cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7122506.v1
title: SI1-7.zip

description: Supplemental material for CP article: <br><br>Bouchal, J.M., Güner, T.H., Denk, T. 2018. Middle Miocene climate of southwestern Anatolia from multiple botanical proxies. Climates of the Past. https://doi.org/10.5194/cp-2018-76 <br> <b>S1</b>: A. Number of fossil-taxa (macrofossils and microfossils) from four middle Miocene localities (including one macrofossil horizon and four pollen zones - PZ) in the Yatağan Basin. B. All fossil-taxa recorded from four Yatağan Basin floras (14.8–13.2 Ma; MN6 into MN7–8). <b>S2</b>: Köppen-Geiger climate type signatures of all genera represented in micro and macrofloras of the Yatağan Basin. <b>S3</b>: Coding of leaf physiognomic characters for morphotypes from three macrofloras. Output pdf files from online CLAMP analysis (http://clamp.ibcas.ac.cn). <b>S4</b>: Heat maps showing precise representation of different Köppen-Geiger climate types for all fossil assemblages. <b>S5</b>: Köppen signature diagrams excluding cosmopolitan and gymnospermous taxa. <b>S6</b>: Arboreal to non-arboreal pollen ratios for three sections, of the Yatağan Basin. <b>S7</b>: Modern climate stations comparable to the middle Miocene climate of the Yatağan Basin, southwestern Anatolia. Climate data from Climate-Data.Org (https://sv.climate-data.org/info/sources/) and Ustaoğlu (2012). Selected Walter-Lieth climate diagrams illustrate qualitative difference between Euxinian-Hyrcanian and Japanese (Honshu) <i>Cf</i> climates. <br>
DOI: 10.6084/m9.figshare.7122368
title: Evolutionary trends in the columnar cactus genus <i>Eulychnia</i> (Cactaceae) based on molecular phylogenetics, morphology, distribution, and habitat

description: Populations of the columnar cactus genus <i>Eulychnia</i> (Cactaceae) are an iconic sight in the Chilean Atacama Desert. The most recent taxonomic treatment of the genus suggested to accept up to seven taxa at species level based on morphological data. To date, species boundaries and infrageneric relationships in <i>Eulychnia</i> have not been investigated using a molecular approach. In this study, sequence data were generated for six chloroplast markers (<i>rpl32-trnL</i>, <i>trnH-psbA</i>, <i>trnL-trnF</i>, <i>trnQ-rps16</i>, <i>trnS-trnG</i>, and <i>ycf1</i>) for the seven species. Where possible, samples were collected from the south and north of the distribution range of widely distributed species, as well as plants from two morphologically distinct populations in the Atacama and Coquimbo Regions. Evolutionary trends of morphological characters were investigated using ancestral state reconstruction, and the habitat of the Chilean taxa was taken into account based on latitudinal and altitudinal distribution, precipitation regime, and vegetation zones. Two major clades were retrieved in the molecular phylogenetic hypotheses, a northern clade and a southern clade, which can easily be distinguished morphologically by differences in rib shape and type of the indumentum of the pericarpel and the hypanthium. The only <i>Eulychnia</i> taxon found outside Chile is most commonly accepted as <i>Eulychnia iquiquensis</i> subsp. <i>ritteri</i>. However, its isolated geographic distribution and the fact that this taxon is not most closely related to <i>E. iquiquensis</i> but was retrieved as sister to the rest of the northern clade in our molecular phylogenetic results support the recognition of <i>E. ritteri</i> at species level. Our results also provide some support for the two recently published species, <i>E. chorosensis</i> (previously placed in <i>E. acida</i> s.l.) and <i>E. taltalensis</i> (previously considered to be part of <i>E. breviflora</i> s.l.). The relationships in the southern clade need further study.
DOI: 10.6084/m9.figshare.7122368.v1
title: Evolutionary trends in the columnar cactus genus <i>Eulychnia</i> (Cactaceae) based on molecular phylogenetics, morphology, distribution, and habitat

description: Populations of the columnar cactus genus <i>Eulychnia</i> (Cactaceae) are an iconic sight in the Chilean Atacama Desert. The most recent taxonomic treatment of the genus suggested to accept up to seven taxa at species level based on morphological data. To date, species boundaries and infrageneric relationships in <i>Eulychnia</i> have not been investigated using a molecular approach. In this study, sequence data were generated for six chloroplast markers (<i>rpl32-trnL</i>, <i>trnH-psbA</i>, <i>trnL-trnF</i>, <i>trnQ-rps16</i>, <i>trnS-trnG</i>, and <i>ycf1</i>) for the seven species. Where possible, samples were collected from the south and north of the distribution range of widely distributed species, as well as plants from two morphologically distinct populations in the Atacama and Coquimbo Regions. Evolutionary trends of morphological characters were investigated using ancestral state reconstruction, and the habitat of the Chilean taxa was taken into account based on latitudinal and altitudinal distribution, precipitation regime, and vegetation zones. Two major clades were retrieved in the molecular phylogenetic hypotheses, a northern clade and a southern clade, which can easily be distinguished morphologically by differences in rib shape and type of the indumentum of the pericarpel and the hypanthium. The only <i>Eulychnia</i> taxon found outside Chile is most commonly accepted as <i>Eulychnia iquiquensis</i> subsp. <i>ritteri</i>. However, its isolated geographic distribution and the fact that this taxon is not most closely related to <i>E. iquiquensis</i> but was retrieved as sister to the rest of the northern clade in our molecular phylogenetic results support the recognition of <i>E. ritteri</i> at species level. Our results also provide some support for the two recently published species, <i>E. chorosensis</i> (previously placed in <i>E. acida</i> s.l.) and <i>E. taltalensis</i> (previously considered to be part of <i>E. breviflora</i> s.l.). The relationships in the southern clade need further study.
DOI: 10.6084/m9.figshare.7122332
title: Biopolymer networks. Skeletons and spatial graphs

description: Biopolymer networks from Actin and polysacharides: Pectin and Carragenan. Denoised, binarized, skeletonized (thinning), and converted into a spatial graph for statistical analysis. <br><br>Read more in the chapter 5 of my thesis (TODO: update to final Massey University link).<br><br>Thesis (overleaf): https://www.overleaf.com/7261677bpwjxpsxjwqc#/25095960/<br><br>
DOI: 10.6084/m9.figshare.7122302
title: Interventions to improve diagnostic decision making: A systematic review and meta-analysis on reflective strategies

description: <b>Aims:</b> To identify, appraise and describe studies of cognitive interventions to improve diagnostic decision making (DDM) amongst medical professionals, assess their effectiveness and identify methodological limitations in existing studies. <b>Methods:</b> We systematically searched for studies (publication date 2000–2016) in multiple databases including Cochrane Controlled Trials, EMBASE, ERIC, Medline, PubMed and PsycINFO, and used additional strategies such as hand searching and snowballing. Included studies evaluated cognitive interventions to enhance DDM amongst medical professionals, using defined outcomes such as diagnostic accuracy. A meta-analysis assessed the impact of <i>“</i>reflection<i>”</i>. <b>Results:</b> Forty-four studies out of 10,114 screened citations, involving 4380 medical professionals, were included. Studies evaluated reasoning workshops/curricula, de-biasing workshops, checklists, reflection, feedback, and instructions to induce analytical thinking. Guided reflection was demonstrated to improve DDM [effect size 0.38(95%CI 0.23–0.52), <i>p</i><b><i> </i></b> <b>Conclusions:</b> Educational interventions incorporating practising deliberate reflection on a formulated diagnosis, modeled reflection on contrasting examples and immediate feedback are promising strategies for improving DDM. The effectiveness of other strategies is unknown, with more methodological refinements required in future research.
DOI: 10.6084/m9.figshare.7122236
title: Performance evaluation of propensity score methods for estimating average treatment effects with multi-level treatments<sup>*</sup>

description: The propensity score (PS) method is widely used to estimate the average treatment effect (TE) in observational studies. However, it is generally confined to the binary treatment assignment. In an extension to the settings of a multi-level treatment, Imbens proposed a generalized propensity score which is the conditional probability of receiving a particular level of the treatment given pre-treatment variables. The average TE can then be estimated by conditioning solely on the generalized PS under the assumption of weak unconfoundedness. In the present work, we adopted this approach and conducted extensive simulations to evaluate the performance of several methods using the generalized PS, including subclassification, matching, inverse probability of treatment weighting (IPTW), and covariate adjustment. Compared with other methods, IPTW had the preferred overall performance. We then applied these methods to a retrospective cohort study of 228,876 pregnant women. The impact of the exposure to different types of the antidepressant medications (no exposure, selective serotonin reuptake inhibitor (SSRI) only, non-SSRI only, and both) during pregnancy on several important infant outcomes (birth weight, gestation age, preterm labor, and respiratory distress) were assessed.
DOI: 10.6084/m9.figshare.7122302.v1
title: Interventions to improve diagnostic decision making: A systematic review and meta-analysis on reflective strategies

description: <b>Aims:</b> To identify, appraise and describe studies of cognitive interventions to improve diagnostic decision making (DDM) amongst medical professionals, assess their effectiveness and identify methodological limitations in existing studies. <b>Methods:</b> We systematically searched for studies (publication date 2000–2016) in multiple databases including Cochrane Controlled Trials, EMBASE, ERIC, Medline, PubMed and PsycINFO, and used additional strategies such as hand searching and snowballing. Included studies evaluated cognitive interventions to enhance DDM amongst medical professionals, using defined outcomes such as diagnostic accuracy. A meta-analysis assessed the impact of <i>“</i>reflection<i>”</i>. <b>Results:</b> Forty-four studies out of 10,114 screened citations, involving 4380 medical professionals, were included. Studies evaluated reasoning workshops/curricula, de-biasing workshops, checklists, reflection, feedback, and instructions to induce analytical thinking. Guided reflection was demonstrated to improve DDM [effect size 0.38(95%CI 0.23–0.52), <i>p</i><b><i> </i></b> <b>Conclusions:</b> Educational interventions incorporating practising deliberate reflection on a formulated diagnosis, modeled reflection on contrasting examples and immediate feedback are promising strategies for improving DDM. The effectiveness of other strategies is unknown, with more methodological refinements required in future research.
DOI: 10.6084/m9.figshare.7122143
title: UAV multispectral

description: This folder included the data and processing code for manuscript "Multispectral imaging and unmanned aerial systems for cotton plant phenotyping"<br>Each subfolder was orgnized as follows:crop.m -- matlab script to read uav images and seperate into plotsdem.tif -- digital elevetion model of the field generated by the PhotoScangct_crop.mat -- matlab varible scores the position of the GCT in the ortho-mosaic/demgct_height.txt -- maunal measurement of the GCTgeo.tif -- ortho-mosaic of the field generated by the PhotoScanheight.txt -- manual measurement of the plant height for each plot<br><br>The processing code is UAVHeight.m. This code was tested in Matlab R2016a<br>
DOI: 10.6084/m9.figshare.7121942
title: Additional file 7 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of bacterocins for APD3_BACTERIOCIN. Evaluation of different models with APD3_BACTERIOCIN after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 31 kb)
DOI: 10.6084/m9.figshare.7121942.v1
title: Additional file 7 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of bacterocins for APD3_BACTERIOCIN. Evaluation of different models with APD3_BACTERIOCIN after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 31 kb)
DOI: 10.6084/m9.figshare.7121936
title: Additional file 6 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of bacterocins for DAMPD_BACTERIOCIN. Evaluation of different models with DAMPD_BACTERIOCIN after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 22 kb)
DOI: 10.6084/m9.figshare.7121936.v1
title: Additional file 6 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of bacterocins for DAMPD_BACTERIOCIN. Evaluation of different models with DAMPD_BACTERIOCIN after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 22 kb)
DOI: 10.6084/m9.figshare.7121930
title: Additional file 5 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antibacterial activity for APD3_ANTIBACTERIAL. Evaluation of different models with APD3_ANTIBACTERIAL after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 34 kb)
DOI: 10.6084/m9.figshare.7121927
title: Additional file 4 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antibacterial activity for DAMPD_ANTIBACTERIAL. Evaluation of different models with DAMPD_ANTIBACTERIAL after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 32 kb)
DOI: 10.6084/m9.figshare.7121927.v1
title: Additional file 4 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antibacterial activity for DAMPD_ANTIBACTERIAL. Evaluation of different models with DAMPD_ANTIBACTERIAL after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 32 kb)
DOI: 10.6084/m9.figshare.7121918
title: Additional file 3 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antimicrobial activity for APD3_AMP. Evaluation of different models with APD3_AMP after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 34 kb)
DOI: 10.6084/m9.figshare.7121918.v1
title: Additional file 3 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antimicrobial activity for APD3_AMP. Evaluation of different models with APD3_AMP after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 34 kb)
DOI: 10.6084/m9.figshare.7121912
title: Additional file 2 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antimicrobial activity for DAMPD_AMP. Evaluation of different models with DAMP_AMP after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 33 kb)
DOI: 10.6084/m9.figshare.7121915
title: Additional file 2: of Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

description: (Sheet 1) Top 30 selected features; (Sheet 2) Performance comparison; (Sheet 3) Sensitivity Comparison. (XLS 45 kb)
DOI: 10.6084/m9.figshare.7121915.v1
title: Additional file 2: of Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

description: (Sheet 1) Top 30 selected features; (Sheet 2) Performance comparison; (Sheet 3) Sensitivity Comparison. (XLS 45 kb)
DOI: 10.6084/m9.figshare.7121909
title: Additional file 1: of Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

description: (Sheet 1) Whole set of features; (Sheet 2) Remaining features after elimination. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.7121912.v1
title: Additional file 2 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antimicrobial activity for DAMPD_AMP. Evaluation of different models with DAMP_AMP after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 33 kb)
DOI: 10.6084/m9.figshare.7121909.v1
title: Additional file 1: of Genome-scale MicroRNA target prediction through clustering with Dirichlet process mixture model

description: (Sheet 1) Whole set of features; (Sheet 2) Remaining features after elimination. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.7121861
title: Additional file 2 of Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer’s disease through ensemble graphs

description: mRNA merged and filtered data R-Data file with the datasets from [7] and [8] merged and filtered following the data processing presented in the “Methods” section. (RDATA 322 KB)
DOI: 10.6084/m9.figshare.7121861.v1
title: Additional file 2 of Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer’s disease through ensemble graphs

description: mRNA merged and filtered data R-Data file with the datasets from [7] and [8] merged and filtered following the data processing presented in the “Methods” section. (RDATA 322 KB)
DOI: 10.6084/m9.figshare.7121846
title: Additional file 1 of Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer’s disease through ensemble graphs

description: MicroRNA merged and filtered data R-Data file with the datasets from [5] and [6] merged and filtered following the data processing presented in the “Methods” section. (RDATA 22 KB)
DOI: 10.6084/m9.figshare.7121846.v1
title: Additional file 1 of Revealing post-transcriptional microRNA–mRNA regulations in Alzheimer’s disease through ensemble graphs

description: MicroRNA merged and filtered data R-Data file with the datasets from [5] and [6] merged and filtered following the data processing presented in the “Methods” section. (RDATA 22 KB)
DOI: 10.6084/m9.figshare.7121777
title: ERA Model 2018 - personalised patient outcomes prediction after endovascular aneurysm repair of abdominal aortic aneurysms

description: The interactive Endovascular Aneurysm Repair Risk Assessment (ERA) Model, originally developed in 2008, is updated and improved. Vascular surgeons enter preoperative variables for a patient undergoing EndoVascular Aneurysm Repair (EVAR) and the ERA Model estimates that patient's individualised expected outcomes. The new model uses variables that are routinely collected preoperatively, and hence can be used to support surgeon-patient discussions prior to the operation. Patients can be fully informed of potential risks based on individualised assessments of likely outcomes following elective EVAR surgery. Outcomes include: 1 and 3 year survival, 30 and 90 day mortality, Early and mid-term endoleaks, operative and complication likelihoods. Pre-operative variables are fitness (fit or unfit), ASA, history of stroke-TIA, age, aneurysm angle, infrarenal neck length, white cell count, respiratory assessment, diabetes and use of statins.
DOI: 10.6084/m9.figshare.7121777.v1
title: ERA Model 2018 - personalised patient outcomes prediction after endovascular aneurysm repair of abdominal aortic aneurysms

description: The interactive Endovascular Aneurysm Repair Risk Assessment (ERA) Model, originally developed in 2008, is updated and improved. Vascular surgeons enter preoperative variables for a patient undergoing EndoVascular Aneurysm Repair (EVAR) and the ERA Model estimates that patient's individualised expected outcomes. The new model uses variables that are routinely collected preoperatively, and hence can be used to support surgeon-patient discussions prior to the operation. Patients can be fully informed of potential risks based on individualised assessments of likely outcomes following elective EVAR surgery. Outcomes include: 1 and 3 year survival, 30 and 90 day mortality, Early and mid-term endoleaks, operative and complication likelihoods. Pre-operative variables are fitness (fit or unfit), ASA, history of stroke-TIA, age, aneurysm angle, infrarenal neck length, white cell count, respiratory assessment, diabetes and use of statins.
DOI: 10.6084/m9.figshare.7121792.v2
title: CRI iAtlas: an interactive portal for immuno-oncology research

description: CRI iAtlas poster presentation for CSBC/PS-ON Junior Investigator meeting, September 2018.<br>