cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12037281
title: Data from: Universal and taxon-specific trends in protein sequences as a function of age

description: This dataset contains the following:<br><br><b>Metrics databases</b>, as calculated over all pfam and full gene sequences used in this analysis, stored as tab-delimited flat files with headers.- EnsemblGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - EnsemblGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.<br>- NCBIGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - NCBIGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.<br><br>-S2_SpeciesList:Gives the species, and their reference species UIDs (unique identifier numbers), which are used in the above datatables.<br><br><b>Homology dictionary datasets</b> for each metric. These were created for: ISD, amino acid composition, and hydrophobic clustering. files are organised into a single gzipped folder:<br>-HomologyDictionaryFiles.zip: <br><br>Contents:<br>Filenames are descriptive, and state: 1) whether the homology groups were calculated over genes or pfams, 2) the metric, 3) whether the data was transformed, 4) over which kingdom the homology groups were calculated over (if any, this is either 'animal' or 'plant'), 5) whether it was specified if the genes or pfams included in the analysis were transmembrane (TransmembraneOnly, or Trans) or not (NonTransmembrane, or NonTrans).<br>-Filenames starting with 'MetricVsTime: Each file consists of two columns, 'Metric', (as specified in the file title, as either isd, isd without cysteine or clustering), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.<br>-Filenames starting with 'AAComp': Summaries of phylostratigraphy slopes for each amino acid slope<br><br>-Files in AACompFiles folder: Each file consists of two columns, 'Metric', (amino acid composition for amino acid specified in file title), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.<br>Sequence data was accessed from Ensembl and NCBI. All scripts used to generate the datasets are available at https://github.com/MaselLab/ProteinEvolution<br>
DOI: 10.6084/m9.figshare.21828126
title: Supplementary Material for: Late PAMM-Like Lesions in a Patient with HIV Retinopathy

description: This report describes a case of a newly diagnosed 49-year-old HIV patient, who presented with decreased visual acuity and retinal lesions characterized by ischemia at the level of the deep retinal capillary plexus, documented with optical coherence tomography (OCT), OCT angiography, fluorescein angiography, and visual fields testing. These lesions closely resembled the morphologic and clinical characteristics of late paracentral acute middle maculopathy. The presence of these lesions suggests that HIV microangiopathy can potentially affect both superficial and deep retinal capillary plexuses.
DOI: 10.6084/m9.figshare.21968105
title: Supplementary Material for: Temporary Myopic Shift in a Patient with Multiple Parallel-Line Endotheliitis

description: Here, we report the case of a patient with multiple parallel-line endotheliitis with myopic shift, which has not been previously reported. A 36-year-old man visited our clinic with blurred vision in his left eye. A slit lamp examination revealed an interesting pattern of multiple parallel lines of keratic precipitates, along with subtle corneal edema. The spherical equivalents measured in the right and left eyes were -9.25 and -11.875 diopter, respectively, with the left eye showing more myopic progression. On specular microscopy, endothelial cell loss was found in the left eye. After administration of a weak topical steroid, keratic precipitates and corneal edema resolved completely within 2 days. The myopic shift in his left eye recovered to -10.0 diopters. Multiple parallel-line endotheliitis can be easily treated with a weak topical steroid in a short period. A temporary myopic shift may occur, which in this case resolved upon disease recovery. However, corneal endothelial cell loss is inevitable; therefore, careful monitoring is needed.
DOI: 10.6084/m9.figshare.22210117
title: Supplementary Material for: A simplified clinical prediction rule for prognosticating dependent daily living in patients with thoracic spinal cord injury: A multicenter nationwide Japan registry study

description: Introduction Clinical prediction rule (CPR) using decision tree analysis is able to show the branching of the variables under consideration in a clear, hierarchical manner, including specific reference values, which can be used as classifiers in clinical practice. However, CPR developed by decision tree analysis for predicting the degree of independent living of patients with thoracic spinal cord injury (SCI) are few. The purpose of this study was to develop a simplified CPR for prognosticating dependent daily living in patients with thoracic SCI. Methods We extracted data on patients with thoracic SCI from a national multicenter registry database, the Japan Rehabilitation Database (JRD). All patients with thoracic SCI who were hospitalized within 30 days after injury onset were included. The independent living was categorized in the JRD as follows: independent socially, independent at home, needing care at home, independent at the facility, and needing care at the facility. These categories were used as the objective variables in classification and regression tree (CART) analysis. The CART algorithm was applied to develop the CPR for predicting whether patients with thoracic SCI achieve independent living at hospital discharge. Results Three hundred ten patients with thoracic SCI were included in the CART analysis. The CART model identified, in a hierarchical order, patient’s age, residual function level, and the bathing sub-score of Functional Independence Measure as the top three factors with moderate classification accuracy and area under the curve. Conclusions We developed a simplified, moderately accurate CPR for predicting whether patients with thoracic SCI achieve independent living at hospital discharge.
DOI: 10.15785/sbgrid/963
title: X-Ray Diffraction data from WTsoak Nramp/MntH divalent transition metal transporter from Deinococcus radiodurans, source of 8E5V structure

description: High resolution dataset of a single LCP crystal of WT mock-soaked in precipitant
description: Data was processed using XDS, indexed using POINTLESS in P22121 spacegroup and scaled using AIMLESS at 2.38A.
DOI: 10.15785/sbgrid/964
title: X-Ray Diffraction data from Manganese-bound WT Nramp/MntH divalent transition metal transporter from Deinococcus radiodurans, source of 8E60 structure

description: High resolution dataset of a single LCP crystal of WT soaked in precipitant containing manganese
description: Data was processed using XDS, indexed using POINTLESS in space group P22121, scaled using AIMLESS at 2.38A
DOI: 10.15785/sbgrid/966
title: X-Ray Diffraction data from Mn-bound A47W mutant Nramp/MntH divalent transition metal transporter from Deinococcus radiodurans, source of 8E6H structure

description: High resolution dataset of Mn-bound A47W mutant collected from a single LCP crystal
description: Data was processed using XDS, indexed using POINTLESS in P22121 spacegroup, scaled using AIMLESS at 2.39A
DOI: 10.15785/sbgrid/968
title: X-Ray Diffraction data from Mn-bound D296A mutant Nramp/MntH divalent transition metal transporter from Deinococcus radiodurans, source of 8E6L structure

description: Datasets of Mn-bound D296A was collected from 3 LCP crystals. Image files that start C7run1_17 are from the first crystal, C7run2_19 are from the second crystal and C7run4_20 are from the third crystal.
description: Data was processed using XDS, indexed using POINTLESS in space group P22121, scaled using AIMLESS at 3.11A.
DOI: 10.15785/sbgrid/969
title: X-Ray Diffraction data from Cadmium-bound WT Nramp/MntH divalent transition metal transporter from Deinococcus radiodurans, source of 8E6M structure

description: High resolution dataset collected from a single WT LCP crystal soaked in precipitant having cadmium.
description: Data was processed using XDS, indexed using POINTLESS in space group P22121, and scaled using AIMLESS at 2.48A.
DOI: 10.18112/openneuro.ds001132.v1.0.0
title: Sherlock
DOI: 10.18112/openneuro.ds004592.v1.0.1
title: SONG dataset
DOI: 10.25824/redu/2mrgl4
title: Physiological data and transcriptional profile collected from the anaerobic chemostat cultures of Saccharomyces cerevisiae strain SA-1 supplemented with 5 mM of p-coumaric acid

description: Physiological data collected from the anaerobic chemostat cultures of Saccharomyces cerevisiae strain SA-1. The yeast culture was cultivated using a chemostat system, with 1L working volume in anaerobic conditions (800 rpm and D ~0.1/h.) The two control samples used verduyn medium supplemented with glucose (25 g/L), KOH (2 mM) and a working pH of 5.0; the treated samples received the same medium with the addition of 5 mM of p-coumaric acid.
DOI: 10.25824/redu/emxway
title: IndyDB - a comparative genomics database for industrial yeast strains

description: INDYdb is a database project which aims to provide users with a platform to perform comparative genomic analyses of multiple yeast strains used in biotechnology industry. Although our main focus is on strains used in bioethanol production, we plan to grow and expand the database to include industrial yeasts all types of applications. Our main goal is to provide structural and functional gene annotations for each of the assemblies using an unified pipeline that can produce consistent results, allowing easy comparison among strains for scientists and professionals around the world .
DOI: 10.5281/zenodo.10002180
title: A database of the healthy human spinal cord morphometry in the PAM50 template space

description: About: This dataset is a collection of tabular files containing normative values of normalized metrics of human spinal cord MRI morphological measurements  (cross-sectional area, AP diameter, transverse diameter, compression ratio, eccentricity, and solidity) of 105 male and 98 female participants. Aggregated metrics (for provenance recording) and demographics are also provided.
Dataset provided for NeuroLibre preprint. Author repo: https://github.com/valosekj/PAM50-normalized-metrics-paper NeuroLibre fork:https://github.com/roboneurolibre/PAM50-normalized-metrics-paper
For details, please visit the corresponding NeuroLibre technical screening.
https://neurolibre.org
DOI: 10.5281/zenodo.8214764
title: Supplementary data - Biochar and its potential to deliver negative emissions and better soil quality in Europe

description: Additional data from - Matlab script of the logistic transport model for the transportation of forest and crop residues to biochar production plants - Gridded data from the maps in the publication and its supplementary information as geotiff, projection system "ETRS89-extended / LAEA Europe"
description: This research is part of the Carbo-Fertil project, funded by the Norwegian Research Council, grant number 281113. The computations were performed on resources provided by the Industrial Ecology Digital Laboratory.
DOI: 10.5525/gla.researchdata.1448
title: Neuropeptide Y-expressing dorsal horn inhibitory interneurons gate spinal pain and itch signalling

description: Data accompanying a paper published in eLife
DOI: 10.6084/m9.figshare.21855495
title: PRISMA_2020_checklist Benefit of Asian Pigmented Rice Bioactive Compound and Its Implication in Breast Cancer: A Systematic Review

description: PRISMA_2020_checklist Benefit of Asian Pigmented Rice Bioactive Compound and Its Implication in Breast Cancer: A Systematic Review
DOI: 10.6084/m9.figshare.21855528.v1
title: The Summary of Studies Discovered Benefit of Asian Pigmented Rice Physicochemical Properties and Its Implication in Breast Cancer

description: The Summary of Studies Discovered Benefit of Asian Pigmented Rice Physicochemical Properties and Its Implication in Breast Cancer
DOI: 10.6084/m9.figshare.21989753
title: Supplementary Material for: Confirmation of Natural Hybridization between <b><i>Kengyilia</i></b> (StStYYPP) and <b><i>Campeiostachys</i></b> (StStYYHH) (Triticeae: Poaceae) Based on Morphological and Molecular Cytogenetic Analyses

description: Natural hybridization has been frequently observed in Triticeae; however, few studies have investigated the origin of natural intergeneric Triticeae hybrids. In the present study, we discovered three putative hybrid Triticeae plants in the Western Sichuan Plateau of China. Morphologically, the putative hybrids were intermediate between <i>Kengyilia melanthera</i> (2n = 6x = 42; StStYYPP) and <i>Campeiostachys dahurica</i> var. <i>tangutorum</i> (2n = 6x = 42; StStYYHH) with greater plant height and tiller number. Cytological analyses demonstrated that the hybrids were hexaploid with 42 chromosomes (2n = 6x = 42). At metaphase I, 12.10–12.58 bivalents and 13.81–14.18 univalents per cell were observed in the hybrid plants. Genomic in situ hybridization demonstrated that the hybrids had StStYYHP genomes. Phylogenetic analysis of <i>Acc1</i> sequences indicated that the hybrids were closely related to <i>K. melanthera</i> and <i>C. dahurica</i> var. <i>tangutorum.</i> Our morphological, cytological, and molecular analyses indicate that these hexaploid natural hybrid plants may be hybrids of <i>K. melanthera</i> and <i>C. dahurica</i> var. <i>tangutorum.</i>
DOI: 10.6084/m9.figshare.22013369
title: Supplementary Material for: High Expression of CD300A Predicts Poor Survival in Acute Myeloid Leukemia

description: Introduction: Recent studies have suggested that CD300A was an oncogene in acute myeloid leukemia (AML) development. However, the clinical relevance and biological insight into CD300A expression in AML are still not well understood. The present study aimed to examine the expression characteristics of CD300A in AML and confirmed its clinical significance for AML. Methods: Quantification of the CD300A transcript was performed in 119 AML patients by real-time quantitative PCR in bone marrow blasts. The predictive significance of CD300A expression on the clinical outcomes of AML was assessed using overall survival (OS) and relapse-free survival (RFS). The published Cancer Genome Atlas (TCGA) data were used as an external validation for survival analysis and pathway analyses. Results: In comparison to monocytes from healthy peripheral blood (PB) cells, the expression levels of CD300A in AML cells were higher. Patients in the intermediate and adverse risk categories by WHO criteria (2018) had higher CD300A expression levels than those in the favorable risk category (p &lt; 0.001). AML patients with high expression of CD300A had a higher early death (ED) rate (P=0.029), lower complete remission (CR) rate (p=0.042), higher death rate (p &lt; 0.001) and relapse rate (p=0.002), and shorter OS (p＜0.0001) and RFS (p＜0.0001). Through multivariable analysis, high CD300A expression in AML was also an independent poor prognostic factor. The CAMP and CGMP-PKG signaling pathways may be stimulated by increased CD300A expression levels, which may be important for the development of AML. Conclusions: The expression levels of CD300A were associated with risk stratification and the clinical relevance of AML. High CD300A expression may act as an independent adverse prognostic factor for OS and RFS in AML.
DOI: 10.6084/m9.figshare.22039793
title: Supplementary Material for: Using Direct and Indirect Estimates for Alcohol-Attributable Mortality: A Modelling Study Using the Example of Lithuania

description: <b><i>Introduction:</i></b> Comparative risk assessments (CRAs) for alcohol use are based on indirect estimates of attributable harm, and usually combine country-specific exposure estimates and global risk relations derived from meta-analyses. CRAs for Eastern European countries, such as Lithuania, base their risk relations not on global risk relations, but on a large Russian cohort study. The availability of a direct estimate of alcohol-attributable mortality following the 2017 implementation of a large increase in alcohol excise taxes in Lithuania has allowed a comparison of these indirect estimates with a country-specific gold standard. <b><i>Methods:</i></b> A statistical modelling study compared direct (predictions based on a time-series methodology) and indirect (predictions based on an attributable-fraction methodology) estimates of alcohol-attributable mortality before and after a large increase in alcohol excise taxes in Lithuania. Specifically, Russia-specific versus global relative risks were compared against the gold standard of time-series based predictions. <b><i>Results:</i></b> Compared to direct estimates, indirect estimates markedly underestimated the reduction of alcohol-attributable mortality 12 months post intervention by at least 63%. While both of the indirect estimates differed markedly from the direct estimates, the Russia-specific estimates were closer to the direct estimates, primarily due to higher estimates for alcohol-attributable cardiovascular mortality. <b><i>Discussion:</i></b> As all indirect estimates were markedly lower than direct estimates, current overall relative risks and price elasticities should be re-evaluated. In particular, global estimates should be replaced by new regional estimates based on cohort studies.
DOI: 10.6084/m9.figshare.22133933
title: Supplementary Material for: Pigmented Nevus of the Caruncle and Plica Semilunaris: A Case Report

description: Conjunctival nevi are benign, heterogenous tumors that uncommonly arise from the lacrimal caruncle and plica semilunaris. We present a case of a patient diagnosed and managed for an unusual, pigmented nevus of the left caruncle involving the plica. An 84-year-old woman presented with a rapidly growing, pigmented lesion in her left nasal canthus. Examination demonstrated a raised, dark, pigmented area arising from the left caruncle and seeming to involve the plica semilunaris without scleral extension. The lesion was completely excised for histopathology, which confirmed the diagnosis of a compound nevus with pigment incontinence. Given the unfavorable anatomical position and prognostic significance in the case of malignancy, pigmented caruncular lesions should be thoroughly investigated with a low threshold for surgical removal.
DOI: 10.6084/m9.figshare.22274965
title: Supplementary Material for: BASELINE PREDICTORS OFLONGITUDINAL COGNITIVE OUTCOMES IN PERSONS WITH MILD COGNITIVE IMPAIRMENT (MCI)

description: Introduction To explore longitudinal cognitive outcomes and to ascertain predictors of conversion to dementia in a hospital-based MCI cohort classified according to the neuropsychological phenotype at baseline Materials & Methods Subjects aged &gt;55 years who had a clinical diagnosis of MCI at initial visit between 2010-2018, with at least one formal neuropsychological assessment at baseline and follow up of a minimum of 2 years were included. The prospective study was completed based on evaluation at last follow up to gauge conversion to dementia, quantification of performance on activities of daily living and where available longitudinal neuropsychological test scores. Results Ninety-five patients with MCI met the inclusion criteria with a mean age of 68.4 ±6.4yrs at baseline and a mean duration of follow-up for 6.4 ±3.2 yrs. The cumulative conversion rate to dementia was 22.2% (21/95) and the annualized conversion rate (ACR) was 3.3 % per year of follow up. The majority of subjects who had converted had multidomain MCI (66%). Only white-matter changes on MRI brain revealed correlation with baseline neuropsychology tests. The multivariate logistic regression analysis revealed the utility of lower baseline list recognition (adjusted odds ratio-0.735[95% confidence interval-0.589-0.916]; p-0.006), lower immediate logical memory (0.885[0.790-0.990]; p-0.03) and high perseverative error scores on set-shifting (3.116[1.425-6.817]; p-0.004) as predictors of conversion. A model score of +2.615 could predict conversion with sensitivity of 72% and specificity of 98% over 6.4 years follow up. Conclusion There was a higher risk of conversion associated with multidomain MCI. Logistic regression-based estimations of dementia risk utilizing domain-based neuropsychology test scores in MCI have high specificity for diagnosis at baseline.
DOI: 10.6084/m9.figshare.22502590
title: Supplementary Material for: A case of a low Vault after posterior chamber acrylic phakic intraocular lens implantation

description: When implanting a posterior chamber pIOL, it is crucial to maintain a safe distance. The patient was a 29-year-old man with high-degree bilateral myopia. In February 2021, posterior chamber acrylic pIOLs (Eyecryl Phakic TORIC; Biotech Vision Care, Gujarat, India) were implanted in both his eyes. After the surgery, the right eye vault was 6 μm, and the left eye vault was 350 μm. Moreover, the ACDendo values were 2270 and 2220 μm for the right and left eyes, respectively. In our case, we found a fairly high CLR in both eyes, but it was greater in the right eye. The CLR value was +455 in the right eye and +350 in the left eye. In our patient, anterior segment anatomical parameters were higher in the right eye than in the left eye, and a greater pIOL length was calculated for the right eye, but the vault was very low. In our opinion, this was associated with the high CLR in the right eye. If an even larger pIOL were implanted, there would have been a greater narrowing of the anterior chamber angle. Therefore, pIOL implantation in the right eye is contraindicated.
DOI: 10.6084/m9.figshare.22560817
title: Supplementary Material for: Asteroid Hyalosis Migration into the Anterior Chamber during Cataract Surgery Case Report

description: A 70-year-old male presented for cataract surgery in the right eye with pre-operative assessment significant for nuclear sclerotic cataract and asteroid hyalosis. Upon irrigation and aspiration during cataract surgery, yellow-white spheres consistent with asteroid hyalosis were visualized circulating into the anterior chamber despite an intact capsule and no apparent zonular weakness. The asteroides particles were completely aspirated by the irrigation and aspiration port and an intraocular lens was implanted into the capsular bag. Post-operatively, the patient did well with final visual acuity of 20/20 with no vitreous prolapse, retinal tears or detachments noted. There are only four cases in the literature of asteroid hyalosis migrating in the anterior chamber, none of these cases are associated with migration during intraocular surgery. We hypothesize that the asteroid hyalosis migrated anteriorly and around the zonules due to the synuretic nature of the vitreous and microscopic gaps in the zonular fibers. This case demonstrates the importance of the cataract surgeon to be aware of potential migration of asteroid hyalosis into the anterior chamber during surgery.