cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25003331
title: Supplementary Material for: Chinese Multidisciplinary Expert Consensus on Immune Checkpoint Inhibitor (ICI)-Based Combination Therapy for Hepatocellular Carcinoma (2023 Edition)

description: Immune checkpoint inhibitor (ICI)-based combination therapy modalities for hepatocellular carcinoma (HCC) have achieved significant efficacy in clinical research and practice and have become the mainstay for the treatment of unresectable HCC. To better help clinicians use combination immunotherapy drugs and regimens rationally, effectively, and safely, the editorial board facilitated a discussion with multidisciplinary experts in the field, adopted the "Delphi" consensus formation method, and finally revised and completed the "Chinese Multidisciplinary Expert Consensus on the Immune Checkpoint Inhibitors (ICIs)-Based Combination Therapy for Hepatocellular Carcinoma (2023 Edition)" on the basis of the 2021 edition. This consensus primarily focuses on the principles and methods of clinical practice of combination therapy based on ICIs, aiming to summarize the recommendations for clinical application based on the latest research and expert experience and provide application guidance for clinicians.
DOI: 10.6084/m9.figshare.25126634
title: Supplementary Material for: Genetic variability of SOX10 related disorders within an Italian family: straddling the line between Kallmann and Waardenburg syndrome.

description: Introduction: Kallmann syndrome (KS) is a genetically heterogeneous developmental disorder that most often manifests hypogonadotropic hypogonadism (HH) and hypo-/anosmia due to early embryonic impairment in the migration of gonadotropin-releasing hormone (GNRH) neurons. SOX10 (SRY-Box 10; MIM*602229), a key transcriptional activator involved in the development of neural crest cells, has been associated with KS and is identified as one of the causative genes of Waardenburg syndrome (WS). 
Case Presentation: A 28-year-old female patient, who was clinically diagnosed with KS in her childhood, presented with HH and anosmia, mild bilateral sensorineural hearing loss (SNHL) and pigmentation abnormalities. Next-generation sequencing analysis detected a missense heterozygous SOX10 pathogenic variant (NM_006941.4:c.506C&gt;T) in the proposita and in her mother, whose phenotype included exclusively anosmia and hypopigmented skin patches. The same variant has been described by Pingault et al. (2015) in a patient with apparently isolated bilateral severe SNHL. 
Conclusion: Our finding substantiates the extreme phenotypic variability of SOX10-related disorders, which range from classical KS and/or WS to contracted endophenotypes that could share a common pathway in the development of neural crest cells and highlights the need for careful evaluation and long-term follow-up of SOX10 patients, with special focus on atypical/additional and/or late-onset phenotypic traits.
DOI: 10.6084/m9.figshare.25211519
title: Supplementary Material for: Temporal Trends in Severe Brain Injury and Associated Outcomes in Very Preterm Infants

description: Introduction: Severe brain injury (SBI), including severe intraventricular haemorrhage (sIVH) and cystic periventricular leukomalacia, poses significant challenges for preterm infants, yet recent data and trends are limited.

Methods: Analyses were conducted using the Australian and New Zealand Neonatal Network data on preterm infants born &lt;32 weeks’ gestation admitted at Monash Children’s Hospital, Australia, from January 2014 to April 2021. We assessed the occurrence and trends of SBI and sIVH among preterm infants, along with the rates and trends of death and neurodevelopmental impairment (NDI) in SBI infants.

Results: Of 1609 preterm infants, 6.7% had SBI, and 5.6% exhibited sIVH. 37.6% of infants with SBI did not survive to discharge, with 92% of these deaths occurring following redirection of clinical care. Cerebral palsy was diagnosed in 65.2% of SBI survivors, while 86.4% of SBI survivors experienced NDI. No statistically significant differences were observed in the temporal trends of SBI (adjusted OR (95% CI) 1.08 (0.97-1.20); P=0.13) or sIVH (adjusted OR (95% CI) 1.09 (0.97-1.21); P=0.11). Similarly, there was no statistically significant difference noted in the temporal trend of the composite outcome, which included death or NDI among infants with SBI (adjusted OR (95% CI) 0.90 (0.53-1.53); P=0.71).

Conclusion: Neither the rates of SBI nor its associated composite outcome of death or NDI improved over time. A notable proportion of preterm infants with SBI faced redirection of care and subsequent mortality, while most survivors exhibited adverse neurodevelopmental challenges. Development of better therapeutic interventions is imperative to improve outcomes for these vulnerable infants.
DOI: 10.6084/m9.figshare.25816315
title: Supplementary Material for: Kratom (Mitragyna speciosa) Use and Mental Health: A Systematic Review and Multilevel Meta-Analysis

description: Introduction: Kratom (Mitragyna speciosa) is a medicinal tree native to Southeast Asia. The present multilevel meta-analysis describes the association between kratom use and the positive and negative indicators of mental health. Methods: A total of thirty-six articles were included in the meta-analysis to examine the associations, using a random-effects model. Results: The pooled effect size showed a very small positive association between kratom use and negative indicators of mental health (r=0.092, 95%CI=[0.020, 0.164], p&lt;0.05), while no significant association was found with positive indicators of mental health (r=-0.031, 95%CI=[-0.149, 0.087], p&gt;0.05). Pooled effect sizes of specific mental health outcomes indicated that kratom use showed only a small positive correlation with externalizing disorders (r=0.201, 95%CI=[0.107, 0.300], p&lt;0.001). No significant association was found between kratom use and quality of life (r=0.069, 95%CI=[-0.104, 0.242], p&gt;0.05) and internalizing disorders (r=-0.001, 95%CI=[-0.115, 0.095], p&gt;0.05). Multilevel moderator analysis showed that the pooled effect size of the association between kratom use and substance use disorder (SUD) was stronger in Malaysia (r=0.347, 95%CI=[0.209, 0.516], p&lt;0.001), and with the mean age (β1=-0.035, 95%CI=[-0.055, -0.014], p=0.003), and the drug profile of those who were not co-using other drugs (r=0.347, 95%CI=[0.209, 0.516], p&lt;0.001). Conclusion: The meta-analysis supports the kratom instrumentalization concept, in that a positive gain from kratom consumption can be achieved without any significant adverse associations with mental health.
DOI: 10.6084/m9.figshare.26055961
title: Supplementary Material for: Treatment Seeking Nitrous Oxide Users in Addiction Care: A Comparison with Cocaine Users on Clinical and Treatment Characteristics

description: Introduction: Over the past decade, frequent use of large quantities of nitrous oxide (N2O) has become more common in the Netherlands. Although N2O poses several negative health consequences for a subgroup of problematic N2O users, there is a lack of knowledge on what characterizes these intensive users. This study therefore aims to provide the demographic and substance use characteristics and experiences during treatment of treatment seeking problematic N2O users, and to compare this with a matched group of treatment seeking problematic cocaine users. 

Methods: A retrospective chart review was performed of patients who were referred for treatment of problematic N2O use at a large Dutch addiction care facility from January 2020 to September 2022, extracting demographics, pattern of use and follow-up data. Additionally, a subgroup of N2O users was propensity-score matched (1:1) with a subgroup of treatment seeking problematic cocaine users, both groups excluding users with substance use disorders or frequent use of substances other than N2O and cocaine, respectively. 

Results: 128 patients with a N2O use disorder were included in the total sample and a subgroup of 77 N2O-only users were propensity-score matched on age and sex to 77 cocaine-only users. N2O users were typically young (mean age 26.2 years), male (66.4%), unmarried (82.9%), with a low education level (59.0%) and born in the Netherlands (88.2%), with parents born in Morocco (45.3%). N2O was used intermittently (median 10 days/month, IQR 4.0 – 17.5 days) and often in very large quantities (median 5 kg [ca. 750 balloons] per average using day, IQR 2 – 10 kg). Compared to the patients with a cocaine use disorder, matched N2O users were lower educated, more often from Moroccan descent, and less likely to be alcohol or polysubstance users. Despite receiving similar treatments, N2O users were twice as likely to discontinue treatment before completion compared to cocaine users (63% vs. 35%, P=0.004).

Conclusion: Treatment seeking problematic N2O users are demographically different from treatment seeking problematic cocaine users and are much more likely to dropout from psychological treatment. Further research is needed into the needs and other factors of problematic N2O users that relate to poor treatment adherence in problematic N2O users.
DOI: 10.15156/bio/sh0957478.10fu
title: SH0957478.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.1594/pangaea.63129
title: Varve data of cores SO90-39KG/56KA
DOI: 10.21227/3q77-z917
title: Data for "Efficient Modeling of Depolarizing Mueller BRDFs"

description: Light-matter interactions within indoor environments are significantly depolarizing. Nonetheless, the relatively small polarization attributes are informative. To make use of this information, polarized-BRDF (pBRDF) models for common indoor materials are sought. Fresnel reflection and diffuse partial polarization are popular terms in pBRDF models, but the relative contribution of each is highly material-dependent and changes based on scattering geometry and albedo. An efficient pBRDF would describe these dependencies with as few parameters as possible while retaining physical significance and task-relevant information. This work compares a triply-degenerate (TD)-Mueller matrix (MM) model to measurements of 3D printed objects. In this TD-MM model, the radiometric, polarimetric, and depolarization attributes are decoupled to reduce the number of parameters. The depolarization is quantified by a single geometry-dependent parameter, four geometry-independent material constants describe the polarization properties, and our TD-MM model is normalized to unit radiance so that the BRDF is decoupled. To test an application of the TD-MM model the material constants are assumed and the geometry-dependent depolarization parameter for a red 3D printed sphere is estimated from linear Stokes images. The geometry-averaged error of the depolarization parameter is 4.2% at 662 nm (high albedo) and 11.7% at 451 nm (low albedo). Since the error is inversely proportional to albedo and depolarization, the TD-MM model is referred to as appropriate for depolarization-dominant materials. The robustness of the TD-MM model is also tested by comparing ground-truth Mueller images to extrapolations of a red 3D printed Stanford bunny under arbitrary polarized illumination.
DOI: 10.25925/20230801
title: Multi-laboratory compilation of atmospheric carbon dioxide data for the period 1957-2022; obspack_co2_1_GLOBALVIEWplus_v9.0_2023-09-09

description: This product is constructed using the Observation Package (ObsPack) framework [Masarie et al., 2014; www.earth-syst-sci-data.net/6/375/2014/]. The framework is designed to bring together atmospheric greenhouse gas (GHG) observations from a variety of sampling platforms, prepare them with specific applications in mind, and package and distribute them in a self-consistent and well-documented product. ObsPack products are intended to support GHG budget studies and represent a new generation of cooperative value-added GHG data products. This product includes 612 atmospheric carbon dioxide datasets derived from observations made by 74 laboratories from 28 countries. Data for the period 1957-2022 (where available) are included.
DOI: 10.34945/f51591
title: Moody Project Survival Analysis Morris Water Maze Dataset

description: STUDY PURPOSE: To characterize the behavioral consequences of our injury model on Morris Water Maze (MWM) latency with high power from combining animals from 3 studies. DATA COLLECTED: 46 untreated sham and 61 untreated injured male Sprague-Dawley rats, fluid percussion injury model, learning and memory assessed by spatial hidden platform (3 days of 4 swims per rat per day) Morris Water Maze; outcome measures analyzed included latency recorded in seconds and number of platforms found. PRIMARY CONCLUSION: We suggest the Accelerated Failure Time models should be the preferred analytical methodology for latency to platform associated with MWM studies.
DOI: 10.5067/aqua/modis/l3b/iop/2018
title: MODIS-Aqua Level 3 Binned Inherent Optical Properties Data Version R2018.0
DOI: 10.5067/aqua/modis/l3b/par/2018
title: MODIS-Aqua Level 3 Binned Photosynthetically Available Radiation Data Version R2018.0
DOI: 10.5067/aqua/modis/l3b/zlee/2018
title: MODIS-Aqua Level-3 Binned Euphotic Depth (ZLEE) Data Version R2018.0
DOI: 10.5281/zenodo.10028517
title: Tabular analysis of polyketide synthase domain active site residues for the PKZILLAs

description: In brief, the presence or absence of expected conserved enzyme active site residues within domains of the PKZILLAs, were matched to the polyketide ketosynthase (KS), acyl carrier protein (ACP), dehydratase (DH), ketoreductase (KR), flavin oxygenase (FLX), and enoyl (ER) domains, using either multiple sequence alignment liftover of active site location & residue as defined by InterProScan annotations, or, locations & residues defined as active site residues from literature sources.

./KS_ALL represents the scripts and source files used to generate the analyses. See run.sh , within.

Post_process_KS-ALL_analysis.ipynb represents the Jupyter notebook used to process the raw analyses into the presented tabular (.xlsx) form.

See Manuscript Materials and Methods for further details.

Summary of the active side residue results:

KS:All scored as active on the basis of catalytic cysteine. The below KS domains are scored as KS0, on the basis of variation of the histidine in the HGTGT motif:

PKZILLA-1__KS14 QGLGS

PKZILLA-1__KS19 QGLGS

PKZILLA-1__KS22 QGLGS

PKZILLA-1__KS25 QGLGS

PKZILLA-1__KS28 QGLGS

PKZILLA-1__KS31 GANGS

PKZILLA-1__KS34 QGLGS

PKZILLA-2__KS3 QGLGS

PKZILLA-2__KS6 QGLGS

PKZILLA-2__KS9 QGLGS

PKZILLA-2__KS11 QGLGS

PKZILLA-2__KS12 QGLGS

PKZILLA-3__KS6 AANGS

ACP:All scored as active (PPant prosthetic group attachment residue present)

DH:All scored as active, except possibly:PKZILLA-3__DH9

ER:Active site residues not defined in InterProScan or literature sources.

FLX:Active site residues not defined in InterProScan or literature sources.

KR:

KR domains come in two flavors: the canonical "full-length" contiguous domain, and the non-canonical split domain with two subdomains.KRs are 2 reciprocally similar subdomains - where the N-terminal subdomain "KRn" has a structural role, and the C-terminal subdomain "KRc" has the catalytic role.

Typically, the two KR subdomains are contiguous. 

However, it's precedendented (Porcine FAS) that these two KRn and KRc subdomains can become split with an ER in the middle. In the PKZILLAs, this can be observed for the KR-ER-KR in Module 28, it's actually KRn-ER-KRc. The first KRn-subdomain (KR26) is missing the catalytic residues (as are all of the KRn domains), while the second KRc-subdomain (KR27) has all of them. This split KR domain structure seems to be not that uncommon in the PKZILLAs, and the intervening domain is not limited to being an ER.

The KR.xlsx excel summarizes the status of the KRs, as active or inactive, and full-length (f), n-terminal subdomain (n), or c-terminal subdomain (c). The below KR domains are scored as inactive:

PKZILLA-1__KR26PKZILLA-1__KR29PKZILLA-1__KR31PKZILLA-2__KR6PKZILLA-2__KR11PKZILLA-2__KR20

Summary of the domain phylogenetics results:

Present in separate Zenodo item: https://doi.org/10.5281/zenodo.10152639
DOI: 10.5281/zenodo.10136894
title: Measurement report: Impact of emission control measures on environmental persistent free radicals and reactive oxygen species – A short-term case study in Beijing
DOI: 10.5281/zenodo.11142408
title: GEST Ocean Surface Current 2.0

description: The GEST Ocean Surface Current product 2.0 builds upon the GEST Ocean Surface Current product 1.0 (doi: 10.5281/zenodo.8329991), which estimates ocean surface currents at a 15 m depth using GESTNet, integrating multi-scale physical processes including Geostrophic and Ekman currents, wave-induced Stokes drift, and Tidal currents. This global daily product spans the period from 2006 to 2019, featuring a spatial resolution of 0.25°.  It is anticipated to be a reliable indicator of actual ocean circulation.
DOI: 10.5281/zenodo.2538121
title: Kaneohe Bay Nutrient Data 2014-2016

description: Nutrients were analyzed from surface waters at 4 sites in Kanoehe Bay at time points from 2014-2016. Quantification of phosphate, silicate, nitrate and nitrite, ammonia and total nitrogen (all are in umol/L) were conducted by the SOEST Laboratory for Analytical Biochemistry.
DOI: 10.5281/zenodo.53226
title: Kaneohe Bay Seawater Temperature Data 2014 And 2015

description: Seawater temperature data from loggers placed at 2 meters depth at multiple patch reefs in Kaneohe Bay, Oahu, Hawaii.
DOI: 10.6084/m9.figshare.12925370
title: Porcine Eye Holder - front

description: Porcine eye holder 3D printable front part
DOI: 10.6084/m9.figshare.25102307
title: Supplementary Material for: A Prospective, Single-arm, Phase 2 Study of Modified Transarterial Chemoembolization (TACE) using Low-dose Chemotherapy with Blank Microspheres Plus Low-dose Lenvatinib and Microwave Ablation in Patients with Large (≥ 7 cm) Unresectable Hepatocellular Carcinoma: The TALEM Trial

description: Background: For patients with large unresectable hepatocellular carcinoma (HCC), the effectiveness of conventional transarterial chemoembolization (cTACE) remains suboptimal. This study investigated the efficacy and safety of modified TACE using low-dose chemotherapy with blank microspheres (BMS-TACE) plus low-dose lenvatinib (LD-LEN) and microwave ablation (MWA) in patients with large unresectable HCC. 
Methods: In this prospective, single-arm, phase 2 study, patients with unresectable HCC exceeding the up-to-seven criteria, with maximum tumor diameter ≥ 7 cm, and without macrovascular invasion or extrahepatic metastases, received initial BMS-TACE (lipiodol, low-dose doxorubicin and lobaplatin up to 30 mg each, and blank microspheres; subsequently modified and repeated in most patients) plus LD-LEN (4-8 mg/day) and MWA. The primary endpoint was downstaging rate (DSR); secondary endpoints were objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and adverse events. 
Results: From November 2019 to March 2022, 43 patients were enrolled. Median follow-up was 21.2 months. Median largest tumor diameter was 11.2 cm (interquartile range [IQR], 7-25). Following BMS-TACE and LD-LEN, downstaging occured in 37 (86.0%) patients, 32 of whom received MWA, and 8 of whom had a complete response (CR) without MWA. ORR was 93.0% (CR in 32 [74.4%] and partial response in 8 [18.6%] patients). The 1-, 2- and 3-year PFS rates were 57.5%, 25.9%, and 18.1%, respectively (median PFS, 14.7 months [95% CI, 8.1-19.5]). The 1-, 2-, and 3-year OS rates were 85.8%, 67.7% and 61.6%, respectively (median OS, 36.4 months [95% CI, 26.8-not reached]). After BMS-TACE, a significant decline in CD11b+/CD33+/HLA-DR- myeloid-derived suppressor cells and early elevation in CXCR5+/CD8+ and CXCR5+/CD4+ T cells were observed (both p&lt;0.05).
Conclusions: BMS-TACE plus LD-LEN and MWA resulted in promising efficacy and tolerable toxicity in patients with large unresectable HCC exceeding the up-to-seven criteria with a maximum tumor diameter ≥ 7 cm and without macrovascular invasion or extrahepatic metastases.
DOI: 10.6084/m9.figshare.25609830
title: Supplementary Material for: Impact of arterial calcification on cardiovascular and renal outcomes in kidney transplant patients

description: Introduction: Coronary artery calcification score (CACS) and abdominal aortic calcification score (AACS) are both well-established markers of vascular stiffness, and previous studies have shown that a higher CACS is a risk factor for chronic kidney disease (CKD) progression. However, impact of pre-transplant CACS and AACS on cardiovascular and renal outcomes in kidney transplant patients has not been established. 
Methods: We included 944 kidney transplant recipients from the KoreaN cohort study for Outcome in patients With Kidney Transplantation (KNOW-KT) cohort and categorized them into three groups (low, medium, and high) according to baseline CACS (0, 0 &lt; and ≤ 100, &gt;100) and AACS (0, 1-4, &gt;4). The low (0), medium (0 &lt; and ≤ 100), and high (&gt;100) CACS groups each consisted of 462, 213 and 225 patients, respectively. Similarly, the low (0), medium (1-4), and high (&gt;4) AACS groups included 638, 159 and 147 patients. The primary outcome was the occurrence of cardiovascular events. The secondary outcomes were all-cause mortality and composite kidney outcomes, which comprised of &gt; 50% decline in the estimated glomerular filtration rate and graft loss. Cox regression analysis was used to investigate the association between baseline CACS/AACS and outcomes.
Results: The high CACS group (N = 462) faced a significantly higher risk for cardiovascular outcomes (adjusted hazard ratio [aHR], 5.97; 95% confidence interval [CI], 2.01-17.7) and all-cause mortality (aHR, 2.74; 95% CI, 1.27-5.92) compared to the low CACS group (N = 225). Similarly, the high AACS group (N = 638) had an elevated risk for cardiovascular outcomes (aHR, 2.38; 95% CI, 1.16-4.88). Furthermore, the addition of CACS to prediction models improved prediction indices for cardiovascular outcomes. However, the risk of renal outcomes did not differ among CACS or AACS groups. 
Conclusion: Pre-transplant arterial calcification, characterized by high CACS or AACS, is an independent risk factor for cardiovascular outcomes and mortality in kidney transplant patients.