cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5139856.v1
title: A stand-level model derived from National Forest Inventory data to predict periodic annual volume increment of forests in Italy

description: A model was developed for predicting the periodic annual volume increment (PAI) of forests using variables commonly recorded through field surveys or the remote sensing. The model was developed using the Italian National Forest Inventory (INFC2005) data, publicly available at www.inventarioforestale.org. Data from 5707 plots were split into two groups. The first was used for fitting the model; the second was used for cross validation. Model reliability for applications at the local, in the Alpine and Mediterranean regions, and at the country level was tested. A sensitivity analysis was carried out to investigate the effects of entering inaccurate values of the number of trees per hectare, one of the predictors of the final model, that may occur in case of biased estimates from the remote sensing. During model calibration, the highest proportion of increment variation was captured using forest category (FC) as dummy variable and, in this respect, this study supports the classification of forests on ecological basis as a stratification criterion in environmental sampling. The model explained 72% of PAI and it predicted annual increment at plot level with no statistical difference to the observed value in any FC, at the country level.
DOI: 10.6084/m9.figshare.5139796
title: Supplementary Material for: The Effects of an Internet-Based Imagery Rehearsal Intervention: A Randomized Controlled Trial

description: <b><i>Background:</i></b> Nightmares are extremely dysphoric dreams, which are prevalent and associated with psychological strain. This study investigated (a) the efficacy of an internet-based imagery rehearsal therapy (IRT), (b) the role of imagery rescription, and (c) the role of guidance during internet-based IRT. <b><i>Methods:</i></b> A total of 127 patients suffering from mainly idiopathic nightmares were randomly assigned to 1 of 2 IRT internet-based groups (guided IRT; unguided IRT) or to 1 of 2 active control groups (frequency control group; narrative control group). <b><i>Results:</i></b> IRT was more effective than a nightmare frequency control condition with respect to nightmare frequency and nightmare distress. Compared to the narrative control group, IRT was only superior in improving nightmare distress but not in nightmare frequency because the narrative control group also improved regarding nightmare frequency. Guidance by a nightmare coach did not affect efficacy, compliance, or dropout. <b><i>Conclusion:</i></b> Internet-based IRT seems to be an effective treatment even when offered with minimal guidance by a nightmare coach. Describing the nightmare narrative in detail already decreased nightmare frequency. However, with regard to inducing decreases in nightmare frequency and nightmare distress, IRT was superior to the narrative control group. The results are discussed with reference to the mastery hypothesis.
DOI: 10.6084/m9.figshare.5139817
title: Supplementary Material for: Integrative Assessment of Pretreatment Inflammation-, Nutrition-, and Muscle-Based Prognostic Markers in Patients with Muscle-Invasive Bladder Cancer Undergoing Radical Cystectomy

description: <b><i>Objective:</i></b> The present study evaluated the clinical relevance of an integrative preoperative assessment of inflammation-, nutrition-, and muscle-based markers for patients with muscle-invasive bladder cancer (MIBC) undergoing curative radical cystectomy (RC). <b><i>Methods:</i></b> The analysis enrolled 117 patients and the variables included age, body mass index (BMI), neutrophil-to-lymphocyte ratio, monocyte-to-lymphocyte ratio, platelet-to-lymphocyte ratio, modified Glasgow Prognostic Score (mGPS), prognostic nutritional index (PNI), Controlling Nutritional Status score, psoas muscle index (PMI), and peak expiratory flow (PEF). The correlations among the variables were evaluated and their prognostic values after RC were tested. <b><i>Results:</i></b> Three inflammation markers (ratios of blood cell counts) were positively correlated (<i>p</i> &lt; 0.0001). The PNI and the BMI were positively correlated (<i>p</i> = 0.04), although they were inversely correlated with the three inflammation markers (<i>p</i> &lt; 0.0001). Age was not significantly correlated with the inflammation markers and PMI, although older age was associated with lower PNI and lower PEF. The disease-specific survival was independently predicted by T4 tumor, positive N status, and decreased PNI. Overall survival was independently predicted by T4 tumor, mGPS, and pretreatment sarcopenia status. <b><i>Conclusions:</i></b> The inflammation-, nutrition-, and muscle-based markers would be useful risk assessment tools for MIBC.
DOI: 10.6084/m9.figshare.5139844.v1
title: Supplementary Material for: Uniparental Disomy of Chromosome 15 in Two Cases by Chromosome Microarray: A Lesson Worth Thinking

description: Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurogenetic disorders caused by loss of function of the imprinted genes at 15q11q13. A 5-7 Mb paternal/maternal deletion of chromosomal region 15q11.2q13 is the major genetic cause of PWS/AS, but in a small group of patients, the PWS/AS phenotype can result from maternal/paternal uniparental disomy (UPD) of chromosome 15. Various mechanisms leading to UPD include gametic complementation, trisomy rescue, and compensatory UPD, which can be inferred from the pattern of uniparental heterodisomy (heteroUPD) or uniparental isodisomy (isoUPD). However, heteroUPD and isoUPD, especially mixed heteroUPD and isoUPD, are very rare in patients with PWS/AS. Here, we report 2 children with PWS/AS caused by mixed segmental heteroUPD 15 and isoUPD 15 which failed to be identified by chromosome microarray (CMA) but could be detected by other molecular genetic methods. The present report unravels the mechanism of mixed iso/heteroUPD 15 in PWS/AS and phenotype-genotype correlations. Moreover, our study suggests that CMA is prone to misdiagnosis for imprinting disorders such as PWS/AS, though it is considered a highly useful tool for copy number variations. As a result, other molecular detection methods, such as methylation analysis and STR marker analysis for UPD, should be supplementary used in this situation.
DOI: 10.6084/m9.figshare.5139706
title: DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis?

description: DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis?
DOI: 10.6084/m9.figshare.5139694
title: Nitrogen and phosphorus treatment of marine wastewater by a laboratory-scale sequencing batch reactor with eco-friendly marine high-efficiency sediment

description: We screened and identified a NH<sub>3</sub>–N-removing bacterial strain, <i>Bacillus</i> sp. KGN1, and a removing strain, <i>Vibrio</i> sp. KGP1, from 960 indigenous marine isolates from seawater and marine sediment from Tongyeong, South Korea. We developed eco-friendly high-efficiency marine sludge (eco-HEMS), and inoculated these marine bacterial strains into the marine sediment. A laboratory-scale sequencing batch reactor (SBR) system using the eco-HEMS for marine wastewater from land-based fish farms improved the treatment performance as indicated by 88.2% removal efficiency (RE) of total nitrogen (initial: 5.6 mg/L) and 90.6% RE of total phosphorus (initial: 1.2 mg/L) under the optimal operation conditions (food and microorganism (F/M) ratio, 0.35 g SCOD<sub>Cr</sub>/g mixed liquor volatile suspended solids (MLVSS)·d; dissolved oxygen (DO) 1.0 ± 0.2 mg/L; hydraulic retention time (HRT), 6.6 h; solids retention time (SRT), 12 d). The following kinetic parameters were obtained: cell yield (<i>Y</i>), 0.29 g MLVSS/g SCOD<sub>Cr</sub>; specific growth rate (<i>µ</i>), 0.06 d<sup>−1</sup>; specific nitrification rate (SNR), 0.49 mg NH<sub>3</sub>–N/g MLVSS·h; specific denitrification rate (SDNR), 0.005 mg /g MLVSS·h; specific phosphorus uptake rate (SPUR), 0.12 mg /g MLVSS·h. The nitrogen- and phosphorus-removing bacterial strains comprised 18.4% of distribution rate in the microbial community of eco-HEMS under the optimal operation conditions. Therefore, eco-HEMS effectively removed nitrogen and phosphorus from highly saline marine wastewater from land-based fish farms with improving SNR, SDNR, and SPUR values in more diverse microbial communities. <b>Abbreviations:</b> DO: dissolved oxygen; Eco-HEMS: eco-friendly high efficiency marine sludge; F/M: food and microorganism ratio; HRT: hydraulic retention time; ML(V)SS: mixed liquor (volatile) suspended solids; NCBI: National Center for Biotechnology Information; ND: not determined; qPCR: quantitative real-time polymerase chain reaction; RE: removal efficiency; SBR: sequencing batch reactor; SD: standard deviation; SDNR: specific denitrification rate; SNR: specific nitrification rate; SPUR: specific phosphate uptake rate; SRT: solids retention time; T-N: total nitrogen; T-P: total phosphorus; (V)SS: (volatile) suspended solids; w.w.: wet weight
DOI: 10.6084/m9.figshare.5139706.v1
title: DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis?

description: DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis?
DOI: 10.6084/m9.figshare.5139694.v1
title: Nitrogen and phosphorus treatment of marine wastewater by a laboratory-scale sequencing batch reactor with eco-friendly marine high-efficiency sediment

description: We screened and identified a NH<sub>3</sub>–N-removing bacterial strain, <i>Bacillus</i> sp. KGN1, and a removing strain, <i>Vibrio</i> sp. KGP1, from 960 indigenous marine isolates from seawater and marine sediment from Tongyeong, South Korea. We developed eco-friendly high-efficiency marine sludge (eco-HEMS), and inoculated these marine bacterial strains into the marine sediment. A laboratory-scale sequencing batch reactor (SBR) system using the eco-HEMS for marine wastewater from land-based fish farms improved the treatment performance as indicated by 88.2% removal efficiency (RE) of total nitrogen (initial: 5.6 mg/L) and 90.6% RE of total phosphorus (initial: 1.2 mg/L) under the optimal operation conditions (food and microorganism (F/M) ratio, 0.35 g SCOD<sub>Cr</sub>/g mixed liquor volatile suspended solids (MLVSS)·d; dissolved oxygen (DO) 1.0 ± 0.2 mg/L; hydraulic retention time (HRT), 6.6 h; solids retention time (SRT), 12 d). The following kinetic parameters were obtained: cell yield (<i>Y</i>), 0.29 g MLVSS/g SCOD<sub>Cr</sub>; specific growth rate (<i>µ</i>), 0.06 d<sup>−1</sup>; specific nitrification rate (SNR), 0.49 mg NH<sub>3</sub>–N/g MLVSS·h; specific denitrification rate (SDNR), 0.005 mg /g MLVSS·h; specific phosphorus uptake rate (SPUR), 0.12 mg /g MLVSS·h. The nitrogen- and phosphorus-removing bacterial strains comprised 18.4% of distribution rate in the microbial community of eco-HEMS under the optimal operation conditions. Therefore, eco-HEMS effectively removed nitrogen and phosphorus from highly saline marine wastewater from land-based fish farms with improving SNR, SDNR, and SPUR values in more diverse microbial communities. <b>Abbreviations:</b> DO: dissolved oxygen; Eco-HEMS: eco-friendly high efficiency marine sludge; F/M: food and microorganism ratio; HRT: hydraulic retention time; ML(V)SS: mixed liquor (volatile) suspended solids; NCBI: National Center for Biotechnology Information; ND: not determined; qPCR: quantitative real-time polymerase chain reaction; RE: removal efficiency; SBR: sequencing batch reactor; SD: standard deviation; SDNR: specific denitrification rate; SNR: specific nitrification rate; SPUR: specific phosphate uptake rate; SRT: solids retention time; T-N: total nitrogen; T-P: total phosphorus; (V)SS: (volatile) suspended solids; w.w.: wet weight
DOI: 10.6084/m9.figshare.5139613
title: surveyRawData.csv

description: Anonymous online survey for the publication: Percentage-based Author Contribution Index: a universal measure of author contribution to scientific articles (https://researchintegrityjournal.biomedcentral.com/articles/10.1186/s41073-017-0042-y)
DOI: 10.6084/m9.figshare.5139553
title: Visualização de Dados Meteorológicos

description: PDF output of LaTeX document for the 4-hour minicourse given to undergraduate students in Environmental Engineering. Data files will be uploaded at a later time.<br>
DOI: 10.6084/m9.figshare.5139613.v1
title: surveyRawData.csv

description: Anonymous online survey
DOI: 10.6084/m9.figshare.5139505
title: Supplementary material for: Scaling range sizes to threats for robust predictions of risks to biodiversity

description: Supplementary material for: Scaling range sizes to threats for robust predictions of risks to biodiversity.<br>R code for estimating Area of Occupancy accounting for uncertainty in the location of grid origin. See the R package 'redlistr' for maintained version. https://cran.r-project.org/package=redlistr <br>Raster files of a simulated landscape with six distribution patterns (30 .tif files)<br>For further information see:<br>Keith, D. A., Akçakaya, H. R. and Murray, N. J. (2017), Scaling range sizes to threats for robust predictions of risks to biodiversity. Conservation Biology. doi:10.1111/cobi.12988<br><br>
DOI: 10.6084/m9.figshare.5139505.v1
title: Supplementary material for: Scaling range sizes to threats for robust predictions of risks to biodiversity

description: Supplementary material for: Scaling range sizes to threats for robust predictions of risks to biodiversity.<br>R code for estimating Area of Occupancy accounting for uncertainty in the location of grid origin. See the R package 'redlistr' for maintained version. https://cran.r-project.org/package=redlistr <br>Raster files of a simulated landscape with six distribution patterns (30 .tif files)<br>For further information see:<br>Keith, D. A., Akçakaya, H. R. and Murray, N. J. (2017), Scaling range sizes to threats for robust predictions of risks to biodiversity. Conservation Biology. doi:10.1111/cobi.12988<br><br>
DOI: 10.6084/m9.figshare.5139475
title: The fishes of Bukwa, Uganda, a lower Miocene (Burdigalian) locality of East Africa

description: Renewed research at the early Miocene fossil site of Bukwa in northeastern Uganda has resulted in new fossil finds, including fish, with representatives of two families, Cichlidae and Alestidae. Although the two families were previously briefly reported from Bukwa, we here give a more detailed account of the fishes based on newly collected material. The cichlid material, mainly composed of vertebrae, can be tentatively assigned to one or more species of Pseudocrenilabrinae. The alestid material, comprising a diversity of teeth, likely represents several different species of <i>Alestes, Brycinus</i>, and/or <i>Bryconaethiops</i>. Although the ichthyofaunal diversity of Bukwa is low, the fishes are important for indicating the paleoenvironment and hydrographic connections of Bukwa. The early Miocene was a critical time for African faunas, because it was during this time that the Afro-Arabian and Eurasian plates came into contact with one another, ending the long isolation of Africa, which, along with rifting in East Africa, created new terrestrial and hydrological connections allowing faunal interchanges. Bukwa is one of only a few African early Miocene localities known that sample fish and, based on these fish, the site probably represents an area of interconnected lakes and large rivers, including floodplains. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Murray, A. M., T. Argyriou, S. Cote, and L. MacLatchy. 2017. The fishes of Bukwa, Uganda, a lower Miocene (Burdigalian) locality of East Africa. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1324460.
DOI: 10.6084/m9.figshare.5139478
title: Virtual reexamination of a plesiosaurian specimen (Reptilia, Plesiosauria) from the Late Cretaceous (Turonian) of Goulmima, Morocco, using computed tomography

description: Turonian deposits of the Goulmima area, Er-Rachidia Province in southern Morocco, have yielded a diverse marine vertebrate fauna, including chondrichthyans, bony fishes, and large marine reptiles such as plesiosaurians, mosasauroids, and turtles. These fossils are included in ovoid calcareous nodules that are difficult to prepare. Moreover, bones may be partially or totally dissolved, making their study difficult. Using computed tomography, we have reconstructed the entire skull anatomy of SMNS 81783, one of the rare plesiosaurian specimens found in this locality and more generally in Africa. The digital three-dimensional reconstruction of the skull and the mandible offers for the first time the possibility to describe this specimen exhaustively. The new anatomical characters recorded confirm that SMNS 81783 belongs to Elasmosauridae on the basis of (1) slender and triangular skull; (2) beak index equal to 42%; (3) temporal fossa estimated to occupy about 40% of the skull length; (4) long process of the premaxillae extending posteriorly to meet the parietal above the orbit and separating the frontals; and (5) margin of the temporal fenestra lacking obvious contribution from the frontal. A preliminary phylogenetic analysis confirms its elasmosaurid affinity. The relationships between SMNS 81783, <i>Libonectes atlasense</i>, and <i>Libonectes morgani</i>, as well as the presence of stapes and pineal foramen, are discussed. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Allemand, R., N. Bardet, A. Houssaye, and P. Vincent. 2017. Virtual reexamination of a plesiosaurian specimen (Reptilia, Plesiosauria) from the Late Cretaceous (Turonian) of Goulmima, Morocco, using computed tomography. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1325894.
DOI: 10.6084/m9.figshare.5139478.v1
title: Virtual reexamination of a plesiosaurian specimen (Reptilia, Plesiosauria) from the Late Cretaceous (Turonian) of Goulmima, Morocco, using computed tomography

description: Turonian deposits of the Goulmima area, Er-Rachidia Province in southern Morocco, have yielded a diverse marine vertebrate fauna, including chondrichthyans, bony fishes, and large marine reptiles such as plesiosaurians, mosasauroids, and turtles. These fossils are included in ovoid calcareous nodules that are difficult to prepare. Moreover, bones may be partially or totally dissolved, making their study difficult. Using computed tomography, we have reconstructed the entire skull anatomy of SMNS 81783, one of the rare plesiosaurian specimens found in this locality and more generally in Africa. The digital three-dimensional reconstruction of the skull and the mandible offers for the first time the possibility to describe this specimen exhaustively. The new anatomical characters recorded confirm that SMNS 81783 belongs to Elasmosauridae on the basis of (1) slender and triangular skull; (2) beak index equal to 42%; (3) temporal fossa estimated to occupy about 40% of the skull length; (4) long process of the premaxillae extending posteriorly to meet the parietal above the orbit and separating the frontals; and (5) margin of the temporal fenestra lacking obvious contribution from the frontal. A preliminary phylogenetic analysis confirms its elasmosaurid affinity. The relationships between SMNS 81783, <i>Libonectes atlasense</i>, and <i>Libonectes morgani</i>, as well as the presence of stapes and pineal foramen, are discussed. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Allemand, R., N. Bardet, A. Houssaye, and P. Vincent. 2017. Virtual reexamination of a plesiosaurian specimen (Reptilia, Plesiosauria) from the Late Cretaceous (Turonian) of Goulmima, Morocco, using computed tomography. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1325894.
DOI: 10.6084/m9.figshare.5139475.v1
title: The fishes of Bukwa, Uganda, a lower Miocene (Burdigalian) locality of East Africa

description: Renewed research at the early Miocene fossil site of Bukwa in northeastern Uganda has resulted in new fossil finds, including fish, with representatives of two families, Cichlidae and Alestidae. Although the two families were previously briefly reported from Bukwa, we here give a more detailed account of the fishes based on newly collected material. The cichlid material, mainly composed of vertebrae, can be tentatively assigned to one or more species of Pseudocrenilabrinae. The alestid material, comprising a diversity of teeth, likely represents several different species of <i>Alestes, Brycinus</i>, and/or <i>Bryconaethiops</i>. Although the ichthyofaunal diversity of Bukwa is low, the fishes are important for indicating the paleoenvironment and hydrographic connections of Bukwa. The early Miocene was a critical time for African faunas, because it was during this time that the Afro-Arabian and Eurasian plates came into contact with one another, ending the long isolation of Africa, which, along with rifting in East Africa, created new terrestrial and hydrological connections allowing faunal interchanges. Bukwa is one of only a few African early Miocene localities known that sample fish and, based on these fish, the site probably represents an area of interconnected lakes and large rivers, including floodplains. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Murray, A. M., T. Argyriou, S. Cote, and L. MacLatchy. 2017. The fishes of Bukwa, Uganda, a lower Miocene (Burdigalian) locality of East Africa. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1324460.
DOI: 10.6084/m9.figshare.5139499.v1
title: Certain Answers in SPARQL using Maybe Tables

description: This asset contains code and results of experiments. Instructions to replicate the experiments and to interpret the results are in the README file.
DOI: 10.6084/m9.figshare.5139373
title: Data for Figure 5a

description: Data used for Figure 5a. Describes acid stress response of the safA-ydeO promoter in E. coli in WT and three mutants. Data is from Burton et al. referenced below. <br>
DOI: 10.6084/m9.figshare.5139397
title: Morphology and molecular phylogeny of Trentepohliales (Chlorophyta) from China

description: The order Trentepohliales is composed of a complex of five aerial genera of branched filamentous green algae, <i>Trentepohlia, Printzina, Phycopeltis</i>, <i>Cephaleuros</i> and <i>Stomatochroon</i>; polyphyly has been discovered in some of these genera and species. To clarify the diversity and some taxonomic problems in the Trentepohliales, we collected specimens from southern China and successfully cultured the majority of them. We carefully observed morphological traits and performed phylogenetic analyses based on new 18S and ITS rDNA sequences obtained during the present study. Our results suggested that the ostiole position of the zoosporangia might effectively indicate the main lineages of Trentepohliales, with reassessment of the genera <i>Trentepohlia</i> and <i>Printzina</i> required based on this ostiole positioning. However, further molecular investigation, particularly for the genus <i>Phycopeltis</i>, is required. Phenotypic plasticity was very common in <i>Trentepohlia</i> and <i>Cephaleuros</i> and the traditionally circumscribed taxa may not be reliable. In <i>Cephaleuros</i>, the lichenized species do not form a single clade and most species are paraphyletic. Additionally, we suggest that a lack of description of the internal systems could be one reason for the difficulties in species identification. Further taxonomic studies should focus on an emendation of <i>Cephaleuros</i> and elucidating the molecular diversity of <i>Phycopeltis</i>.