cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21558319.v1
title: Identification of intelligence-related proteins through a robust two-layer predictor

description: In this study, we advance a robust methodology for identifying specific intelligence-related proteins across phyla. Our approach exploits a support vector machine-based classifier capable of predicting intelligence-related proteins based on a pool of meaningful protein features. For the sake of illustration of our proposed general method, we develop a novel computational two-layer predictor, Intell_Pred, to predict query sequences (proteins or transcripts) as intelligence-related or non-intelligence-related proteins or transcripts, subsequently classifying the former sequences into learning and memory-related classes. Based on a five-fold cross-validation and independent blind test, Intell_Pred obtained an average accuracy of 87.48 and 88.89, respectively. Our findings revealed that a score &gt;0.75 (during prediction by Intell_Pred) is a well-grounded choice for predicting intelligence-related candidate proteins in most organisms across biological kingdoms. In particular, we assessed seismonastic movements and associate learning in plants and evaluated the proteins involved using Intell_Pred. Proteins related to seismonastic movement and associate learning showed high percentages of similarities with intelligence-related proteins. Our findings lead us to believe that Intell_Pred can help identify the intelligence-related proteins and their classes using a given protein/transcript sequence.
DOI: 10.6084/m9.figshare.21558319
title: Identification of intelligence-related proteins through a robust two-layer predictor

description: In this study, we advance a robust methodology for identifying specific intelligence-related proteins across phyla. Our approach exploits a support vector machine-based classifier capable of predicting intelligence-related proteins based on a pool of meaningful protein features. For the sake of illustration of our proposed general method, we develop a novel computational two-layer predictor, Intell_Pred, to predict query sequences (proteins or transcripts) as intelligence-related or non-intelligence-related proteins or transcripts, subsequently classifying the former sequences into learning and memory-related classes. Based on a five-fold cross-validation and independent blind test, Intell_Pred obtained an average accuracy of 87.48 and 88.89, respectively. Our findings revealed that a score &gt;0.75 (during prediction by Intell_Pred) is a well-grounded choice for predicting intelligence-related candidate proteins in most organisms across biological kingdoms. In particular, we assessed seismonastic movements and associate learning in plants and evaluated the proteins involved using Intell_Pred. Proteins related to seismonastic movement and associate learning showed high percentages of similarities with intelligence-related proteins. Our findings lead us to believe that Intell_Pred can help identify the intelligence-related proteins and their classes using a given protein/transcript sequence.
DOI: 10.5281/zenodo.7440303
title: Table S1: Fetal phenotype and genotype

description: Legend to supplementary Table 1 This table contains the 28 fetal cases on whom WES was performed. For each case, the fetal phenotype and the organ system involved are described, as well as the sample type from which the DNA was extracted, the applied gene panel and the result. For the positive cases, the gestational age at ultrasound, the affected gene and variant, the inheritance mode, the associated syndrome, the fetal phenotype as described in the literature and the outcome of the pregnancy are listed as well. AC: amniocytes; AD: autosomal dominant; AR: autosomal recessive; CNS: central nervous system; CV: chorionic villi; hom: homozygous; IF: incidental finding; IUGR: intrauterine growth restriction; LB: live birth; norm: normal; NT: nuchal translucency; pat: paternal; path: pathogenic; TOP: termination of pregnancy; US: ultrasound; VSD: ventricular septal defect; WES: whole exome sequencing; WESSD: WES with skeletal dysplasia panel
DOI: 10.5281/zenodo.7440302
title: Table S1: Fetal phenotype and genotype

description: Legend to supplementary Table 1 This table contains the 28 fetal cases on whom WES was performed. For each case, the fetal phenotype and the organ system involved are described, as well as the sample type from which the DNA was extracted, the applied gene panel and the result. For the positive cases, the gestational age at ultrasound, the affected gene and variant, the inheritance mode, the associated syndrome, the fetal phenotype as described in the literature and the outcome of the pregnancy are listed as well. AC: amniocytes; AD: autosomal dominant; AR: autosomal recessive; CNS: central nervous system; CV: chorionic villi; hom: homozygous; IF: incidental finding; IUGR: intrauterine growth restriction; LB: live birth; norm: normal; NT: nuchal translucency; pat: paternal; path: pathogenic; TOP: termination of pregnancy; US: ultrasound; VSD: ventricular septal defect; WES: whole exome sequencing; WESSD: WES with skeletal dysplasia panel
DOI: 10.6084/m9.figshare.21731249.v1
title: Supplementary Material for: Transcranial MR-Guided Focused Ultrasound and Hyperostosis Calvariae Diffusa: Case Report and Systematic Review of the Literature

description: We describe a 74-year-old male with intractable essential tremor (ET) and hyperostosis calvariae diffusa who was unsuccessfully treated with magnetic resonance-guided focused ultrasound (MRgFUS). A computed tomography performed prior to the procedure demonstrated a skull density ratio (SDR) of 0.37 and tricortical hyperostosis calvariae diffusa. No lesion was evident on post-MRgFUS MRI, and no improvement in the patient’s hand tremor was noted clinically. We systematically reviewed the literature to understand outcomes for those patients with hyperostosis who have undergone MRgFUS. A comprehensive literature search using the PubMed, Cochrane, and Google Scholar databases identified 3 ET patients with hyperostosis who failed treatment with MRgFUS. Clinical findings, skull characteristics, treatment parameters, and outcomes were summarized, demonstrating different patterns/degrees of bicortical hyperostosis and variable SDRs (i.e., from 0.38 to ≥0.45). Although we have successfully treated patients with bicortical hyperostosis frontalis interna (<i>n</i> = 50), tricortical hyperostosis calvariae diffusa appears to be a contraindication for MRgFUS despite acceptable SDRs.
DOI: 10.17632/gcdckhx3pt.1
title: Saline Wastewater Treatment Plant Data

description: RAW data of process data and sequencing results from North Water's SWWTP that is used in the article of 'NGS-enriched activated sludge modelling of industrial wastewater treatment plant'. In the article, these datasets will be interpolated to achieve a more complete dataset (daily dataset).
DOI: 10.17632/gcdckhx3pt.2
title: Saline Wastewater Treatment Plant Data

description: RAW data of process data and sequencing results from North Water's SWWTP that is used in the article of 'NGS-enriched activated sludge modelling of industrial wastewater treatment plant'. In the article, these datasets will be interpolated to achieve a more complete dataset (daily dataset).
DOI: 10.25403/upresearchdata.21586872
title: The movement of the Bangwaketse

description: The datasets include: the least cost paths (LCPs) that were generated to map out the possible routes that were taken by the Bangwaketse in the 18th and 19th century; the Bangwaketse settlements; Digital Elevation Model (DEM) collected from the USGS to create a slope layer on which the routes would be created based on: slope which was created from the DEM; and the maps that were created to present the routes, the settlements and the slope.
DOI: 10.25403/upresearchdata.21586872.v1
title: The movement of the Bangwaketse

description: The datasets include: the least cost paths (LCPs) that were generated to map out the possible routes that were taken by the Bangwaketse in the 18th and 19th century; the Bangwaketse settlements; Digital Elevation Model (DEM) collected from the USGS to create a slope layer on which the routes would be created based on: slope which was created from the DEM; and the maps that were created to present the routes, the settlements and the slope.
DOI: 10.5281/zenodo.6811684
title: Materials Project Dataset

description: Structure-formation energy pairs from February 2022 version of MP database.
DOI: 10.5281/zenodo.6811683
title: Materials Project Dataset

description: Structure-formation energy pairs from February 2022 version of MP database.
DOI: 10.6084/m9.figshare.21293709
title: Supplementary Material for: Effects of lifestyle and educational bridging programs before bariatric surgery on postoperative weight loss - a systematic review and meta-analysis

description: Objective: To fulfill the requirements for bariatric surgery, patients often need to participate in mandatory pre-operative lifestyle interventions (PLI). Currently, the efficacy of multi-month PLI-programs on body mass index (BMI) reduction from the start of the program (T0) through the immediate pre-operative time point (T1) to one-year post-surgery (T2), and how the amount of pre-operative BMI reduction affects post-operative outcome (T1 to T2) is unclear. The aim of this meta-analysis was to analyze the effects of PLI on body mass index (BMI) one-year post-surgery. Method: A systematic literature search was conducted according to PRISMA criteria. Randomized controlled trials that implemented PLI lasting 1-8 months before bariatric surgery were included. The BMI of the intervention group was compared with a control group before participation in the PLI (T0), after completion of the program before surgery (T1) and one-year post-surgery (T2). Finally, the impact of successful BMI reduction at T1 on BMI at T2 was analyzed. Results: N=345 patients derived from 4 studies undergoing PLI reduced their BMI at T1 by 1.5 units compared to the control group (95% CI: -2.73, -0.28). One-year post-surgery, both groups had lost comparable BMI points. The influence of reduced BMI at T1 on weight status at T2 is unclear due to the lack of available studies. Other endpoints and subgroup analyses were rarely examined. Conclusions: PLI reduce BMI before bariatric surgery more effectively than usual care. These differences are not detectable one-year post-surgery. Although a short-term energy reduction period before surgery is clearly important to minimize surgery risks, it is currently unclear whether, and if so under what circumstances, participation in a PLI is beneficial.
DOI: 10.6084/m9.figshare.21729446
title: Structural Health Monitoring test data and procedures

description: Campbell Scientific, Inc. data acquisition system consisting of CR5000 data logger and Loggernet software was used to collect and process strain transducer data to monitor the structural health of girder G5 at Br 1-704.
DOI: 10.6084/m9.figshare.21728240
title: arxiv

description: arxiv
DOI: 10.6084/m9.figshare.21728240.v1
title: arxiv

description: arxiv
DOI: 10.6084/m9.figshare.21729413
title: SEM test data and procedures

description: A Hitachi TM-3000 scanning electron microscope was used to examine the microstructure of aged CFRP from the Foulk Road bridge.
DOI: 10.6084/m9.figshare.21729398
title: Raman Spectroscopy test data and procedures

description: All Raman experiments were carried out on CFRP composite field samples collected from the Foulk Road bridge using a Kaiser spectrometer equipped with a 785 nm laser.
DOI: 10.6084/m9.figshare.21729398.v1
title: Raman Spectroscopy test data and procedures

description: All Raman experiments were carried out on CFRP composite field samples collected from the Foulk Road bridge using a Kaiser spectrometer equipped with a 785 nm laser.
DOI: 10.6084/m9.figshare.21462999
title: Supplementary Material for: New view on the impact of the low-frequency electromagnetic field (50 Hz) on stress responses – hormesis effect

description: Introduction: Low-frequency electromagnetic field (50 Hz) (EMF) can modify crucial neuronal processes. Existing data indicate that exposure to EMF may represent a mild stressor and contribute to disturbances of hypothalamic-pituitary-adrenal (HPA) axis. The important regulatory pathways controlling HPA axis activity include two types of corticosteroid receptors: mineralocorticoid (MR) and glucocorticoid (GR) receptors. There are particularly abundant in the hippocampus, a key locus of HPA axis feedback control. The research aimed at determining whether 1) EMF exhibits hormesis, it means bidirectional action depending on EMF intensity (1 or 7 mT), and 2) repeated EMF exposure changes stress response to subsequent stress factors. Methods: The exposure (7-day, 1h/day) of adult rats to EMF (1 mT and 7 mT) was repeated 3 times. HPA axis hormones and their receptors were analysed after each following exposure. Moreover, the impact of EMF exposure on hormonal and behavioural responses to subsequent stress factor - open-field test was evaluated. Results/Discussion: Our data suggest that exposure to EMF can establish a new “set-point” for HPA axis activity. The direction and dynamics of this process depend on the intensity of EMF and the number of exposures. EMF of 1 mT induced an adaptive stress response, but 7 mT EMF caused sensitization. Consequently, EMF changed the vulnerability of the organism to a subsequent stress factor. We have also shown the increase of MR mRNA abundance in hippocampus of 1 mT EMF exposed rats, which can represent the possible neuroprotective response and suggest therapeutic properties of electromagnetic fields.
DOI: 10.6084/m9.figshare.21462999.v1
title: Supplementary Material for: New view on the impact of the low-frequency electromagnetic field (50 Hz) on stress responses – hormesis effect

description: Introduction: Low-frequency electromagnetic field (50 Hz) (EMF) can modify crucial neuronal processes. Existing data indicate that exposure to EMF may represent a mild stressor and contribute to disturbances of hypothalamic-pituitary-adrenal (HPA) axis. The important regulatory pathways controlling HPA axis activity include two types of corticosteroid receptors: mineralocorticoid (MR) and glucocorticoid (GR) receptors. There are particularly abundant in the hippocampus, a key locus of HPA axis feedback control. The research aimed at determining whether 1) EMF exhibits hormesis, it means bidirectional action depending on EMF intensity (1 or 7 mT), and 2) repeated EMF exposure changes stress response to subsequent stress factors. Methods: The exposure (7-day, 1h/day) of adult rats to EMF (1 mT and 7 mT) was repeated 3 times. HPA axis hormones and their receptors were analysed after each following exposure. Moreover, the impact of EMF exposure on hormonal and behavioural responses to subsequent stress factor - open-field test was evaluated. Results/Discussion: Our data suggest that exposure to EMF can establish a new “set-point” for HPA axis activity. The direction and dynamics of this process depend on the intensity of EMF and the number of exposures. EMF of 1 mT induced an adaptive stress response, but 7 mT EMF caused sensitization. Consequently, EMF changed the vulnerability of the organism to a subsequent stress factor. We have also shown the increase of MR mRNA abundance in hippocampus of 1 mT EMF exposed rats, which can represent the possible neuroprotective response and suggest therapeutic properties of electromagnetic fields.
DOI: 10.6084/m9.figshare.21729386
title: DMA test data and procedures

description: Dynamic Mechanical Analysis (DMA) was used to obtain the glass transition temperature of unidirectional CFRP composite control samples and field samples collected from Bridge 1-704.
DOI: 10.25934/pr00006774.2
title: Available IPD datapackage for study 'A Multicentre, Randomized, Double-blind, Placebo-controlled, Parallel-group Study Of Oral Cp-690,550 As An Induction Therapy In Subjects With Moderate To Severe Ulcerative Colitis'

description: This study is designed to evaluate the efficacy and safety of tofacitinib (CP-690,550) in patients with moderate to severe ulcerative colitis who have failed or be intolerant to one of following treatments for ulcerative colitis: oral steroids, azathiopurine/6-mercaptopurine, or anti-TNF-alpha therapy.
DOI: 10.25934/pr00008294
title: Extended Validation of an Ulcerative Colitis Vedolizumab Decision Support Tool for Outcome Prediction with Tofacitinib 

description: Vedolizumab is biologic approved for moderate to severe ulcerative colitis, which specifically targets the gut to help improve inflammation. Biologics are drugs that are made of animal and/or human cells, viruses, and proteins. Several other biologics are available with various modes of action and the optimal treatment for some patients remain unclear. The majority of guidance surrounding choice of therapy encourages clinicians to consider all available therapies given currently available evidence as opposed to explicitly outlining which therapies are better suited for specific patient populations. In the absence of explicit guidelines, I previously developed and validated a clinical decision support tool specifically for vedolizumab that has demonstrated the ability to identify ulcerative colitis patients who may derive the greatest benefit with vedolizumab. More importantly, I have demonstrated this tool can predict response specifically to vedolizumab rather than anti-TNF therapy, which are drugs that reduce inflammation in conditions such as ulcerative colitis. However, further validation is needed to compare the prognostic value of this tool for vedolizumab compared to therapies with other modes of action in a post-hoc analysis using robust data from randomized clinical trials. The primary aim of this study is to further validate the ability of the clinical decision support tool to identify ulcerative colitis patients suited for vedolizumab treatment compared to tofacitinib, which is as small molecule drug. These drugs have very low molecular weight and can be taken orally. This validation exercise may benefit ulcerative colitis patients as it can provide greater confidence in the use and uptake of the clinical decision support tool in clinical settings for vedolizumab.
DOI: 10.25934/pr00006775.3
title: Available IPD datapackage for study 'A Multicentre, Randomized, Double-blind, Placebo-controlled, Parallel-group Study Of Oral Cp-690,550 As An Induction Therapy In Subjects With Moderate To Severe Ulcerative Colitis.'

description: This study is designed to evaluate the efficacy and safety of tofacitinib (CP-690,550) in patients with moderate to severe ulcerative colitis who have failed or be intolerant to one of following treatments for ulcerative colitis: oral steroids, azathiopurine/6-mercaptopurine, or anti-TNF-alpha therapy.
DOI: 10.25934/pr00006776.2
title: Available IPD datapackage for study 'A Multicentre, Randomized, Double-blind, Placebo-controlled, Parallel-group Study Of Oral Cp-690,550 As A Maintenance Therapy In Subjects With Ulcerative Colitis'

description: The study proposes to assess whether compared to placebo, CP-690,550 is effective, safe, and tolerable maintenance therapy in subjects with Ulcerative Colitis (UC). The study proposes to assess whether compared to placebo, CP-690,550 maintenance therapy more effectively achieves mucosal healing and improves quality of life in subjects with UC.The study proposes to assess CP-690,550 pharmacokinetic exposure during maintenance therapy in subjects over the age of 18 years with UC.
DOI: 10.5281/zenodo.7417728
title: Switching between Numerical Black-box Optimization Algorithms with Warm-starting Policies - Reproduction artifacts

description: # Reproducibility instructions This document details the steps to reproduce the results presented in the paper 'Chaining of Numerical Black-box Algorithms: Investigating the Impact of Warm-Starting and the Switching Point' ## Algorithm code<br> The code for the individual algorithms and the switching routines is included in the 'dynas.zip' folder. ## Data collection<br> To collect the performance data for the static algorithms, the file 'data_collection.py' can be used. This file runs all 5 static algorithm on the function suite used in the paper, using the 'ioh' package. To run it, please modify the 'ioh_dir' variable to a place where the data should be stored. <br> The resulting data is made available under the 'static.zip' file. ## Processing code<br> The code which processes the performance data into the list of usecases is part of the 'Processing_R' notebook. <br> This results in a set of rds-files with the data in IOHanalyzer's internal format, and in a csv file ('Split_performances_relative.csv') with the selected usecases. This csv file can then be read in using the 'visualization' notebook, which can generate Figure 1 from the paper. This notebook can then be used to count the specific usecases, which is the data shown in Table 1. The csv-file containing the selected usecases ('usecases.csv') is also generated here. The 'usecases' csv file can be used in the 'Data_collection_switch' notebook to run the dynamic configurations. This results in the 'Dynamic.zip' data, which can again be read using IOHanalyzer in the 'Processing_R' notebook. This then generates several csv-files, for both the static and dynamic case, containing the per-run hitting times ('RT_samples.zip'). These are then used in the 'Visualization' notebook to generate figure 3 and 4, as well as table 2. ## Countour plots<br> The code for generating Figure 5 is included in the end of the 'Visualization' notebook. ## Performance comparison plot<br> Figure 6 has been generated using IOHanalyzer web-interface (iohanalyzer.liacs.nl), by uploading the files in 'cma_bfgs.zip'. ## Switch point impact plot<br> Figure 7 has been generated using the 'split_experiment' notebook