cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5082115.v1
title: Supplementary Material for: A Role of Remote Organs Effect in Acute Kidney Injury Outcome?

description: Acute kidney injury (AKI) has been associated with both short- and long-term outcomes. To date, there is still a debate whether the increase risk of morbidity and mortality is directly due to AKI occurrence. There is, however, a potential causal impact of AKI on outcome, but evidence of this association is yet lacking. The hypothesis of remote organ damage and dysfunction (heart, lung, liver, brain, etc.) has emerged over the last decade and may explain the reason for the potential negative impact of AKI on outcome. The aim of this review was to describe findings concerning the remote effect of AKI in animal models and human studies.
DOI: 10.6084/m9.figshare.5082118
title: Serum values of total testosterone in males.sav

description: This dataset contains variables related to male hormonal parameters; especially AMH and total testosterone values<br>
DOI: 10.21421/d2/nibhau
title: Evaluation of sorghum cultivars to determine their reaction to striga

description: The trial was conducted to evaluate the reaction of different sorghum varieties to striga. Significant losses in sorghum biomass and grain yield occur in sub‐Saharan Africa due to infection by the root‐parasitic weed Striga hermonthica. This trial will assist in selecting striga tolerant varieties that can be cultivated in striga infested fields. The ontents of this data set include the plant height, number of plants that germinated, time to flower, date of maturity, pest and disease scores, grain weight and the yield. The trial was conducted in Alupe (Nairobi) from July, 2018. Data collection began from the second week after planting. Sixteen different sorghum varieties were evaluated.
DOI: 10.6084/m9.figshare.5082118.v1
title: AMH_TT_Men.sav

description: This dataset contains variables related to male hormonal parameters; especially AMH and total testosterone values<br>
DOI: 10.6084/m9.figshare.5082331.v5
title: Fileset "3D fractal dimensions of stony corals" - 3D meshes and raw data

description: The 3D meshes of the stony corals analysed in the publication of Reichert, J; Backes, A.; Schubert, P. & Wilke, T.<strong></strong><strong></strong> (accepted): The power of 3D fractal dimensions for comparative shape and structural complexity analyses of irregularly shaped organisms. Methods in Ecology and Evolution.
DOI: 10.6084/m9.figshare.5082061
title: Supplementary Material for: Ureteroscopic Lithotripsy versus Laparoscopic Ureterolithotomy or Percutaneous Nephrolithotomy in the Management of Large Proximal Ureteral Stones: A Systematic Review and Meta-Analysis

description: <b><i>Objectives:</i></b> To provide a systematic review and meta-analysis of studies comparing ureterolithotripsy (URS) with percutaneous nephrolithotripsy (PCNL) or laparoscopic ureterolithotomy (LU) techniques for the management of large proximal ureteral stones (diameter greater than 10 mm). <b><i>Methods:</i></b> A literature search was performed using PubMed, EMBASE, EBSCO, Web of Science, and Cochrane Library to identify suitable studies until November 2016. We used weighted mean difference to measure operative time and hospital stay, OR to measure stone free rate (SFR), and complication rate. Subgroup analyses were assessed for heterogeneity. <b><i>Results:</i></b> Fourteen publications strictly met our eligibility criteria of which 7 were randomized control studies (RCTs) and 7 non-RCTs. Meta-analysis of extractable data showed that LU and PCNL had higher SFR than URS. URS led to a similar hospital stay like that of LU. However, it had a shorter operative time and lower complication rate than LU. When we compared URS with PCNL, we found a shorter hospital stay in the URS group. However, there was no significant difference in terms of the operative time and complication rate between URS and PCNL. <b><i>Conclusion:</i></b> URS should be considered standard therapy for treating large proximal ureteral stones.
DOI: 10.6084/m9.figshare.5082070
title: Supplementary table 1.xlsx

description: Differentially expressed genes (DEGs) between sepsis patients and sepsis+ALI patients.
DOI: 10.6084/m9.figshare.5082064
title: Size-based indicators in the deep sea

description: Supporting data for the paper: Mindel, B.L., Neat, F.C., Webb, T.J. & Blanchard, J.L. Sized-based indicators show depth-dependent change over time in the deep sea. ICES Journal of Marine Science, 2017, DOI 10.1093/icesjms/fsx110.<br>Datasets have been summarised to enable replication of figures and analyses from this paper. Data are provided by Marine Scotland from their ongoing deepwater trawl survey. <br><br>Haul level indicators:Data to produce Fig. 2 A, B, C and Fig. 3 from the paper. Values are given at the level of the haul and include temperature, depth, mean body length, mean maximum length, LFI (proportion of biomass made up of individuals greater than 40 cm in length) and LFI60 (proportion of biomass made up of individuals greater than 60 cm in length). <br>Year level indicators:Slope of the normalised biomass spectrum for each year of the survey (as detailed in the Methods section of the paper) to produce Fig. 2D.
DOI: 10.6084/m9.figshare.5082169.v2
title: Importance of Life Stage Capture in Dragonfly Specimen Digitization

description: Life stage is apparently rarely captured during the digitization of natural history collections, but it can highlight sampling biases, life history changes, and gaps in taxonomy and systematics. Through the digitization of non-adult specimens of clubtail dragonflies, for example, it is possible to identify the taxa that lack diagnostic keys for all life stages. While likely only a small proportion of an entomological collection includes all life stages for a single taxon, the larvae and exuviae (the skin shed upon emergence from the aquatic larval stage to the adult terrestrial stage) can provide a more comprehensive representation of morphological characters for species’ identification and evolutionary questions. Furthermore, recording the life stage of dragonflies in the digitization process enables analysis of the distribution of a dragonfly taxon throughout its life history, which is both aquatic and terrestrial. By digitizing the Gomphidae specimens in collection at the Frost Entomological Museum at Penn State University, proportions of life stages were compared to other digitized collections. This analysis reveals gaps in both keys and collections, as well as the need for increased diagnostic and natural history data for this family.
DOI: 10.6084/m9.figshare.5082064.v1
title: Size-based indicators in the deep sea

description: Supporting data for the paper: Mindel, B.L., Neat, F.C., Webb, T.J. & Blanchard, J.L. Sized-based indicators show depth-dependent change over time in the deep sea. ICES Journal of Marine Science, DOI 10.1093/icesjms/fsx110.<br>Datasets have been summarised to enable replication of figures and analyses from this paper. Data are provided by Marine Scotland from their ongoing deepwater trawl survey. <br><br>Haul level indicators:Data to produce Fig. 2 A, B, C and Fig. 3 from the paper. Values are given at the level of the haul and include temperature, depth, mean body length, mean maximum length, LFI (proportion of biomass made up of individuals greater than 40 cm in length) and LFI60 (proportion of biomass made up of individuals greater than 60 cm in length). <br>Year level indicators:Slope of the normalised biomass spectrum for each year of the survey (as detailed in the Methods section of the paper) to produce Fig. 2D.
DOI: 10.6084/m9.figshare.5082070.v1
title: Supplementary table 1.xlsx

description: Differentially expressed genes (DEGs) between sepsis patients and sepsis+ALI patients.
DOI: 10.6084/m9.figshare.5082055
title: Species Mortality data: infection with S. destruens

description: Mortality data of fish species infected with Sphaerothecum destruens.
DOI: 10.6084/m9.figshare.5082061.v1
title: Supplementary Material for: Ureteroscopic Lithotripsy versus Laparoscopic Ureterolithotomy or Percutaneous Nephrolithotomy in the Management of Large Proximal Ureteral Stones: A Systematic Review and Meta-Analysis

description: <b><i>Objectives:</i></b> To provide a systematic review and meta-analysis of studies comparing ureterolithotripsy (URS) with percutaneous nephrolithotripsy (PCNL) or laparoscopic ureterolithotomy (LU) techniques for the management of large proximal ureteral stones (diameter greater than 10 mm). <b><i>Methods:</i></b> A literature search was performed using PubMed, EMBASE, EBSCO, Web of Science, and Cochrane Library to identify suitable studies until November 2016. We used weighted mean difference to measure operative time and hospital stay, OR to measure stone free rate (SFR), and complication rate. Subgroup analyses were assessed for heterogeneity. <b><i>Results:</i></b> Fourteen publications strictly met our eligibility criteria of which 7 were randomized control studies (RCTs) and 7 non-RCTs. Meta-analysis of extractable data showed that LU and PCNL had higher SFR than URS. URS led to a similar hospital stay like that of LU. However, it had a shorter operative time and lower complication rate than LU. When we compared URS with PCNL, we found a shorter hospital stay in the URS group. However, there was no significant difference in terms of the operative time and complication rate between URS and PCNL. <b><i>Conclusion:</i></b> URS should be considered standard therapy for treating large proximal ureteral stones.
DOI: 10.6084/m9.figshare.5082040
title: Dataset for: Assessing agreement with relative area under the coverage probability curve

description: There has been substantial statistical literature in the last several decades on assessing agreement and coverage probability approach was selected as a preferred index for assessing and improving measurement agreement in a core laboratory setting [1]. With this approach, a satisfactory agreement is based on pre-specified high satisfactory coverage probability (e.g., 95%), given one pre-specified acceptable difference. In practice, we may want to have quality control on more than one pre-specified differences or we may simply want to summarize the agreement based on differences up to a maximum acceptable difference. We propose to assess agreement via the coverage probability curve that provides a full spectrum of measurement error at various differences/disagreement. Relative area under the coverage probability curve is proposed for the summary of overall agreement and this new summary index can be used for comparison of different intra- or inter-methods/labs/observers’ agreement. Simulation studies and a blood pressure example are used for illustration of the methodology.
DOI: 10.6084/m9.figshare.5082031
title: Dataset for: Symbiosis induces widespread changes in the proteome of the model cnidarian <i>Aiptasia</i>

description: Coral reef ecosystems are metabolically founded on the mutualism between corals and photosynthetic dinoflagellates of the genus <i>Symbiodinium</i>. The glass anemone <i>Aiptasia</i> sp. has become a tractable model for this symbiosis, and recent advances in genetic information have enabled the use of mass spectrometry-based proteomics in this model. We utilized label-free liquid chromatography electrospray-ionization tandem mass spectrometry to analyze the effects of symbiosis on the proteomes of symbiotic and aposymbiotic <i>Aiptasia</i>. We identified and obtained relative quantification of more than 3,300 proteins in 1,578 protein clusters, with 81 protein clusters showing significantly different expression between symbiotic states. Symbiotic anemones showed significantly higher expression of proteins involved in lipid storage and transport, nitrogen transport and cycling, intracellular trafficking, endocytosis and inorganic carbon transport. These changes reflect shifts in host metabolism and nutrient reserves due to increased nutritional exchange with the symbionts, as well as mechanisms for supplying inorganic nutrients to the algae. Aposymbiotic anemones exhibited increased expression of multiple systems responsible for mediating reactive oxygen stress, suggesting that the host derives direct or indirect protection from oxidative stress while in symbiosis. Aposymbiotic anemones also increased their expression of an array of proteases and chitinases, indicating a metabolic shift from autotrophy to heterotrophy. These results provide a comprehensive <i>Aiptasia</i> proteome with more direct relative quantification of protein abundance than transcriptomic methods. The extension of “omics” techniques to this model system will allow more powerful studies of coral physiology, ecosystem function, and the effects of biotic and abiotic stress on the coral-dinoflagellate mutualism.
DOI: 10.6084/m9.figshare.5082040.v1
title: Dataset for: Assessing agreement with relative area under the coverage probability curve

description: There has been substantial statistical literature in the last several decades on assessing agreement and coverage probability approach was selected as a preferred index for assessing and improving measurement agreement in a core laboratory setting [1]. With this approach, a satisfactory agreement is based on pre-specified high satisfactory coverage probability (e.g., 95%), given one pre-specified acceptable difference. In practice, we may want to have quality control on more than one pre-specified differences or we may simply want to summarize the agreement based on differences up to a maximum acceptable difference. We propose to assess agreement via the coverage probability curve that provides a full spectrum of measurement error at various differences/disagreement. Relative area under the coverage probability curve is proposed for the summary of overall agreement and this new summary index can be used for comparison of different intra- or inter-methods/labs/observers’ agreement. Simulation studies and a blood pressure example are used for illustration of the methodology.
DOI: 10.6084/m9.figshare.5082055.v1
title: Species Mortality data: infection with S. destruens

description: Mortality data of fish species infected with Sphaerothecum destruens.
DOI: 10.6084/m9.figshare.5082025
title: Dataset for: Q-learning Residual Analysis: Application to The Effectiveness of Sequences of Antipsychotic Medications for Patients with Schizophrenia

description: Q-learning is a regression-based approach that uses longitudinal data to construct dynamic treatment regimes, which are sequences of decision rules that use patient information to inform future treatment decisions. An optimal dynamic treatment regime is composed of a sequence of decision rules that indicate how to {optimally} individualize treatment using the patients' baseline and time-varying characteristics to optimize the final outcome. Constructing optimal dynamic regimes using Q-learning depends heavily on the assumption that regression models at each decision point are correctly specified; yet model checking in the context of Q-learning has been { largely} overlooked in the current literature. In this article, we show that residual plots obtained from standard Q-learning models may fail to adequately check the quality of the model fit. We present a modified Q-learning procedure that accommodates residual analyses using standard tools. We present simulation studies showing the advantage of the proposed modification over standard Q-learning. We illustrate this new Q-learning approach using data collected from a sequential multiple assignment randomized trial of patients with schizophrenia.
DOI: 10.6084/m9.figshare.5082031.v1
title: Dataset for: Symbiosis induces widespread changes in the proteome of the model cnidarian <i>Aiptasia</i>

description: Coral reef ecosystems are metabolically founded on the mutualism between corals and photosynthetic dinoflagellates of the genus <i>Symbiodinium</i>. The glass anemone <i>Aiptasia</i> sp. has become a tractable model for this symbiosis, and recent advances in genetic information have enabled the use of mass spectrometry-based proteomics in this model. We utilized label-free liquid chromatography electrospray-ionization tandem mass spectrometry to analyze the effects of symbiosis on the proteomes of symbiotic and aposymbiotic <i>Aiptasia</i>. We identified and obtained relative quantification of more than 3,300 proteins in 1,578 protein clusters, with 81 protein clusters showing significantly different expression between symbiotic states. Symbiotic anemones showed significantly higher expression of proteins involved in lipid storage and transport, nitrogen transport and cycling, intracellular trafficking, endocytosis and inorganic carbon transport. These changes reflect shifts in host metabolism and nutrient reserves due to increased nutritional exchange with the symbionts, as well as mechanisms for supplying inorganic nutrients to the algae. Aposymbiotic anemones exhibited increased expression of multiple systems responsible for mediating reactive oxygen stress, suggesting that the host derives direct or indirect protection from oxidative stress while in symbiosis. Aposymbiotic anemones also increased their expression of an array of proteases and chitinases, indicating a metabolic shift from autotrophy to heterotrophy. These results provide a comprehensive <i>Aiptasia</i> proteome with more direct relative quantification of protein abundance than transcriptomic methods. The extension of “omics” techniques to this model system will allow more powerful studies of coral physiology, ecosystem function, and the effects of biotic and abiotic stress on the coral-dinoflagellate mutualism.
DOI: 10.6084/m9.figshare.5081998
title: OULAD: Open University Learning Analytics Dataset

description: Open University Learning Analytics Dataset (OULAD) contains data about courses, students and their interactions with Virtual Learning Environment (VLE) for seven selected courses (called modules). Presentations of courses start in February and October - they are marked by “B” and “J” respectively. The dataset consists of tables connected using unique identifiers. All tables are stored in the csv format.<br>
DOI: 10.6084/m9.figshare.5082025.v1
title: Dataset for: Q-learning Residual Analysis: Application to The Effectiveness of Sequences of Antipsychotic Medications for Patients with Schizophrenia

description: Q-learning is a regression-based approach that uses longitudinal data to construct dynamic treatment regimes, which are sequences of decision rules that use patient information to inform future treatment decisions. An optimal dynamic treatment regime is composed of a sequence of decision rules that indicate how to {optimally} individualize treatment using the patients' baseline and time-varying characteristics to optimize the final outcome. Constructing optimal dynamic regimes using Q-learning depends heavily on the assumption that regression models at each decision point are correctly specified; yet model checking in the context of Q-learning has been { largely} overlooked in the current literature. In this article, we show that residual plots obtained from standard Q-learning models may fail to adequately check the quality of the model fit. We present a modified Q-learning procedure that accommodates residual analyses using standard tools. We present simulation studies showing the advantage of the proposed modification over standard Q-learning. We illustrate this new Q-learning approach using data collected from a sequential multiple assignment randomized trial of patients with schizophrenia.
DOI: 10.6084/m9.figshare.5081992
title: Genomic information of strains SH4916 and SH5446

description: Description of the methods used to analyze the high-throughput sequencing information of strains SH4916 and SH5446. Annotated contigs of each of the strains are provided.<br>
DOI: 10.6084/m9.figshare.5081989
title: Biosynthesized gold and silver nanoparticles by aqueous fruit extract of <i>Chaenomeles sinensis</i> and screening of their biomedical activities

description: The design of mild and non-toxic synthesis of metallic nanoparticles is a topical subject in the nanotechnology field. The objective of this present study is to screen the bioactivity of biosynthesized nanoparticles by aqueous fruit extract of <i>Chaenomeles sinensis</i>. The reducing and stabilizing ability of <i>C. sinensis</i> to fabricate gold (Cs-AuNps) and silver (Cs-AgNps) nanoparticles was confirmed by UV–visible (UV–Vis) spectroscopy at 562 nm and 477 nm, respectively. The field-emission transmission electron microscopy (FE-TEM) and X-ray diffraction analysis (XRD) verify the nano-scale morphology and crystallinity of Cs-AuNps (20–40 nm) and Cs-AgNps (5–20 nm). Furthermore, we evaluated the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging capacity, antimicrobial activity against <i>Staphylococcus aureus</i> and <i>Escherichia coli</i> and cytotoxicity against breast cancer cells. The results showed that Cs-AuNps (IC<sub>50</sub>: 725.93 μg/mL) displayed superior inhibitory activities on DPPH than Cs-AuNps. The biosynthesized Cs-AuNps successfully inhibited the growth of pathogenic bacteria <i>S. aureus</i> (ATCC 6538) and <i>E. coli</i> (BL21). The cytotoxic effect of Cs-AuNps and Cs-AgNps was evaluated in murine macrophage (RAW264.7) and human breast cancer cell lines (MCF7) by MTT assay. Thus, the present study explores the biomedical applications of gold and silver nanoparticles synthesized by <i>C. sinensis</i>.
DOI: 10.6084/m9.figshare.5081968
title: Complete C. carnifex Data Set

description: Complete data set of the <i>C. carnifex </i>feeding preference experiments.<br>
DOI: 10.6084/m9.figshare.5081992.v1
title: Genomic information of strains SH4916 and SH5446

description: Description of the methods used to analyze the high-throughput sequencing information of strains SH4916 and SH5446. Annotated contigs of each of the strains are provided.<br>
DOI: 10.6084/m9.figshare.5081968.v1
title: Complete C. carnifex Data Set

description: Complete data set of the <i>C. carnifex </i>feeding preference experiments.<br>
DOI: 10.6084/m9.figshare.5080756
title: Molecular evidence of the presence of <i>Dictyota dichotoma</i> (Dictyotales: Phaeophyceae) in Argentina based on sequences from mtDNA and cpDNA and a discussion of its possible origin

description: <i>Dictyota</i> is a brown algae genus inhabiting tropical to warm temperate environments where it is an important food source, shelter and substrate to several species of invertebrates and other algae. The taxonomy of this genus is troublesome, with poor species delimitation and doubtful records in the literature. <i>Dictyota dichotoma</i>, the type species of the genus, was commonly accepted as a cosmopolitan species because of the inaccurate geographical distributional range as a consequence of misidentification in several parts of the world. Recent studies with molecular data revealed new species and a new understanding of the evolution and biogeography of the genus <i>Dictyota</i>. These studies confined natural populations of <i>D. dichotoma</i> to Europe (Atlantic and Mediterranean coasts) and Macaronesian islands (Azores, Madeira and Canary archipelagos). Also, they confirmed its presence in South Africa, but whether the species was native or introduced in South Africa could not be verified. In the present study two regions of cpDNA (<i>psb</i>A, <i>rbc</i>L) and one region of mtDNA (<i>nad</i>1) from Argentinian samples, identified morphologically as <i>D. dichotoma</i>, were analysed and compared to other <i>Dictyota</i> species. The identity of these samples as <i>D. dichotoma</i> was confirmed. A haplotype network analysis using all available <i>psb</i>A sequences distinguished seven haplotypes divided into two geographic groups: Atlantic–Mediterranean and Canarian. In Argentina and South Africa only the most common haplotype of the Atlantic–Mediterranean group was observed. According to the paleoceanographic currents and the presence of a European haplotype, the introduced nature of <i>D. dichotoma</i> is indicated.