cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21252378
title: Supplementary Material for: Mechanism of glycitein in the treatment of colon cancer based on network pharmacology and molecular docking

description: Introduction: The prevalence of colon cancer remains high across the world. The early diagnosis of colon cancer is challenging. Moreover, patients with colon cancer frequently suffer from poor prognoses. Methods: Differentially expressed genes (DEGs) in colon cancer were acquired based on TCGA-COAD dataset screening. DEGs were input into the Connectivity Map (CMap) database to screen small molecule compounds with the potential to reverse colon cancer pathological function. Glycitein ranked first among the screened small molecule compounds. We downloaded the main targets of glycitein from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database and constructed protein-protein interaction (PPI) networks of those which were closely related to targets by Search Tool for the Retrieval of Interaction Gene/Proteins (STRING). Five potential targets of glycitein for treating colon cancer were identified (CCNA2, ESR1, ESR2, MAPK14, and PTGS2). These targets were used as seeds for random walk with restart (RWR) analysis of PPI networks. Then, the interaction network of glycitein-colon cancer-related genes was constructed based on the top 50 genes in affinity coefficients. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on the potential genes targeted by glycitein in colon cancer treatment and those were closely bound up with targets. Results: GO analysis demonstrated that the enrichment of these genes was primarily discovered in biological functions including regulation of fibroblast proliferation, response to oxygen levels, and epithelial cell proliferation. KEGG analysis results illustrated that the signaling pathways where these genes were mostly involved consisted of the mitogen-activated protein kinases signaling pathway, the phosphatidylinositol-3-kinase-Akt signaling pathway, and the p53 signaling pathway. Finally, stable binding of glycitein to five potential targets in colon cancer was verified by molecular docking. Conclusion: This study elucidated the key targets and main pathways of glycitein on the basis of network pharmacology and preliminarily analyzed molecular mechanisms in the treatment of colon cancer. A scientific basis is provided for glycitein application in treating colon cancer.
DOI: 10.6084/m9.figshare.21304314
title: Supplementary Material for: Intravitreal dexamethasone implant has better retinal perfusion than anti-vascular endothelial growth factor treatment for macular edema secondary to retinal vein occlusion: a five-year real-world study

description: Purpose: To investigate the long-term effect of intravitreal dexamethasone (DEX) implant and anti-vascular endothelial growth factor (VEGF) injection on macular edema (ME) secondary to retinal vein occlusion (RVO) in a real-world setting. Methods: The medical records of RVO-ME cases, with intravitreal injections and followed-up for at least 5 years, were retrospectively reviewed. Changes in best-corrected visual acuity (BCVA) and central macular thickness (CMT) were primary outcomes. Images of fluorescence angiography (FA) and swept-source optical coherence tomography angiography (OCTA) were analyzed. Foveal avascular zone (FAZ) metrics and perfusion density at the last visit were also compared between the two treatments. Results: A total of 16 patients were recruited, 8 in the anti-VEGF group and 8 in the DEX group. At the 5th year, the BCVA and the CMT in the DEX group were not different from those in the anti-VEGF group (0.69 ± 0.36 LogMAR vs 0.57 ± 0.30 LogMAR, P = 0.574; 183.25 ± 97.31 μm vs 195.38 ± 40.92 μm, P = 0.442). Compared with the anti-VEGF group, the DEX group had higher FAZ circularity index (0.57 ± 0.14 vs 0.68 ± 0.14, P = 0.130) and higher retinal perfusion density (0.45 ± 0.02 vs 0.39 ± 0.03, P = 0.001), especially in the deep capillary plexus. Conclusion: DEX implant and anti-VEGF injection had comparative long-term effects on RVO-ME. Compared with the anti-VEGF treatment, the DEX treatment had advantages in maintaining retinal perfusion in patients with RVO.
DOI: 10.6084/m9.figshare.21311088
title: Supplementary Material for: Obesity Exacerbates Lupus Activity in Fc Gamma Receptor IIb Deficient Lupus Mice Partly through Saturated Fatty Acid-Induced Gut Barrier Defect and Systemic Inflammation

description: The prevalence of obesity is increasing, and the coexistence of obesity and systemic lupus erythematosus (lupus) is possible. A high-fat diet (HFD) was orally administered for 6 months in female 8-week-old Fc gamma receptor IIb deficient (FcgRIIb−/−) lupus or age and gender-matched wild-type (WT) mice. Lupus nephritis (anti-dsDNA, proteinuria, and increased creatinine), gut barrier defect (fluorescein isothiocyanate dextran), serum lipopolysaccharide (LPS), serum interleukin (IL)-6, liver injury (alanine transaminase), organ fibrosis (liver and kidney pathology), spleen apoptosis (activated caspase 3), and aorta thickness (but not weight gain and lipid profiles) were more prominent in HFD-administered FcgRIIb−/− mice than the obese WT, without injury in regular diet-administered mice (both FcgRIIb−/− and WT). In parallel, combined palmitic acid (PA; a saturated fatty acid) with LPS (PA + LPS) induced higher tumor necrotic factor-α, IL-6, and IL-10 in the supernatant, inflammatory genes (inducible nitric oxide synthase and IL-1β), reactive oxygen species (dihydroethidium), and glycolysis with reduced mitochondrial activity (extracellular flux analysis) when compared with the activation by each molecule alone in both FcgRIIb−/− and WT macrophages. However, the alterations of these parameters were more prominent in PA + LPS-administered FcgRIIb−/− than in the WT cells. In conclusion, obesity accelerated inflammation in FcgRIIb−/− mice, partly due to the more potent responses from the loss of inhibitory FcgRIIb against PA + LPS with obesity-induced gut barrier defect.
DOI: 10.6084/m9.figshare.21334266
title: Supplementary Material for: Getting in a Spin Over the Therapeutic Process: QBism and a Gyroscopic Model of the Vital Force

description: Background: In the previous paper, a relatively new interpretation of quantum theory called QBism, was introduced as an alternative quantum metaphor for the therapeutic process (TP). This is because previous metaphors have been based on conventional quantum theory and its notion that quantum states belong to a strongly objective shared reality. QBism suggests otherwise, quantum states being merely subjective degrees of belief made by the individual agents assigning those states. It suggests QBism’s explicit subjectivity is more in line with practitioners’ (Pr) and patient’s (Px) implicitly subjective experience of the TP. Objective: To investigate the impact on this suggestion of a previously developed gyroscopic model of the Vital Force, Vf. Method: Based on an original starting wavefunction for the Vf, a sequence of equations and transformations between them are generated and then interpreted as the Vf interacting with and moving into and out of dis-ease (Dx) states, in essence, a physics of health. Results/Discussion & Conclusion: These equations and their transformations manage to predict (a) homeopathic aggravation from the curative remedy (Rx), and (b) the logic behind Hahnemann’s development of the LM potencies. Further, displaying these equations and their interactions pictorially and geometrically (as a stellated octahedron) suggests that the recently developed gyroscopic model for the Vf supports a metaphor for the therapeutic process (based on the subjectivity explicit in QBism), that is indeed viable and potentially superior to previous metaphors based on the strong objectivity of conventional quantum theory (CQT).
DOI: 10.6084/m9.figshare.21359745
title: Supplementary Material for: Hospital-based study of risk factors associated with development of myopic macular neovascularization in highly myopic eyes

description: Introduction: Myopic macular neovascularization (MNV) is the most common cause of a reduction of central vision in eyes with pathologic myopia, and it can progress to macular atrophy in the long-term. The aim of this study was to determine the risk factors associated with the development of MNVs. Methods: There were 17,198 follow-up records from 5,409 eyes of 2,784 highly myopic patients that were reviewed. The general information and ophthalmic information in the records were studied. The significance of the correlations of factors associated with the development and predicting the development of myopic MNV were determined. Results: Being a woman (odds ratio [OR]: 0.727, P&lt;0.001), having a longer axial length (OR = 0.948, P&lt;0.001), a poorer baseline best-correct visual acuity (BCVA, OR = 2.098, P&lt;0.001), having severe myopic maculopathy (overall: P&lt;0.001), prior myopic MNV in the fellow eye (OR = 4.105, P&lt;0.001), presence of patchy atrophy (overall P&lt;0.001), lacquer cracks (OR = 1.718, P&lt;0.001), prior foveal retinal detachment (RD, OR = 3.269, P&lt;0.001), prior macular hole (MH, OR = 0.641, P &lt;0.001), prior macular retinoschisis (OR = 1.533, P&lt;0.001), and prior macular edema (OR = 1.508, P&lt;0.001) were significantly correlated with the development of myopic MNV. Eyes with MNV and patchy atrophy would require an intensive follow-up examination for myopic patients as the fellow eye would have a risk of &gt;70% for the development of myopic MNV in 3-years and nearly 80% in 5-years. Conclusions: Clinicians need to pay special attention to eyes with severe grades of myopic maculopathy, prior myopic MNV in the fellow eye, presence of patchy atrophy, and prior foveal retinal detachment to determine the onset of myopic MNV.
DOI: 10.6084/m9.figshare.21435369
title: Supplementary Material for: Reduction of missed diagnosis of G6PD deficiency in heterozygous females by G6PD/6PGD ratio assay combined with ARMS-PCR

description: Objective: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder that results in impaired enzyme activity. The G6PD/6PGD ratio assay was routinely used for G6PD deficiency screening in China, but there is an apparent defect of missed diagnosis in heterozygous females. The study aims to explore the means to improve its accuracy. Methods: A total of 4161 Chinese females of childbearing age were collected in this retrospective study. All samples were first subjected to G6PD/6PGD ratio assay and then screened by amplification refractory mutation system PCR (ARMS-PCR) for six hotspot mutants in Chinese population (c.1376G&gt;T, c.1388G&gt;A, c.95A&gt;G, c.1024C&gt;T, c.392G&gt;T, and c.871G&gt;A). For the samples with G6PD/6PGD ratio &lt;1.0 and no mutations were found by ARMS-PCR, next-generation sequencing (NGS) was performed. Sanger sequencing was finally used to verify all the variants. Results: The prevalence of G6PD deficiency in Shenzhen females of childbearing age was 7.31%. The proportion of the six hotspot mutations accounted for 98.03% of all 304 G6PD variants carriers. Taking the ARMS-PCR/NGS results as a reference, the missed diagnosis rate of the G6PD/6PGD ratio assay was 33.88%. Using ARMS-PCR to retest the samples with a G6PD/6PGD ratio between 1.00~1.10 or 1.00~1.15 could reduce the missed diagnosis rate from the original 33.88% to 18.09% or 12.05% separately. Conclusion: ARMS-PCR is an appropriate supplementary method for discovering most carriers missed by the G6PD/6PGD ratio assay.
DOI: 10.6084/m9.figshare.21673232
title: Supplementary Material for: The Effect of Prostaglandin Analogues on Central Corneal Thickness of Patients with Glaucoma or Ocular Hypertension: a systematic review

description: Purpose: A meta-analysis of observational studies was conducted to evaluate the effect of prostaglandin analogues (PGAs) on central cornea thickness (CCT) of patients with glaucoma and ocular hypertension (OHT). Methods: A literature search was performed through Pubmed, Embase, Cochrane Library, the System for Information on Grey Literature in Europe (Open Grey), ClinicalTrials.gov, and reference lists of retrieved studies. Observational studies were included in our meta-analysis. The final CCT of patients and 95% confidence interval (CI) from each study were extracted. Study quality was assessed using The Newcastle-Ottawa Scale (NOS) and the Agency for Healthcare Research and Quality (AHRQ). A fixed-effects model was used to calculate the weighted mean difference (WMD) and 95% confidence interval (CI). Subgroup analyses based on several stratified factors were also performed. Results: Five cohort studies, five case-control, three cross-sectional studies involving 2722 subjects were included. The pooled effect of all thirteen studies showed PGAs can reduce CCT of patients with glaucoma or OHT slightly but significantly (WMD, -9.37; 95% CI [-12.18, -6.57], P =0.00; I2 = 45.5%). And significant results were observed in all specific study design ( WMD, -5.17; 95% CI [-9.52, -0.82] for cohort study; WMD, -15.31; 95% CI [-22.66, -7.97] for case–control study; WMD, -8.65; 95% CI [-17.30, -0.01] for cross-sectional study). Also, subgroup analysis of exposure time showed the effect of PGAs was more obvious in the first two years (WMD, -5.81; 95% CI [-9.49, -2.14] for 1 year; WMD, -13.02; 95% CI [-20.03, -6.01] for 2 years). Conclusions: The pooled effects from current literature suggest that PGAs use could reduce CCT of patients with glaucoma or OHT slightly but significantly, and this effect is more pronounced in the first two years. This reminds us that we need to pay attention to the changes in CCT during the first two years of PGA use in case we misestimate intraocular pressure (IOP) and the efficacy of the PGA.
DOI: 10.6084/m9.figshare.21673241
title: Supplementary Material for: DISCORDANCE BETWEEN ANTERIOR SEGMENT ANATOMY AND AXIAL LENGTH IN CATARACT SURGERY CANDIDATES IN FRANCE

description: Introduction: To study ocular biometric data and their association with age and sex in a population of cataract surgery candidates. To assess the proportion of inhomogeneous eyes and the ratio anterior segment (AS) to axial length (AL). Multicentric cross-sectional analysis between April 2008 and May 2021 in public and private ophthalmic institutions in Montpellier, France. Individuals ≥ 40 years old who underwent ocular biometry before cataract surgery were included. Methods: Right phakic eyes were included. Ocular biometrics were measured by using the Lenstar LS900 device. We defined AS as anterior chamber depth (ACD) plus lens thickness (LT) and calculated the ratio of AS to AL. We defined inhomogeneous eyes as those with deep AS (≥ 4th quartile) and short AL (≤ 1st quartile) (AS+) or with short AS and high AL (AL+). Results: We included 11,650 individuals (11,650 eyes) (mean [SD] age 71.64 [10.50] years; 54.51% women). Older age was associated with shorter AL (p&lt;0.01), shallower ACD (p &lt; 0.01), thinner central corneal thickness (p&lt; 0.01) and larger LT (p&lt;0.001). Women had shorter AL, shallower ACD, and thinner central corneal thickness than men (p&lt;0.001). In total, 778 (6.68%) eyes were inhomogeneous (3.22% AS+ and 3.46% AL+), for a mean (SD) AS/AL ratio of 0.36 (0.01) and 0.28 (0.01), respectively, as compared with 0.32 (0.02) for homogeneous eyes (p&lt;0.001). Conclusion: The AS/AL ratio could be useful to screen inhomogeneous eyes before cataract surgery and justify the use of new generation formulas in these eyes to avoid the risk of refractive error.
DOI: 10.6084/m9.figshare.21908616
title: Supplementary Material for: Risk Factors for Fellow Eye Involvement in Patients with Nonarteritic Anterior Ischemic Optic Neuropathy

description: <b><i>Introduction:</i></b> The aim of the study was to investigate the possible risk factors for fellow eye involvement in patients with nonarteritic anterior ischemic optic neuropathy (NAION). <b><i>Methods:</i></b> A total of 113 patients with unilateral NAION attack were included and divided into two groups according to whether fellow eye involvement was present over a mean follow-up period of 2.70 years (P25–P75: 0.77–3.54 years). General characteristics (including age, sex, diabetes, hypertension, hyperlipidemia, and obstructive sleep apnea syndrome [OSAS]) and ocular characteristics (including initial best-corrected visual acuity, initial visual field damage of the first eye, and the presence/absence of a crowded disc) were analyzed and compared between the two groups. Cox regression was used to assess the risk factors for fellow eye involvement. <b><i>Results:</i></b> During the follow-up period, 40 patients developed fellow eye involvement. The initial best-corrected visual acuity (<i>p</i> = 0.048) and mean deviation of the visual field (VF) (<i>p</i> = 0.039) of the first eye in patients with fellow eye involvement were worse than those in patients without it. Diabetes (HR = 3.06, 95% CI: 1.50, 6.26, <i>p</i> = 0.002) and increased VF damage (moderate vs. mild, HR = 2.92, 95% CI: 1.03, 8.25, <i>p</i> = 0.043; severe vs. mild, HR = 5.01, 95% CI: 1.65, 15.20, <i>p</i> = 0.004) were associated with a significantly increased risk of fellow eye involvement. In 57 patients with apnea-hypopnea index (AHI) data for further study, an AHI score ≥23.2 was also found to be a risk factor (HR = 3.36, 95% CI: 1.17, 9.69, <i>p</i> = 0.025). <b><i>Conclusion:</i></b> Diabetes, severer initial VF damage, and more severe OSAS were risk factors for fellow eye involvement in NAION. For patients with these risk factors, more intensive follow-ups might be warranted.
DOI: 10.6086/n13j3b0g
title: NYCTaxi
title: Pickup and drop-off locations of taxi rides in New York City

description: This dataset represents pickup and dropoff locations of NYC Taxi in 2013
DOI: 10.18739/a2kh0f08v
title: DataHawk2 Uncrewed Aircraft System data from the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) campaign, B1 level

description: This dataset is derived from DataHawk2 fixed-wind uncrewed aircraft system (UAS) flights that were conducted in the central Arctic Ocean over sea ice during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The data include Coordinated Universal Time (UTC), aircraft position and attitude, atmospheric thermodynamic conditions (pressure, temperature, humidity) from various sensors, approximate brightness temperature of the surface and overlying atmosphere, and estimated horizontal winds. A flight flag is included to indicate when the aircraft is in flight. All the data have been synchronized, quality controlled, and interpolated at 10 hertz (Hz). Data at their native frequency are provided in the A1 level files, and are available in the Arctic Data Center at doi:10.18739/A22Z12Q8X. The purpose of this dataset is to provide information on the thermodynamic and kinematic states of the lower atmosphere, and provide detailed observations of turbulence between the surface and one kilometer. Two flight patterns were implemented during the campaign with the DataHawk2: an orbital profile extending from the ice surface to 1000 meter(m) or cloud base if lower, and a “racetrack” pattern where the aircraft was held at a constant altitude while sampling horizontally between two circles. The latter was used to collect data on the spatial variability of thermodynamic properties over the ice surface, particularly over inhomogeneities in the surface such as leads. Displaying latitude, longitude and altitude will help users to identify the flight pattern. Thermodynamic and kinematic measurements have been validated with radiosonde-based measurements. More information on the data and methods used for synchronization and quality control can be found in de Boer, G. R. Calmer, G. Jozef, J. Cassano, J. Hamilton, D. Lawrence, S. Borenstein, A. Doddi, C. Cox, J. Schmale, A. Preußer and B. Argrow (2021): Observing the Central Arctic Atmosphere and Surface with University of Colorado Uncrewed Aircraft Systems, Nature Scientific Data, in prep.
DOI: 10.5281/zenodo.4461575
title: The FireTracks Scientific Dataset

description: The <strong>FireTracks Scientific Dataset</strong> is based on the MODIS Fire Products MOD14A1/MYD14A1 and the MODIS Land Cover Product MCD12Q1. It entails HDF5-tables/GeoPackages of active fire events, spatiotemporal components of fire events and associated land cover information. For detailed information, please see https://github.com/dominiktraxl/firetracks. A command line interface (CLI) to convert the HDF5 files provided in this repository to CSV files is available at the above link. Version of original data used to create the FireTracks Scientific Dataset (v1.0.0): MOD14A1: Collection 6 (C6) MYD14A1: Collection 6 (C6) MCD12Q1: Collection 6 (C6) The FireTracks Scientific Dataset (v1.0.0) covers the years from 2002 to the end of the year 2020.
DOI: 10.5281/zenodo.4555536
title: Dataset for "Terrestrial laser scanning to reconstruct branch architecture from harvested branches"

description: Datasets supporting the publication "Terrestrial laser scanning to reconstruct branch architecture". <em>Polygon File Format </em>(.ply) files can be viewed in software such as CloudCompare. For each branch ther Unfiltered point clouds are clipped from the original data and have had no post processing applied Filtered point clouds have been filtered according to the steps in manuscript QSM were produced using <em>treegraph</em> Manual measurements
DOI: 10.5281/zenodo.7093590
title: Postprocessed data for "Tracing the rain formation pathways in numerical simulations of deep convection"

description: This dataset is associated with the journal paper "Tracing the rain formation pathways in numerical simulations of deep convection". There are six .npz files containing data for the 5 simulations (CTRL, CTRLrfix, K13, CTRL800, K13800)<br> and one npz file containing data for constructing the rain pdfs of simulation CTRL (Figure 6). This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52‐07NA27344 IM Release number LLNL-MI-843623
DOI: 10.5291/ill-data.8-03-807
title: Towards a Fuller Understanding of Salt-Bridges in Proteins
DOI: 10.5441/002/edbt.2017.08
title: Lightweight Data Compression Algorithms: An Experimental Survey (Experiments and Analyses)
DOI: 10.6084/m9.figshare.20254467
title: Supplementary Material for: <b><i>Slc6a13</i></b> Deficiency Attenuates <b><i>Pasteurella multocida</i></b> Infection-Induced Inflammation via Glycine-Inflammasome Signaling

description: We have previously demonstrated that Slc6a13-deficient (Slc6a13<sup>−/−</sup>; KO) mice are resistant to <i>P</i>. <i>multocida</i> infection, which might be in connection with macrophage-mediated inflammation; however, the specific metabolic mechanism is still enigmatic. Here we reproduce the less sensitive to <i>P</i>. <i>multocida</i> infection in overall survival assays as well as reduced bacterial loads, tissue lesions, and inflammation of lungs in KO mice. The transcriptome sequencing analysis of wild-type (WT) and KO mice shows a large number of differentially expressed genes that are enriched in amino acid metabolism by functional analysis. Of note, glycine levels are substantially increased in the lungs of KO mice with or without <i>P</i>. <i>multocida</i> infection in comparison to the WT controls. Interestingly, exogenous glycine supplementation alleviates <i>P</i>. <i>multocida</i> infection-induced inflammation. Mechanistically, glycine reduces the production of inflammatory cytokines in macrophages by blocking the activation of inflammasome (NALP1, NLRP3, NLRC4, AIM2, and Caspase-1). Together, Slc6a13 deficiency attenuates <i>P</i>. <i>multocida</i> infection through lessening the excessive inflammatory responses of macrophages involving glycine-inflammasome signaling.