cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13502475
title: Supplementary Material for: A Meta-Analysis of Prognostic Factors in Patients with Posterior Circulation Stroke after Mechanical Thrombectomy

description: <b><i>Background:</i></b> Posterior circulation stroke is characterized by poor prognosis because its optimal thrombolysis “time window” is always missed. After mechanical thrombectomy (MT), the recanalization rate of posterior circulation obstruction is significantly increased, but prognosis remains poor. To best manage patients, prognostic factors are needed to inform MT triaging after posterior circulation stroke. <b><i>Methods:</i></b> A systematic literature search was done for the period through April 2020. Studies included those with posterior circulation stroke cases that underwent MT. The primary outcome measure in this study was the modified Rankin Scale on day 90. <b><i>Results:</i></b> No outcome differences were found in gender, atrial fibrillation, smoking, and coronary artery disease (OR = 1.07, 95% CI: 0.90–1.28; OR = 1.02, 95% CI: 0.82–1.26; OR = 1.26, 95% CI: 0.94–1.68; and OR = 0.84, 95% CI: 0.58–1.22, respectively). Hypertension, diabetes mellitus, and previous stroke correlated with poorer prognosis (OR = 0.61, 95% CI: 0.48–0.77; OR = 0.60, 95% CI: 0.50–0.73; and OR = 0.74, 95% CI: 0.55–0.99, respectively). However, hyperlipidemia correlated with better prognosis (OR = 1.28, 95% CI: 1.04–1.58). <b><i>Conclusion:</i></b> Our analysis indicates that hypertension, diabetes mellitus, or previous stroke correlate with poorer outcomes. Intriguingly, hyperlipidemia correlates with better prognosis. These factors may help inform triage decisions when considering MT for posterior circulation stroke patients. However, large, multicenter, randomized controlled trials are needed to validate these observations.
DOI: 10.6084/m9.figshare.13502463
title: Supplementary Material for: Lentinan Inhibited the Activation of Th2 Cells in Allergic Mice by Reducing the Amplitude of Changes in Biological Rhythm

description: <b><i>Introduction:</i></b> Biological rhythm is inextricably linked to the physiological mechanisms of allergic diseases, but the exact mechanisms are still poorly understood. Clinical studies have reported rhythmic fluctuations in allergic diseases. The search for natural and harmless active ingredients based on biological rhythm with which to regulate allergic diseases is essential for the control of food allergy. <b><i>Methods:</i></b> In this study, mice were treated at different time points to determine the link between the severity of allergic reactions and the circadian clock genes. The mice were treated with lentinan, either continuously or discontinuously, to assess their clinical symptoms, vascular permeability, immune cells, cytokines, and clock genes. Specifically, rat basophilic leukemia (RBL-2H3) cells were treated with lentinan and the rhythmic changes of cell degranulation were measured. <b><i>Results:</i></b> The results in different models showed that the allergic reactions in mice treated at different time points were significantly different and thus related to fluctuations in biological rhythm. Treatment with lentinan was found to reduce the amplitude of changes in the clock genes, such as the activation of Per and Cry proteins in allergic mice, as well as to regulate biological rhythm in cells, inhibit the activation of Th2 cells, and alleviate allergic reactions. Furthermore, lentinan changed the rhythm of degranulation in RBL-2H3 cells. <b><i>Conclusion:</i></b> Lentinan was, therefore, determined to successfully alleviate allergic reactions by reducing the amplitude of changes in the body’s biological rhythm, inhibiting the activation of Th2 cells, and affecting the immune microenvironment.
DOI: 10.6084/m9.figshare.13502463.v1
title: Supplementary Material for: Lentinan Inhibited the Activation of Th2 Cells in Allergic Mice by Reducing the Amplitude of Changes in Biological Rhythm

description: <b><i>Introduction:</i></b> Biological rhythm is inextricably linked to the physiological mechanisms of allergic diseases, but the exact mechanisms are still poorly understood. Clinical studies have reported rhythmic fluctuations in allergic diseases. The search for natural and harmless active ingredients based on biological rhythm with which to regulate allergic diseases is essential for the control of food allergy. <b><i>Methods:</i></b> In this study, mice were treated at different time points to determine the link between the severity of allergic reactions and the circadian clock genes. The mice were treated with lentinan, either continuously or discontinuously, to assess their clinical symptoms, vascular permeability, immune cells, cytokines, and clock genes. Specifically, rat basophilic leukemia (RBL-2H3) cells were treated with lentinan and the rhythmic changes of cell degranulation were measured. <b><i>Results:</i></b> The results in different models showed that the allergic reactions in mice treated at different time points were significantly different and thus related to fluctuations in biological rhythm. Treatment with lentinan was found to reduce the amplitude of changes in the clock genes, such as the activation of Per and Cry proteins in allergic mice, as well as to regulate biological rhythm in cells, inhibit the activation of Th2 cells, and alleviate allergic reactions. Furthermore, lentinan changed the rhythm of degranulation in RBL-2H3 cells. <b><i>Conclusion:</i></b> Lentinan was, therefore, determined to successfully alleviate allergic reactions by reducing the amplitude of changes in the body’s biological rhythm, inhibiting the activation of Th2 cells, and affecting the immune microenvironment.
DOI: 10.6084/m9.figshare.13502478
title: Supplementary Material for: Medical Care and Survival of Soft-Tissue and Bone Sarcoma Patients: Results and Methodological Aspects of a German Subnational Cohort Study Based on Administrative Healthcare Data

description: <b><i>Introduction:</i></b> Medical care of soft-tissue sarcoma (STS) and bone sarcoma (BS) patients in Germany has rarely been investigated. The objectives of this article were (1) to investigate medical care and survival in STS and BS patients, and (2) to examine methodological aspects of corresponding analyses based on administrative healthcare data. <b><i>Methods:</i></b> We analyzed data from a statutory health insurance located in Saxony, Germany, covering approximately 2 million individuals. We identified incident STS and BS patients in the period 2012–2016 using 4 different case definitions. We examined treatment rates and visits to medical oncologists and medical practices descriptively, and then compared results between case definitions. We investigated survival prospects using a relative survival analysis and estimated hazard ratios (HRs) for risk factors for mortality using Cox regression. <b><i>Results:</i></b> Across case definitions, the number of included sarcoma patients (STS: <i>n</i> = 871–1,757; BS: <i>n</i> = 216–689) and applied treatments (STS: 42.2–83.1%; BS: 28.3–77.8%) varied substantially. Irrespective of the case definition, the minority of patients visited medical oncologists (STS: 9.8–10.8% BS: 4.4–7.9%) and “experienced” medical practices (STS: 27.7–38.4%; BS: 18.3–23.6%). Survival prospects were better for patients who visited “experienced” medical practices (STS: HR = 0.55; BS: HR = 0.42). <b><i>Conclusion:</i></b> Treatment rates clearly &lt;100% and evidence from survival analyses indicate the potential for improvements in the care of sarcoma patients in Germany, e.g., by physicians in “experienced” medical practices.
DOI: 10.6084/m9.figshare.13502478.v1
title: Supplementary Material for: Medical Care and Survival of Soft-Tissue and Bone Sarcoma Patients: Results and Methodological Aspects of a German Subnational Cohort Study Based on Administrative Healthcare Data

description: <b><i>Introduction:</i></b> Medical care of soft-tissue sarcoma (STS) and bone sarcoma (BS) patients in Germany has rarely been investigated. The objectives of this article were (1) to investigate medical care and survival in STS and BS patients, and (2) to examine methodological aspects of corresponding analyses based on administrative healthcare data. <b><i>Methods:</i></b> We analyzed data from a statutory health insurance located in Saxony, Germany, covering approximately 2 million individuals. We identified incident STS and BS patients in the period 2012–2016 using 4 different case definitions. We examined treatment rates and visits to medical oncologists and medical practices descriptively, and then compared results between case definitions. We investigated survival prospects using a relative survival analysis and estimated hazard ratios (HRs) for risk factors for mortality using Cox regression. <b><i>Results:</i></b> Across case definitions, the number of included sarcoma patients (STS: <i>n</i> = 871–1,757; BS: <i>n</i> = 216–689) and applied treatments (STS: 42.2–83.1%; BS: 28.3–77.8%) varied substantially. Irrespective of the case definition, the minority of patients visited medical oncologists (STS: 9.8–10.8% BS: 4.4–7.9%) and “experienced” medical practices (STS: 27.7–38.4%; BS: 18.3–23.6%). Survival prospects were better for patients who visited “experienced” medical practices (STS: HR = 0.55; BS: HR = 0.42). <b><i>Conclusion:</i></b> Treatment rates clearly &lt;100% and evidence from survival analyses indicate the potential for improvements in the care of sarcoma patients in Germany, e.g., by physicians in “experienced” medical practices.
DOI: 10.15161/oar.it/73373
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.5281/zenodo.4399886
title: Microbial ecosystem in Triassic halite subsurface system

description: This dataset includes two metagenomes from a Triassic halite mine in N.Ireland as part of a study on the insights into the mechanisms supporting microbial ecosystem in a NaCl stalactite within Triassic halite. One of which is metagenomic data from a brine sample and the other is from a subsurface NaCl stalactite here referred to as a saltcile. The brine DNA was sent to MR DNA Lab (Shallowater, TX, USA) for sequencing library preparation (Nextera XT) and subsequent metagenomic shotgun sequencing on the Illumina MiSeq platform. The salticle metagenome was prepared using the TruSeq® DNA PCR-Free library prep kit, and the shotgun sequencing was completed on an Illumina (San Diego, CA, USA) MiSeq platform at the Genomics Core Technology Unit, Queen’s University Belfast. In both cases, a MiSeq Reagent Kit v2 (500-cycles) (Illumina, San Diego, CA, USA) was used to generate paired-end, 2 x 250 base pair (bp) reads.
DOI: 10.5281/zenodo.4399885
title: Microbial ecosystem in Triassic halite subsurface system

description: This dataset includes two metagenomes from a Triassic halite mine in N.Ireland as part of a study on the insights into the mechanisms supporting microbial ecosystem in a NaCl stalactite within Triassic halite. One of which is metagenomic data from a brine sample and the other is from a subsurface NaCl stalactite here referred to as a saltcile. The brine DNA was sent to MR DNA Lab (Shallowater, TX, USA) for sequencing library preparation (Nextera XT) and subsequent metagenomic shotgun sequencing on the Illumina MiSeq platform. The salticle metagenome was prepared using the TruSeq® DNA PCR-Free library prep kit, and the shotgun sequencing was completed on an Illumina (San Diego, CA, USA) MiSeq platform at the Genomics Core Technology Unit, Queen’s University Belfast. In both cases, a MiSeq Reagent Kit v2 (500-cycles) (Illumina, San Diego, CA, USA) was used to generate paired-end, 2 x 250 base pair (bp) reads.
DOI: 10.6084/m9.figshare.13502487
title: Supplementary Material for: Proof of Concept for an “eyePhone” App to Measure Video Head Impulses

description: <b><i>Objective:</i></b> Differentiating benign from dangerous causes of dizziness or vertigo presents a major diagnostic challenge for many clinicians. Bedside presentations of peripheral vestibular disorders and posterior fossa strokes are often indistinguishable other than by a few subtle vestibular eye movements. The most challenging of these to interpret is the head impulse test (HIT) of vestibulo-ocular reflex (VOR) function. There have been major advances in portable video-oculography (VOG) quantification of the video HIT (vHIT), but these specialized devices are not routinely available in most clinical settings. As a first step towards smartphone-based diagnosis of strokes in patients presenting vestibular symptoms, we sought proof of concept that we could use a smartphone application (“app”) to accurately record the vHIT. <b><i>Methods:</i></b> This was a cross-sectional agreement study comparing a novel index test (smartphone-based vHIT app) to an accepted reference standard test (VOG-based vHIT) for measuring VOR function. We recorded passive (examiner-performed) vHIT sequentially with both methods in a convenience sample of patients visiting an otoneurology clinic. We quantitatively correlated VOR gains (ratio of eye to head movements during the HIT) from each side/ear and experts qualitatively assessed the physiologic traces by the two methods. <b><i>Results:</i></b> We recruited 11 patients; 1 patient’s vHIT could not be reliably quantified with either device. The novel and reference test VOR gain measurements for each ear (<i>n</i> = 20) were highly correlated (Pearson’s <i>r</i> = 0.9, <i>p</i> = 0.0000001) and, qualitatively, clinically equivalent. <b><i>Conclusions:</i></b> This preliminary study provides proof of concept that an “eyePhone” app could be used to measure vHIT and eventually developed to diagnose vestibular strokes by smartphone.
DOI: 10.5519/qd.wwahhiun
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (756 records)
DOI: 10.6084/m9.figshare.13502397
title: Pre-harvest measures against Fusarium spp. infection and related mycotoxins implemented by Dutch wheat farmers

description: Fusarium spp. are one of the most widespread mycotoxin-producing fungi in small-grain cereals like wheat. Theirrate of infection and production of mycotoxins is mainly influenced by weather and pre-harvest agronomicmeasures. Consequently, farmers’ prevention and control of mycotoxins are imperative since it is difficult toremove mycotoxins further down the cereal supply chain. This study aimed to (i) identify which pre-harvestpreventive and control measures Dutch wheat farmers currently apply against Fusarium spp. infection andmycotoxin contamination and to (ii) examine which farm and farmer characteristics explain the implementationof these measures. Field data on pre-harvest measures, like the selection of resistant varieties, fungicide use, andcrop rotation, along with farm and farmer characteristics were collected from Dutch wheat farmers via an onlinequestionnaire. Probit models were applied to examine farm and farmer characteristics that explain the implementationof pre-harvest measures. Results showed that most farmers applied six or more different measuresagainst Fusarium spp. infection and mycotoxin contamination in wheat and that the use of pre-harvest measuresis related to at least one other measure. However, results indicated that about 44% of farmers could become moreeffective if they implemented a benchmark approach consisting of a combination of fungicide use duringflowering, selection of a Fusarium resistant wheat variety, and plowing or crop rotation. Five out of the tenevaluated farm and farmer characteristics significantly (p &lt; 0.05) explained the implementation of at least one ofthe eight pre-harvest control measures. These five farm and farmer characteristics include wheat as main incomecrop, the use of a decision support system, the education level of the farmer, the farmer’s knowledge aboutmycotoxins, and the farmer’s level of risk aversion. Insight into relevant characteristics can be used by farmercooperatives, processing industries and government agencies to improve the overall mycotoxin management ofwheat farmers.
DOI: 10.6084/m9.figshare.13502397.v1
title: Pre-harvest measures against Fusarium spp. infection and related mycotoxins implemented by Dutch wheat farmers

description: Fusarium spp. are one of the most widespread mycotoxin-producing fungi in small-grain cereals like wheat. Theirrate of infection and production of mycotoxins is mainly influenced by weather and pre-harvest agronomicmeasures. Consequently, farmers’ prevention and control of mycotoxins are imperative since it is difficult toremove mycotoxins further down the cereal supply chain. This study aimed to (i) identify which pre-harvestpreventive and control measures Dutch wheat farmers currently apply against Fusarium spp. infection andmycotoxin contamination and to (ii) examine which farm and farmer characteristics explain the implementationof these measures. Field data on pre-harvest measures, like the selection of resistant varieties, fungicide use, andcrop rotation, along with farm and farmer characteristics were collected from Dutch wheat farmers via an onlinequestionnaire. Probit models were applied to examine farm and farmer characteristics that explain the implementationof pre-harvest measures. Results showed that most farmers applied six or more different measuresagainst Fusarium spp. infection and mycotoxin contamination in wheat and that the use of pre-harvest measuresis related to at least one other measure. However, results indicated that about 44% of farmers could become moreeffective if they implemented a benchmark approach consisting of a combination of fungicide use duringflowering, selection of a Fusarium resistant wheat variety, and plowing or crop rotation. Five out of the tenevaluated farm and farmer characteristics significantly (p &lt; 0.05) explained the implementation of at least one ofthe eight pre-harvest control measures. These five farm and farmer characteristics include wheat as main incomecrop, the use of a decision support system, the education level of the farmer, the farmer’s knowledge aboutmycotoxins, and the farmer’s level of risk aversion. Insight into relevant characteristics can be used by farmercooperatives, processing industries and government agencies to improve the overall mycotoxin management ofwheat farmers.
DOI: 10.5281/zenodo.4395254
title: Laser-free super-resolution microscopy

description: Raw data for "Laser-free super-resolution microscopy" https://www.biorxiv.org/content/10.1101/121061v3.full.pdf
DOI: 10.5281/zenodo.4395253
title: Laser-free super-resolution microscopy

description: Raw data for "Laser-free super-resolution microscopy" https://www.biorxiv.org/content/10.1101/121061v3.full.pdf
DOI: 10.6084/m9.figshare.13502547
title: Supplementary Material for: Utilization of Machine Learning-Based Computer Vision and Voice Analysis to Derive Digital Biomarkers of Cognitive Functioning in Trauma Survivors

description: <b><i>Background:</i></b> Alterations in multiple domains of cognition have been observed in individuals who have experienced a traumatic stressor. These domains may provide important insights in identifying underlying neurobiological dysfunction driving an individual’s clinical response to trauma. However, such assessments are burdensome, costly, and time-consuming. To overcome barriers, efforts have emerged to measure multiple domains of cognitive functioning through the application of machine learning (ML) models to passive data sources. <b><i>Methods:</i></b> We utilized automated computer vision and voice analysis methods to extract facial, movement, and speech characteristics from semi-structured clinical interviews in 81 trauma survivors who additionally completed a cognitive assessment battery. A ML-based regression framework was used to identify variance in visual and auditory measures that relate to multiple cognitive domains. <b><i>Results:</i></b> Models derived from visual and auditory measures collectively accounted for a large variance in multiple domains of cognitive functioning, including motor coordination (<i>R</i><sup>2</sup> = 0.52), processing speed (<i>R</i><sup>2</sup> = 0.42), emotional bias (<i>R</i><sup>2</sup> = 0.52), sustained attention (<i>R</i><sup>2</sup> = 0.51), controlled attention (<i>R</i><sup>2</sup> = 0.44), cognitive flexibility (<i>R</i><sup>2</sup> = 0.43), cognitive inhibition (<i>R</i><sup>2</sup> = 0.64), and executive functioning (<i>R</i><sup>2</sup> = 0.63), consistent with the high test-retest reliability of traditional cognitive assessments. Face, voice, speech content, and movement have all significantly contributed to explaining the variance in predicting functioning in all cognitive domains. <b><i>Conclusions:</i></b> The results demonstrate the feasibility of automated measurement of reliable proxies of cognitive functioning through low-burden passive patient evaluations. This makes it easier to monitor cognitive functions and to intervene earlier and at a lower threshold without requiring a time-consuming neurocognitive assessment by, for instance, a licensed psychologist with specialized training in neuropsychology.
DOI: 10.6084/m9.figshare.13502529
title: Supplementary Material for: Prophylactic Topical Treatment for EGFR Inhibitor-Induced Papulopustular Rash: A Randomized Clinical Trial

description: <b><i>Background:</i></b> The incidence of epidermal growth factor receptor inhibitor (EGFRI)-induced papulopustular rash is 60–85%. <b><i>Objective:</i></b> To investigate prophylactic topical treatment for EGFRI-induced rash. <b><i>Methods:</i></b> A single-center, randomized, double-blind, placebo-controlled trial. Adult cancer patients initiating treatment with EGFRIs were randomized to receive facial topical treatment with chloramphenicol 3% + prednisolone 0.5% (CHL-PRED) ointment, chloramphenicol 3% (CHL) ointment, or aqua cream (AQUA). The primary end points were the incidence of ≥grade 3 rash using the Common Terminology Criteria for Adverse Events (CTCAE), on days 14 and 30. A subanalysis was conducted for incidence of a protocol-specified significant rash, defined as ≥10 facial papulopustular lesions. <b><i>Results:</i></b> The per-protocol analysis on day 14 included 69 patients, who received CHL-PRED (21), CHL (23), or AQUA (25). The incidence of CTCAE ≥grade 3 rash was not statistically significant between arms; however, the incidence of the protocol-specified significant rash was: CHL-PRED 14%, CHL 39%, and AQUA 48% (<i>p</i> = 0.03, CHL-PRED vs. AQUA). At 30 days, the CTCAE ≥grade 3 incidence was similar, but the incidences of protocol-specified significant rash were 6%, 16%, and 43% (<i>p</i> = 0.03, CHL-PRED vs. AQUA). No significant differences were found between CHL and CHL-PRED and between CHL and AQUA. <b><i>Conclusions:</i></b> Prophylactic topical CHL-PRED was efficacious when compared to AQUA, in the treatment of EGFRI-induced facial papulopustular rash.