoboling granodiorite porphyry, eventually followed by amphibole- and biotite-dominated crystallization, with minor accessory mineral contribution, producing the (younger) Zhongliao porphyritic biotite-granodiorite. Asthenospheric mantle sources may have also contributed to generating the melts as indicated by initial Pb isotopic compositions and Hf isotopic compositions. The generation of these intrusions was associated with the Pacific subduction in an extensional setting during the Cretaceous.
DOI: 10.6084/m9.figshare.1263505.v2
title: A subduction-related metasomatically enriched mantle origin for the Luoboling and Zhongliao Cretaceous granitoids from South China: implications for magma evolution and Cu–Mo mineralization

description: The Luoboling granodiorite porphyry and Zhongliao porphyritic biotite-granodiorite occur within the Zijinshan ore field in Fujian Province, southeast China. LA–ICP–MS zircon U–Pb dating yields ages of 103.1 ± 1.1 Ma (2σ, MSWD = 3.1) and 95.9 ± 0.6 Ma (2σ, MSWD = 1.2) for the Luoboling and Zhongliao intrusions, respectively. All rocks show high SiO<sub>2</sub>, K<sub>2</sub>O, and light rare earth element levels, variable CaO and Fe<sub>2</sub>O<sub>3</sub><sup>T</sup>, but low heavy rare earth element and high field strength element (Nb, Ta, Ti) concentrations. They also exhibit uniform initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7064–0.7068) and ε<sub>Nd</sub>(t) values (−4.0 to −2.6), falling within the compositional field of Cretaceous basalts and mafic dikes in the Cathaysia Block. Together with their relatively high Hf isotopic ratios (ε<sub>Hf</sub>(t) = −5.8 to +0.7), these data suggest that the Luoboling and Zhongliao intrusions were derived from a subduction-enriched mantle source. We infer fractional crystallization processes involving early fractionation of clinopyroxene and olivine, and subsequent fractionation of garnet forming the Luoboling granodiorite porphyry, eventually followed by amphibole- and biotite-dominated crystallization, with minor accessory mineral contribution, producing the (younger) Zhongliao porphyritic biotite-granodiorite. Asthenospheric mantle sources may have also contributed to generating the melts as indicated by initial Pb isotopic compositions and Hf isotopic compositions. The generation of these intrusions was associated with the Pacific subduction in an extensional setting during the Cretaceous.
DOI: 10.6084/m9.figshare.1263505.v1
title: A subduction-related metasomatically enriched mantle origin for the Luoboling and Zhongliao Cretaceous granitoids from South China: implications for magma evolution and Cu–Mo mineralization

description: The Luoboling granodiorite porphyry and Zhongliao porphyritic biotite-granodiorite occur within the Zijinshan ore field in Fujian Province, southeast China. LA–ICP–MS zircon U–Pb dating yields ages of 103.1 ± 1.1 Ma (2σ, MSWD = 3.1) and 95.9 ± 0.6 Ma (2σ, MSWD = 1.2) for the Luoboling and Zhongliao intrusions, respectively. All rocks show high SiO<sub>2</sub>, K<sub>2</sub>O, and light rare earth element levels, variable CaO and Fe<sub>2</sub>O<sub>3</sub><sup>T</sup>, but low heavy rare earth element and high field strength element (Nb, Ta, Ti) concentrations. They also exhibit uniform initial <sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7064–0.7068) and ε<sub>Nd</sub>(t) values (−4.0 to −2.6), falling within the compositional field of Cretaceous basalts and mafic dikes in the Cathaysia Block. Together with their relatively high Hf isotopic ratios (ε<sub>Hf</sub>(t) = −5.8 to +0.7), these data suggest that the Luoboling and Zhongliao intrusions were derived from a subduction-enriched mantle source. We infer fractional crystallization processes involving early fractionation of clinopyroxene and olivine, and subsequent fractionation of garnet forming the Luoboling granodiorite porphyry, eventually followed by amphibole- and biotite-dominated crystallization, with minor accessory mineral contribution, producing the (younger) Zhongliao porphyritic biotite-granodiorite. Asthenospheric mantle sources may have also contributed to generating the melts as indicated by initial Pb isotopic compositions and Hf isotopic compositions. The generation of these intrusions was associated with the Pacific subduction in an extensional setting during the Cretaceous.
DOI: 10.6084/m9.figshare.1263573
title: The survival motor neuron gene <i>smn-1</i> interacts with the U2AF large subunit gene <i>uaf-1</i> to regulate <i>Caenorhabditis elegans</i> lifespan and motor functions

description: Spinal muscular atrophy (SMA), the most frequent human congenital motor neuron degenerative disease, is caused by loss-of-function mutations in the highly conserved survival motor neuron gene <i>SMN1</i>. Mutations in <i>SMN</i> could affect several molecular processes, among which aberrant pre-mRNA splicing caused by defective snRNP biogenesis is hypothesized as a major cause of SMA. To date little is known about the interactions of <i>SMN</i> with other splicing factor genes and how SMN affects splicing <i>in vivo</i>. The nematode <i>Caenorhabditis elegans</i> carries a single ortholog of <i>SMN</i>, <i>smn-1</i>, and has been used as a model for studying the molecular functions of SMN. We analyzed RNA splicing of reporter genes in an <i>smn-1</i> deletion mutant and found that <i>smn-1</i> is required for efficient splicing at weak 3′ splice sites. Genetic studies indicate that the defective lifespan and motor functions of the <i>smn-1</i> deletion mutants could be significantly improved by mutations of the splicing factor U2AF large subunit gene <i>uaf-1</i>. In <i>smn-1</i> mutants we detected a reduced expression of U1 and U5 snRNAs and an increased expression of U2, U4 and U6 snRNAs. Our study verifies an essential role of <i>smn-1</i> for RNA splicing <i>in vivo</i>, identifies the <i>uaf-1</i> gene as a potential genetic modifier of <i>smn-1</i> mutants, and suggests that SMN-1 has multifaceted effects on the expression of spliceosomal snRNAs.
DOI: 10.6084/m9.figshare.1263573.v1
title: The survival motor neuron gene <i>smn-1</i> interacts with the U2AF large subunit gene <i>uaf-1</i> to regulate <i>Caenorhabditis elegans</i> lifespan and motor functions

description: Spinal muscular atrophy (SMA), the most frequent human congenital motor neuron degenerative disease, is caused by loss-of-function mutations in the highly conserved survival motor neuron gene <i>SMN1</i>. Mutations in <i>SMN</i> could affect several molecular processes, among which aberrant pre-mRNA splicing caused by defective snRNP biogenesis is hypothesized as a major cause of SMA. To date little is known about the interactions of <i>SMN</i> with other splicing factor genes and how SMN affects splicing <i>in vivo</i>. The nematode <i>Caenorhabditis elegans</i> carries a single ortholog of <i>SMN</i>, <i>smn-1</i>, and has been used as a model for studying the molecular functions of SMN. We analyzed RNA splicing of reporter genes in an <i>smn-1</i> deletion mutant and found that <i>smn-1</i> is required for efficient splicing at weak 3’ splice sites. Genetic studies indicate that the defective lifespan and motor functions of the <i>smn-1</i> deletion mutants could be significantly improved by mutations of the splicing factor U2AF large subunit gene <i>uaf-1</i>. In <i>smn-1</i> mutants we detected a reduced expression of U1 and U5 snRNAs and an increased expression of U2, U4 and U6 snRNAs. Our study verifies an essential role of <i>smn-1</i> for RNA splicing <i>in vivo</i>, identifies the <i>uaf-1</i> gene as a potential genetic modifier of <i>smn-1</i> mutants, and suggests that SMN-1 has multifaceted effects on the expression of spliceosomal snRNAs.
DOI: 10.6084/m9.figshare.1263573.v2
title: The survival motor neuron gene <i>smn-1</i> interacts with the U2AF large subunit gene <i>uaf-1</i> to regulate <i>Caenorhabditis elegans</i> lifespan and motor functions

description: Spinal muscular atrophy (SMA), the most frequent human congenital motor neuron degenerative disease, is caused by loss-of-function mutations in the highly conserved survival motor neuron gene <i>SMN1</i>. Mutations in <i>SMN</i> could affect several molecular processes, among which aberrant pre-mRNA splicing caused by defective snRNP biogenesis is hypothesized as a major cause of SMA. To date little is known about the interactions of <i>SMN</i> with other splicing factor genes and how SMN affects splicing <i>in vivo</i>. The nematode <i>Caenorhabditis elegans</i> carries a single ortholog of <i>SMN</i>, <i>smn-1</i>, and has been used as a model for studying the molecular functions of SMN. We analyzed RNA splicing of reporter genes in an <i>smn-1</i> deletion mutant and found that <i>smn-1</i> is required for efficient splicing at weak 3′ splice sites. Genetic studies indicate that the defective lifespan and motor functions of the <i>smn-1</i> deletion mutants could be significantly improved by mutations of the splicing factor U2AF large subunit gene <i>uaf-1</i>. In <i>smn-1</i> mutants we detected a reduced expression of U1 and U5 snRNAs and an increased expression of U2, U4 and U6 snRNAs. Our study verifies an essential role of <i>smn-1</i> for RNA splicing <i>in vivo</i>, identifies the <i>uaf-1</i> gene as a potential genetic modifier of <i>smn-1</i> mutants, and suggests that SMN-1 has multifaceted effects on the expression of spliceosomal snRNAs.
DOI: 10.6084/m9.figshare.1263573.v4
title: The survival motor neuron gene <i>smn-1</i> interacts with the U2AF large subunit gene <i>uaf-1</i> to regulate <i>Caenorhabditis elegans</i> lifespan and motor functions

description: Spinal muscular atrophy (SMA), the most frequent human congenital motor neuron degenerative disease, is caused by loss-of-function mutations in the highly conserved survival motor neuron gene <i>SMN1</i>. Mutations in <i>SMN</i> could affect several molecular processes, among which aberrant pre-mRNA splicing caused by defective snRNP biogenesis is hypothesized as a major cause of SMA. To date little is known about the interactions of <i>SMN</i> with other splicing factor genes and how SMN affects splicing <i>in vivo</i>. The nematode <i>Caenorhabditis elegans</i> carries a single ortholog of <i>SMN</i>, <i>smn-1</i>, and has been used as a model for studying the molecular functions of SMN. We analyzed RNA splicing of reporter genes in an <i>smn-1</i> deletion mutant and found that <i>smn-1</i> is required for efficient splicing at weak 3′ splice sites. Genetic studies indicate that the defective lifespan and motor functions of the <i>smn-1</i> deletion mutants could be significantly improved by mutations of the splicing factor U2AF large subunit gene <i>uaf-1</i>. In <i>smn-1</i> mutants we detected a reduced expression of U1 and U5 snRNAs and an increased expression of U2, U4 and U6 snRNAs. Our study verifies an essential role of <i>smn-1</i> for RNA splicing <i>in vivo</i>, identifies the <i>uaf-1</i> gene as a potential genetic modifier of <i>smn-1</i> mutants, and suggests that SMN-1 has multifaceted effects on the expression of spliceosomal snRNAs.
DOI: 10.6084/m9.figshare.1263573.v3
title: The survival motor neuron gene <i>smn-1</i> interacts with the U2AF large subunit gene <i>uaf-1</i> to regulate <i>Caenorhabditis elegans</i> lifespan and motor functions

description: Spinal muscular atrophy (SMA), the most frequent human congenital motor neuron degenerative disease, is caused by loss-of-function mutations in the highly conserved survival motor neuron gene <i>SMN1</i>. Mutations in <i>SMN</i> could affect several molecular processes, among which aberrant pre-mRNA splicing caused by defective snRNP biogenesis is hypothesized as a major cause of SMA. To date little is known about the interactions of <i>SMN</i> with other splicing factor genes and how SMN affects splicing <i>in vivo</i>. The nematode <i>Caenorhabditis elegans</i> carries a single ortholog of <i>SMN</i>, <i>smn-1</i>, and has been used as a model for studying the molecular functions of SMN. We analyzed RNA splicing of reporter genes in an <i>smn-1</i> deletion mutant and found that <i>smn-1</i> is required for efficient splicing at weak 3′ splice sites. Genetic studies indicate that the defective lifespan and motor functions of the <i>smn-1</i> deletion mutants could be significantly improved by mutations of the splicing factor U2AF large subunit gene <i>uaf-1</i>. In <i>smn-1</i> mutants we detected a reduced expression of U1 and U5 snRNAs and an increased expression of U2, U4 and U6 snRNAs. Our study verifies an essential role of <i>smn-1</i> for RNA splicing <i>in vivo</i>, identifies the <i>uaf-1</i> gene as a potential genetic modifier of <i>smn-1</i> mutants, and suggests that SMN-1 has multifaceted effects on the expression of spliceosomal snRNAs.
DOI: 10.6084/m9.figshare.1263577
title: Transcriptome-wide N<sup>6</sup>-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

description: <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m<sup>6</sup>A modification becomes feasible. Here we present a transcriptome-wide m<sup>6</sup>A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m<sup>6</sup>A-modified genes, respectively. The m<sup>6</sup>A peak (m<sup>6</sup>A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m<sup>6</sup>A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m<sup>6</sup>A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m<sup>6</sup>A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m<sup>6</sup>A-modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m<sup>6</sup>A modification.
DOI: 10.6084/m9.figshare.1263577.v1
title: Transcriptome-wide N<sup>6</sup>-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

description: <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m<sup>6</sup>A modification becomes feasible. Here we present a transcriptome-wide m<sup>6</sup>A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m<sup>6</sup>A-modified genes, respectively. The m<sup>6</sup>A peak (m<sup>6</sup>A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m<sup>6</sup>A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m<sup>6</sup>A-modified genes between the two samples, we define 1,792 and 6,508 tissue-specific m<sup>6</sup>A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m<sup>6</sup>A-modified (SMGs) only in one of the two tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further our knowledge on the function of RNA m<sup>6</sup>A modification.
DOI: 10.6084/m9.figshare.1263577.v2
title: Transcriptome-wide N<sup>6</sup>-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

description: <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m<sup>6</sup>A modification becomes feasible. Here we present a transcriptome-wide m<sup>6</sup>A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m<sup>6</sup>A-modified genes, respectively. The m<sup>6</sup>A peak (m<sup>6</sup>A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m<sup>6</sup>A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m<sup>6</sup>A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m<sup>6</sup>A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m<sup>6</sup>A-modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m<sup>6</sup>A modification.