cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23735721
title: Supplementary Material for: A patient with Crohn’s disease who gave birth despite sigmoid volvulus, venous thrombosis, non-traumatic fracture of the rib, and sepsis during pregnancy

description: The patient was a woman in her 40s who was diagnosed with Crohn’s disease (CD) of the large and small intestines in 1996. In 2005, she was referred to our hospital for treatment. We treated her for 17 years with corticosteroids, biologics, immunosuppressive agents, 5-aminosalicylic acid, and nutrition care. However, her Crohn’s Disease Activity Index remained between 200 and 250, indicating refractory CD. During her medical treatment, the patient also underwent 3 operations. One year ago, the patient became pregnant through in vitro fertilization. Even after pregnancy was confirmed, the patient continued her treatment for refractory CD with ustekinumab, granulocyte apheresis, and budesonide. Nonetheless, her CD was highly active during pregnancy, and she experienced various complications: sigmoid volvulus at gestational week 15, venous thrombosis at gestational week 17, non-traumatic rib fracture due to fetal movement at gestational week 32, and sepsis from central venous catheter infection at gestational week 37. At gestational week 38, the patient gave birth by emergency cesarian delivery. This paper reports details of the case in which delivery was achieved after various complications were overcome and discusses previous relevant reports.
DOI: 10.6084/m9.figshare.23806986
title: Supplementary Material for: Mild Synovitis Impairs Chondrogenic Joint Environment

description: The impact of mild synovitis on the chondrogenic environment in the joint pertaining to cartilage repair is often neglected. In this study, 21 synovial samples were collected from foot surgeries, for histology and isolation of fibroblast-like synoviocytes (FLS). Of the 21 samples, 13 were normal and eight mild synovitis according to their synovitis scores. In mild synovitis, CD3+lymphocytes were increased in the sublining layer. When chondrocytes were cultured and treated with the conditioned medium produced by FLS, their glycosaminoglycan production was negatively correlated with the synovitis scores of the synovium, from which FLS were isolated. In conclusion, mild synovitis in common joint conditions compromises the process of chondrogenesis, via inhibiting chondrocyte matrix production by FLS. The results suggest that the concomitant synovitis, even being mild, could significantly alter the joint environment for chondrogenesis and impair the outcome of cartilage repair.
DOI: 10.6084/m9.figshare.23904570
title: Supplementary Material for: Plunging Ranula Presenting as a Giant Anterior Cervical Cystic Mass: A Case Report and Literature Review

description: Plunging ranula, a subtype of ranula, commonly presents as a submandibular or submental cystic mass without oral counterpart, and its clinical management remains challenging. Herein, the authors report an extremely rare case of 30-year-old female patient with plunging ranula involving the root of left anterior neck.
DOI: 10.6084/m9.figshare.23998344
title: Supplementary Material for: Identification and validation of an aging-associated circRNA-miRNA-mRNA network in neovascular age-related macular degeneration

description: Introduction: Neovascular age-related macular degeneration (NVAMD) is a leading cause of severe vision impairment in the elderly. Aging is one of the most pivotal underlying molecular mechanisms of NVAMD. Methods: In this study, we identified the potential aging-related genes involved in NVAMD. Considering that non-coding RNAs are vital regulators of NVAMD progression, we explored and constructed an aging-originated circRNA-miRNA-mRNA network of NVAMD. Differential expression of 23 aging-associated genes was identified based on sequencing data and the Human Aging Genomic Resources tool at a threshold of P &lt;0.05, and log2|fold change| &gt; 1. Results: We screened 12 microRNAs (miRNAs) using public datasets and the miRNet database. A total of 13 circRNAs were subsequently mined using the StarBase tool. Merging these 13 circRNAs, 12 miRNAs, and 15 genes together, we obtained 281 pairs of circRNA-miRNA and 30 pairs of miRNA-mRNA. Conclusion: We created an aging-related circRNA-miRNA-mRNA network, which could be a promising target for future AMD treatments.
DOI: 10.6084/m9.figshare.23998353
title: Supplementary Material for: The global prevalence and severity of dental caries among racially minoritized children: A systematic review and meta-analysis

description: Racially minoritized children often bear a greater burden of dental caries, but the overall magnitude of racial gaps in oral health and their underlying factors are unknown. A systematic review and meta-analysis were conducted to fill these knowledge gaps. We compared racially minoritized (E) children aged 5 to 11 years (P) with same-age privileged groups (C) to determine the magnitude and correlates of racial inequities in dental caries (O) in observational studies (S). Using the PICOS selection criteria, a targeted search was performed from inception to December 1st, 2021, in nine major electronic databases and an online web search for additional grey literature. The primary outcome measures were caries severity, as assessed by mean decayed, missing, and filled teeth (dmft) among children and untreated dental caries prevalence (% d&gt;0). The meta-analysis used the random-effects model to calculate standardized mean differences (SMD) and 95% confidence intervals (95% CI). Subgroup analysis, tests for heterogeneity (I2, Galbraith plot), leave-one-out sensitivity analysis, cumulative analysis, and publication bias (Egger’s test and funnel plots) tests were carried out. The New Castle Ottawa scale was used to assess risk of bias. This review was registered with PROSPERO, CRD42021282771. A total of 75 publications were included in the descriptive analysis. The SMD of dmft score was higher by 2.30 (95% CI: 0.45, 4.15), and the prevalence of untreated dental caries was 23% (95% CI: 16, 31) higher among racially minoritized children, compared to privileged groups. Cumulative analysis showed worsening caries outcomes for racially marginalized children over time and larger inequities in dmft among high-income countries. Our study highlights the high caries burden among minoritized children globally by estimating overall trends and comparing against factors including time, country, and world income. The large magnitude of these inequities, combined with empirical evidence on the oral health impacts of racism and other forms of oppression, reinforce that oral health equity can only be achieved with social and political changes at a global level.
DOI: 10.6084/m9.figshare.24013881
title: Supplementary Material for: Fat intake and fat quality in pregnant and lactating women, infants, children, adolescents and related health outcomes: a scoping review of systematic reviews of prospective studies

description: Introduction: Dietary fat intake during pregnancy and childhood is important for health. However several health aspects are inconclusive. Methods: We systematically searched Medline, Cochrane Library and Epistemonikos for systematic reviews (SRs) of randomized controlled trials (RCTs) and/or prospective cohort studies published from 01.01.2015 to 31.12.2019 assessing the association of dietary fat intake (including dietary supplements) during pregnancy and across childhood with pregnancy, perinatal, and child health outcomes. Results: Thirty-one SRs, mainly of RCTs, were included. Omega-3 fatty acids supplementation during pregnancy reduced the risk of early preterm birth, and in some SRs also any preterm birth, increased gestation length and birth weight, but mostly was not associated with other pregnancy/perinatal outcomes. Pre- and postnatal polyunsaturated fatty acids (PUFA) intake was not consistently associated with growth, neurological, visual and cognitive outcomes, allergic diseases, cardiovascular and metabolic health in childhood. Reduced saturated fatty acids (SFA) intake and its replacement with PUFA/monounsaturated fatty acids had favourable effects on blood pressure and blood lipids in children. No apparent effects of total or trans-fat on health outcomes across target groups were observed. Conclusion: Omega-3 PUFA supplementation during pregnancy and SFA intake reduction in childhood require further consideration in dietary recommendations targeting these populations.
DOI: 10.6084/m9.figshare.24024387
title: Supplementary Material for: Extracorporeal blood purification with CytoSorb in 359 critically ill patients

description: Introduction. Critically ill patients with inflammatory dysregulation and organ disfunction may benefit from blood purification, although the use of this technique has not been described in large case series. We evaluated clinical outcomes and survival in high-risk intensive care unit (ICU) patients who underwent extracorporeal blood purification. Methods. 359 consecutive ICU patients treated with CytoSorb™ were included. Results. Main admission diagnoses were: 120 (34%) refractory cardiac arrest under mechanical chest compression; 101 (28%) profound cardiogenic shock; 81 (23%) post-cardiotomy cardiogenic shock; and 37 (10%) respiratory failure. Fifteen patients (4%) were positive for SARS-CoV2 infection. We observed 49% 30-days mortality, 57% ICU mortality, and 62% hospital mortality, all lower than the 71% mortality predicted by SAPS II and 68% predicted from SOFA score. Parameters of shock and organ failure, above all vasoactive inotropic score, reduced during CytoSorb treatment. Multivariable analysis identified SAPS II, lactate dehydrogenase, ICU stay duration, vasoactive inotropic score, lactates, intraaortic counterpulsation on top of VA ECMO, and total bilirubin as predictors of mortality. No CytoSorb-related complications occurred. Discussion/Conclusion. CytoSorb treatment was effective in reducing laboratory parameters of shock and vasoactive inotropic score with possible survival implications in a large population of critically ill patients.
DOI: 10.6084/m9.figshare.24071115
title: Supplementary Material for: EBV positive lymphoproliferative disorder following lymphodepletion for MAGE A4 adoptive cellular therapy in a patient with synovial sarcoma: Case Report

description: Lymphoproliferative disorder associated with viral reactivation is a known risk of immunocompromised patients. With development of novel cellular therapies utilizing lymphodepletion regimens in advanced cancer, the risk of lymphoproliferative disorders should be a consideration. Here we report a case of a 61-year-old treated male with history of metastatic synovial sarcoma and multiple treatment lines treated with cell therapy (lymphodepleting chemotherapy and afami-cel, formerly ADP-A2M4, T-cell treatment) on clinical study that developed EBV positive lymphoproliferative disorder (LPD). Patient was treated with rituximab and achieved a complete response. New cellular therapies present promising treatment options for patients and adverse events should be monitored carefully.
DOI: 10.6084/m9.figshare.24117477
title: Supplementary Material for: Distinct Biomarkers of ANT Stimulation and Seizure Freedom in an Epilepsy Patient with Ambulatory Hippocampal Electrocorticography

description: Background: Deep brain stimulation (DBS) of the anterior nucleus of the thalamus (ANT) and responsive neurostimulation (RNS) of the hippocampus are the predominant approaches to brain stimulation for treating mesial temporal lobe epilepsy (MTLE). Both are similarly effective at reducing seizures in drug resistant patients, but the underlying mechanisms are poorly understood. In rare cases where it becomes clinically indicated to use RNS and DBS simultaneously, ambulatory electrophysiology from RNS may provide the opportunity to measure the effects of ANT DBS in the putative seizure onset zone and identify biomarkers associated with clinical improvement. Here, one such patient became seizure free, allowing us to identify and compare the changes in hippocampal electrophysiology associated with ANT stimulation and with seizure freedom. Methods: Ambulatory electrocorticography and clinical history were retrospectively analyzed for a patient treated with RNS and DBS for MTLE. DBS artifacts were used to identify ANT stimulation periods on RNS recordings and measure peri-stimulus electrographic changes. Clinical history was used to determine the chronic electrographic changes associated with seizure freedom. Results: ANT stimulation acutely suppressed hippocampal gamma (25-90Hz) power, with minimal theta (4-8Hz) suppression and without clear effects on seizure frequency. Eventually, the patient became seizure free alongside the emergence of chronic gamma increase and theta suppression, which started at the same time as clobazam was introduced. Both seizure freedom and the associated electrophysiology persisted after inadvertent DBS discontinuation, further implicating the clobazam relationship. Unexpectedly, RNS detections and long episodes increased, although they were not considered to be electrographic seizures, and the patient remained clinically seizure-free. Conclusion: ANT stimulation and seizure freedom were associated with distinct, dissimilar spectral changes in RNS-derived electrophysiology. The time course of these changes supported a new medication as the most likely cause of clinical improvement. Broadly, this work showcases the use of RNS recordings to interpret the effects of multimodal therapy. Specifically, it lends additional credence to hippocampal theta suppression as a biomarker previously associated with seizure reduction in RNS patients.
DOI: 10.25326/242
title: Calibrated stable water isotope data in precipitation from the BCO during EUREC4A 

description: Water isotope in precipitation collected at the Barbados Cloud Observatory BCO, includes VSMOW-SLAP normalisation and rain rate derived from the weight of the collected rain amount.
DOI: 10.5067/terra-aqua/ceres/ebaf-toa_l3b004.1
title: CERES Energy Balanced and Filled (EBAF) TOA Monthly means data in netCDF Edition4.1
DOI: 10.5281/zenodo.4662444
title: European Literary Text Collection (ELTeC): April 2021 release with 14 collections of at least 50 novels.

description: This release contains 14 collections of at least 50 novels, 8 of which have reached 100 novels, and a total of over 1200 novels. Collections in this release include: Czech, German, English, French, Hungarian, Norwegian, Polish, Portuguese, Romanian, Slovenian, Spanish, Serbian, Swedish and Ukrainian. Note that this is an umbrella release, referencing the collections included in the release, but not containing the actual files. Citation suggestion for ELTeC: <em>European Literary Text Collection (ELTeC)</em>, version 1.1.0, April 2021, edited by Carolin Odebrecht, Lou Burnard and Christof Schöch. COST Action <em>Distant Reading for European Literary History</em> (CA16204). DOI: doi.org/10.5281/zenodo.4662444. (See also the citation suggestions for individual ELTeC collections in their respective repositories on Github.)
description: Note that this is an umbrella release, referencing the collections included in the release, but not containing the actual files. ELTeC has been created in the context of the COST Action 'Distant Reading for European Literary History' (CA16204), a COST Action funded by the COST Association as part of the Horizon 2020 Framework Programme of the EU.
DOI: 10.5281/zenodo.5523684
title: Assembled transcriptomes of ovary, testis, and brain (male and female) of Amphibolurus muricatus (jacky dragon) generated using Trinity v2.11.0

description: <strong><em>A. muricatus</em> transcriptome assemblies generated using Trinity v2.11.0 (Haas et al. 2013; Grabherr et al. 2011; Henschel et al. 2012)</strong><br> • Amphibolurus-muricatus_brain.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> brain (male and female).<br> • Amphibolurus-muricatus_combined.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> ovary, testis, and brain (male and female).<br> • Amphibolurus-muricatus_female_brain.fa.tar.gz: Trinity assembly of female <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_male_brain.fa.tar.gz: Trinity assembly of male <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_ovary.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> ovary.<br> • Amphibolurus-muricatus_testis.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> testis. <strong>References</strong> Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson et al., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29 (7):644-652. Haas, B.J., A. Papanicolaou, M. Yassour, M. Grabherr, P.D. Blood et al., 2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8 (8):1494-1512. Henschel, R., M. Lieber, L.-S. Wu, P.M. Nista, B.J. Haas et al., 2012 Trinity RNA-Seq assembler performance optimization, pp. 45 in Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. Association for Computing Machinery, Chicag, IL, USA.
DOI: 10.5281/zenodo.8210940
title: Gene annotations of Amphibolurus muricatus (jacky dragon), Intellagama lesueurii (Australian water dragon), Phrynocephalus przewalskii (Przewalski's toadhead agama), and Phrynocephalus vlangalii (Ching Hai toadhead agama)

description: <strong>Annotation file and associated FASTA files for <em>A. muricatus</em> assembly AmpMurF_3.0</strong><br> • AmpMurF3.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file.<br> • AmpMurF3.cds.tar.gz: EVM gene models coding sequences.<br> • AmpMurF3.pep.tar.gz: EVM gene models coding sequences translated into amino acid sequences. <strong>Annotation file and associated FASTA files for <em>A. muricatus</em> assembly AmpMurM_3.0</strong><br> • AmpMurM3.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file.<br> • AmpMurM3.cds.tar.gz: EVM gene models coding sequences.<br> • AmpMurM3.pep.tar.gz: EVM gene models coding sequences translated into amino acid sequences. <strong>Annotation file and associated FASTA files for <em>I. lesueurii</em> (Australian water dragon; assembly EWD_hifiasm_HiC generated as part of the AusARG consortium)</strong><br> • Intellagama_lesueurii.evm.final.add_replace_buscoV5_homolog.final.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file.<br> • Intellagama_lesueurii.evm.final.add_replace_buscoV5_homolog.final.cds.fa.tar.gz: EVM gene models coding sequences.<br> • Intellagama_lesueurii.evm.final.add_replace_buscoV5_homolog.final.pep.fa.tar.gz: EVM gene models coding sequences translated into amino acid sequences. <strong>Annotation file and associated FASTA files for <em>P. przewalskii</em> (Przewalski’s toadhead agama; see PMID ID 30808754 and CNGBdb accession no. CNP0000203) </strong><br> • Phrynocephalus_przewalskii.evm.final.add_replace_buscoV5_homolog.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file.<br> • Phrynocephalus_przewalskii.evm.final.add_replace_buscoV5_homolog.cds.fa.tar.gz: EVM gene models coding sequences.<br> • Phrynocephalus_przewalskii.evm.final.add_replace_buscoV5_homolog.pep.fa.tar.gz: EVM gene models coding sequences translated into amino acid sequences. <strong>Annotation file and associated FASTA files for <em>P. vlangalii</em> (Ching Hai toadhead agama; see PMID ID 30808754 and CNGBdb accession no. CNP0000203)</strong><br> • Phrynocephalus_vlangalii.evm.final.add_replace_busco_homolog.gff3.tar.gz: EVidenceModeler (EVM) gene model annotation file.<br> • Phrynocephalus_vlangalii.evm.final.add_replace_busco_homolog.cds.fa.tar.gz: EVM gene models coding sequences.<br> • Phrynocephalus_vlangalii.evm.final.add_replace_busco_homolog.pep.fa.tar.gz: EVM gene models coding sequences translated into amino acid sequences.
DOI: 10.6084/m9.figshare.22559956
title: Supplementary Material for: Rectal adenocarcinoma presenting as a perirectal abscess

description: Classic symptoms of rectal cancer (RC) such as hematochezia, tenesmus, rectal pain, and bowel habit changes are well known but can be non-specific and misdiagnosed. Rare presentations, in combination with these conventional symptoms, can occur warranting a higher degree of clinical suspicion. Here we report a case of rectal adenocarcinoma presenting as a perirectal abscess. A 52-year-old male with uncontrolled diabetes mellitus presented with a two-year and two-month history of rectal bleeding and changes in bowel habits, respectively, which were attributed to other conditions. He initially presented with left buttock pain and severe sepsis. Subsequent workup for suspected Fournier’s gangrene and perirectal abscess led to the discovery of a rectal adenocarcinoma (pT4N0M0, stage IIB/C). A combination of debridement, antibiotic therapy, neoadjuvant chemoradiation, and abdominoperineal resection resulted in improvement of the patient’s condition and remission. In conclusion, rare presentations of RC, such as a perirectal abscess, especially if present in conjunction with conventional RC symptomology, may necessitate the workup of RC.
DOI: 10.6084/m9.figshare.23259338
title: Supplementary Material for: Risk Factors for Common Kidney Stones Are Correlated with Kidney Function Independent of Stone Composition

description: Background: Kidney stone type varies with age, sex, season, and medical conditions. Lower estimate glomerular filtration rate (eGFR) leads to changes in urine chemistry, and risk factors for kidney stones are thought to vary by stone type. We explore the association between eGFR, urine risk factors, and common stone compositions. Methods: This was a retrospective cohort study of 811 kidney stone patients seen at Yale Medicine between 1994-2021 with serum chemistries and 24-hour urine chemistries matched within one year of baseline stone analysis. Patients’ eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) 2021 equation. Demographics and medical history were compared by Chi-squared tests. 24-hour urine chemistries and stone analyses were analyzed by one-way ANOVA. Linear regressions were performed to control for demographics, comorbidities, and stone composition. Results: With lower eGFR, the proportion of calcium stones declined while uric acid stones increased. On univariable analysis, lower eGFR was associated with lower urine pH, calcium, citrate, uric acid, magnesium, phosphorus, and ammonium. On multivariable analysis, controlling for age, sex, ethnicity, BMI, comorbidities, and stone type, these factors remained significant. Stone formers with lower eGFR had elevated supersaturation for uric acid, but reduced supersaturations for calcium-containing stones. Though urine oxalate was significant on univariable analysis, it was not on multivariable analysis. Discussion/Conclusion: Changes in urine parameters are strongly correlated with eGFR regardless of stone type. Renal function may play a key role in modulating kidney stone risk factors. Strategies to mitigate stone risk may need to vary with kidney function, especially when patient urine or stone composition data is unavailable.