cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127091.v1
title: Supplementary Material for: Duration of Stable Disease Is Associated with Overall Survival in Patients with Advanced Hepatocellular Carcinoma Treated with Sorafenib

description: <b><i>Background:</i></b> Sorafenib is a molecular-targeting agent showing improved overall survival (OS) for advanced hepatocellular carcinoma (HCC). Although tumor dormancy, characterized by stable tumor status or stable disease (SD) without tumor regression, is a unique feature of sorafenib treatment, the contribution of SD to OS remains debatable. This study aimed to clarify the correlation between SD periods and OS in patients with HCC treated with sorafenib. <b><i>Methods:</i></b> From May 2009 to January 2013, 269 patients with advanced-stage HCC were treated with sorafenib at the Kinki University Hospital. The antitumor response of sorafenib was evaluated in 158 patients using the modified Response Evaluation Criteria in Solid Tumors, and patients with SD were divided into two subgroups according to the median duration of SD: short SD (&lt;3 months) and long SD (≥3 months). The relationship between the duration of SD and OS was analyzed among patients with complete (CR) and partial response (PR), and long and short SD using the Kaplan-Meier method. <b><i>Results:</i></b> The median OS was 5.7 months in the short SD, 20.8 months in the long SD and 17.9 months in the CR + PR group. Although the duration of OS was significantly longer in the long SD group than the short SD group, no difference in OS was detected between the patients with CR + PR and patients with long SD. The impact of long SD on OS could be as strong as that of CR + PR. <b><i>Conclusion:</i></b> Achievement of long SD is one of the important goals for improving survival in patients with HCC treated with sorafenib.
DOI: 10.17632/tnxh2mf7cz
title: Sepsis

description: Sepsis patients from the Mimic-iv database
DOI: 10.6084/m9.figshare.17004067.v1
title: Underlying Data

description: This project contains the following underlying data:Data file 1. (Map of city of Medan with its 21 Districts (Kecamatan))Data file 2. (Figure of path diagram from the final bootstrapping)Data file 3. (Final path coefficient)Data file 4. (Final outer loadings)Data file 5. (The third (final) bootstrapping result)Data file 6. (Validation and reliability result)Data file 7. (Dataset for questionnaire validation and reliability (49 respondents) in testing stage)Data file 8. (Intercorrelation testing result)Data file 9. (Research questionnaire on Google form)Data file 10. (Research questionnaire – hard copy)Data file 11. (Anonymized dataset of leanness strategy of Medan MSMEs [169 respondents])Data file 12. (Groups in the Production Sector with 466 businesses identified for study)Data file 13. (Path Coefficient - explanation for exclusion of H3, H5, H6, and H7)Data file 14. Law of the Republic of Indonesia Number 16 of 1997 concerning Statistics
DOI: 10.6084/m9.figshare.27012025.v1
title: <b>Microstructure and properties of Ni-Ti-Cu alloy fabricated in situ by treble-wire arc additive manufacturing</b>

description: This study is the first attempt to manufactureTi50Ni45Cu5, Ti50Ni35Cu15, Ti50Ni25Cu25 alloys by treble-wire arc additive manufacturing (T-WAAM) using pure Ti, pure Ni and pure Cu wires as raw materials. The objective is to study the hysteresis of phase transformation, the microstructure evolution and properties of as-built Ni-Ti-Cu alloy. The results show that for Ti50Ni45Cu5 alloy, NiTi2, (Ni, Cu)2Ti, B2 with CsCl structure and B19′ phases are formed. For Ti50Ni35Cu15 alloy, NiTi2, B19′, Ni4Ti3, CuTi2, (Cu, Ni)Ti2 and (Cu, Ni)Ti phases are formed. For Ti50Ni25Cu25 alloy, Ti2Ni, B19′, R, (Cu, Ni)Ti, Ti2Cu, Ni4Ti3 phases are formed.With an increase of Cu content from 5 at.% to 25 at.%, the phase transition temperature increases sharply. The ultimate tensile strength of Ti50Ni45Cu5, Ti50Ni35Cu15, Ti50Ni25Cu25 are 248.2 MPa, 534.8 MPa and 261.8 MPa, respectively. Their strain is 1.71%, 6.42%, and 3.36%, respectively. For Ti50Ni45Cu5, Ti50Ni35Cu15, Ti50Ni25Cu25 alloy,the fracture mode of the Ti-Ni-Cu alloy is brittle fracture.
DOI: 10.17632/2kfk4vfgf7
title: Reading code for the data used in the manuscript "Whistler echo trains triggered by energetic winter lightning"

description: The file "NC_vlf.pro" is a source code written in the IDL programming tool for reading the magnetic field data analyzed in the manuscript "Whistler echo trains triggered by energetic winter lightning" and stored in the Mendeley Data ( doi: 10.17632/bhd4dt42mg.1; doi: 10.17632/gy27m8vy9v.1)
DOI: 10.17632/6hgyr25h8d
title: Data for: Analysis and modeling of cycle aging of a commercial LiFePO4/graphite cell

description: This data is from a comprehensive cycle aging study on a lithium-ion battery with a test duration of 29 months: Naumann, M. et al.; Analysis and modeling of cycle aging of a commercial LiFePO4/graphite cell; Journal of Power Sources (2020), Volume 451; DOI: 10.1016/j.jpowsour.2019.227666 This aging study presents cycle aging results of a commercial lithium-ion cell from a comprehensive, 29 month aging study and follows up on calendar aging results published previously [1]. We use a widely used commercial LiFePO 4 /graphite cell from Sony/Murata, which promises long calendar and cycle lifetime, that would make it suitable for stationary battery applications. The evolution of the cells’ capacity and impedance are shown in a static cycle aging study for 19 test points with different combinations of temperature, C-rate, depth of discharge and state of charge. Based on the measurement data shown herein and the calendar aging model presented in the previous paper, a semi-empirical combined aging model is presented for the capacity loss and resistance increase. Two dynamic load profiles are used to experimentally validate the combined aging model. Absolute model errors below 1% for the capacity loss and below 2% for the resistance increase in both dynamic load profiles demonstrate that the combined aging model can predict the lifetime of LiFePO 4 /graphite battery cells for different applications and varying operation conditions adequately. In the cycle experiments, an unexpectedly strong, but partly reversible capacity loss is observed with shallow cycles at medium states of charge.
DOI: 10.17632/dc97t6r54x
title: Interleukin-17 pathway inhibition with brodalumab in early systemic sclerosis: analysis of a single-arm, open-label, phase 1 trial

description: Systemic sclerosis (SSc) is an autoimmune disease that causes fibrosis of the skin and internal organs. Despite several studies reporting the role of interleukin-17 (IL-17) in SSc, no consensus exists regarding the role of the IL-17 pathway in SSc pathogenesis and progression. We hypothesize a possible relationship between the activated IL-17 pathway and the pathogenesis of SSc; therefore, this single-center trial assessed the pharmacokinetics, safety, and efficacy of multiple subcutaneous injections of the commonly used dosage of brodalumab, a fully human anti–IL-17 receptor A (IL-17RA) monoclonal antibody, in Japanese patients with SSc. To the best of our knowledge, this is the first study assessing the effect of IL-17RA inhibition with brodalumab on human fibrotic lesions in patients with early diffuse cutaneous SSc with moderate-to-severe skin thickening. Eight patients with early SSc involving moderate-to-severe and progressive skin thickening were enrolled. All patients had diffuse cutaneous SSc and met the ACR/EULAR classification criteria for SSc. Seven of the eight patients were women. All patients were treated with brodalumab. Brodalumab demonstrated a greater than expected rapid and significant reduction in the modified Rodnan Skin Score (mRSS), which decreased rapidly at week 4 and was sustained over 52 weeks. A reduction in dermal thickness in the lesional skin was observed consistently with changes in mRSS. In four of the eight patients with finger digital ulcers at baseline, a decrease in the mean number of digital ulcers from baseline was observed at weeks 24 and 52. No changes were observed in the measures of respiratory function assessed by spirometry. In this trial, brodalumab induced a regulatory T-cell (Treg)–dominant Treg/T helper 17 (Th17) balance, decreased the number of immunoglobulin G+ class–switched memory B cells and plasmablasts, and increased the number of transitional B cells compared with those at baseline. In summary, all patients had a decrease in mRSS that exceeded the minimal clinically important difference, together with a reduction in dermal thickness. This rapid, sustained, and significantly high efficacy of brodalumab in reducing fibrotic lesions in SSc could be attributed to its direct effects on fibroblasts and indirect effects by altering B-cell and T-cell subsets. Brodalumab also ameliorated clinical symptoms without any serious treatment emergent adverse events. These results suggest that brodalumab may represent a new treatment drug for patients with SSc, and it is currently being evaluated in a double-blind, placebo-controlled phase 3 trial with a larger sample size.
DOI: 10.17632/m4rfg9wb29
title: Comparative analysis of kidney organoids by single cell transcriptomics

description: Kidney organoids differentiated from human pluripotent stem cells hold great promise for understanding organogenesis, disease mechanisms and ultimately as a source of replacement tissue but how closely current protocols model adult kidney is undefined. Here we compared two different directed differentiation protocols by analyzing single cell gene expression in 83,130 cells isolated from 65 organoids. Both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios but 10-20% of these cells are non-renal. Evaluation of the differentiation state of organoid kidney cell types against fetal and adult kidney single cell transcriptomes revealed the immaturity of all organoid-derived cell types. Reconstruction of lineage relationships by pseudotemporal ordering identified ligands, receptors and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its receptor neurotrophic tyrosine kinase, receptor, type 2 (NTRK2) was expressed exclusively in off-target neurons, and inhibition of this pathway reduced neurons by 90% without altering kidney differentiation. Our analysis reveals the power of single cell analysis both to characterize and to optimize organoid differentiation protocols.
DOI: 10.6084/m9.figshare.25481632.v1
title: Whole-body patterns of muscle degeneration and progression in sarcoglycanopathies

description: MRI studies were performed following standard protocols, either WB(Carlier & Quijano-Roy, 2019; Chardon et al., 2019; Quijano-Roy et al., 2012) or combination of UB and LB MRI(Tasca et al., 2012, 2014), using different 1.5T or 3T scanners, and T1-weighted images were analyzed.A total of 65 muscles on both sides were independently evaluated for each scan by two independent observers, a radiologist and a pediatric neurologist with experience in muscle imaging (AS and LC). In case of discrepancy between the evaluators, agreement was reached by consensus (AS, DGA and LC). The median scores from both sides were used for data analysis. A four-point modified Lamminen scale was used to evaluate signal abnormalities representative of the extent of intramuscular fatty replacement in each muscle as follows: 0= normal signal intensity, 1=slightly hyperintense, patchy intramuscular signal changes 2=markedly hyperintense and widespread intramuscular signal changes, 3= total, homogeneous hyperintense signal change in whole muscle, equaling the signal intensity of the adjacent subcutaneous or paramuscular fat, or atrophy(Chardon et al., 2019; Lamminen, 1990; Wattjes et al., 2010). The scores of muscles that were not adequately visualized were considered as missing values (NA). The lower limb scans analyzed in the previous imaging study(Tasca et al., 2018) with a 5-point scoring system were re-scored to address the limitations in assessing some of the small and flat muscles in the head, trunk, neck and arms, ensuring uniformity across all body regions.
DOI: 10.6084/m9.figshare.27315027.v1
title: A new name for an old problem − <i>Colletotrichum cigarro </i>is the cause of St John’s wilt of <i>Hypericum perforatum</i>

description: The online version of MAFFT and the programme MEGA X were used to create the alignments and phylogenetic trees.
DOI: 10.6084/m9.figshare.28749464.v1
title: Generally reduced sink capacity of upland soils for atmospheric methane over the past three decades (1993-2022)

description: Upland soils act as the second largest and the only manageable methane (CH4) sink. Quantifying spatiotemporal patterns of the net CH4 exchange in upland soils is critical for refining global CH4 budget estimates and developing climate mitigation strategies. However, global CH4 budget in upland soils remains highly uncertain due to incomplete understanding of CH4-related biogeochemical processes and their responses to climate change. In this study, we generated high-resolution global maps of CH4 fluxes from upland soils by integrating field CH4 flux measurement data spanning over the period of 1993-2022 using machine learning models. Collectively, upland soils exhibited a generally reduced sink capacity for atmospheric methane over the past three decades. Cropping uplands underwent a shift from a weak sink to a source over the past three decades. In contrast, a sharp decrease by 68.8% was observed in sink capacity of forest soils for CH4. Grassland soils changed from a sink to a strong source of CH4, while tundra upland soils acted as a consistent source of CH4, although accompanied by a decrease by 55.3% since 1993. The combined effects of changes in precipitation and temperature can explain more than 70% of spatiotemporal variations of CH4 fluxes in upland soils. Our findings provided a new perspective on the spatiotemporal patterns of CH4 fluxes in global upland soils, which updated the role of upland soils in global CH4 budget, particularly as a potential CH4 sink.
DOI: 10.17632/9x86z33vzm
title: Age-model tiepoints for cores DSDP 594, MD88-770, MD02-2488, MD84-551, ODP site 1094, SO136-003, PS1768-8, PS2102-2 and MD97-2120

description: Tiepoints used to place the cores DSDP 594, MD88-770, MD02-2488, MD84-551, ODP site 1094, SO136-003, PS1768-8, PS2102-2 and MD97-2120 onto the LR04 benthic stack chronology. The δ18O data for each core is correlated to the LR04 benthic stack (Lisiecki & Raymo 2005) using the Analyseries software (Paillard et al. 1996). LR04 ages are presented against depth in the core with the exceptions of cores DSDP 594, MD88-770 and SO136-003 where the LR04 age is presented against the "age" published in Barrows et al. (2007). The MIS stage boundaries use the LR04 ages from Lisiecki & Raymo (2005) and the MIS 5 sub-stage boundaries use the ages from Govin et al. (2009). Benthic δ18O data is used for the correlation of cores DSDP 594 (Nelson et al. 1993), MD88-770 (Labeyrie et al. 1996) and MD02-2488 (Govin et al. 2009) to the LR04 benthic stack. Planktic δ18O data is used for the correlation of cores MD84-551 (Pichon et al. 1992), ODP site 1094 (Kanfoush et al. 2002), SO136-003 (Barrows et al. 2007), PS1768-8 (Mulitza et al. 1999), PS2102-2 (Niebler 1995) and MD97-2120 (Pahnke et al. 2003) to the LR04 benthic stack.


Barrows T.T., et al. 2007. Long-term sea surface temperature and climate change in the Australian-New Zealand region. Paleoceanography, 22(2): PA2215.
Govin A., et al. 2009. Evidence for northward expansion of Antarctic Bottom Water mass in the Southern Ocean during the last glacial inception. Paleoceanography, 24(1): PA1202.
Kanfoush S.L., et al. 2002. Comparison of ice-rafted debris and physical properties in ODP Site 1094 (South Atlantic) with the Vostok ice core over the last four climatic cycles. Palaeogeography, Palaeoclimatology, Palaeoecology, 182: 329-349.
Labeyrie L., et al. 1996. Hydrographic changes of the Southern Ocean (southeast Indian Sector) Over the last 230 kyr. Paleoceanography, 11(1): 57-76.
Lisiecki L.E. & Raymo M.E. 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography, 20(1): PA1003.
Mulitza S., et al. 1999. Foraminifera isotopes of sediment core PS1768-8. PANGAEA.
Nelson C.S., et al. 1993. Oceanographic and climatic changes over the past 160,000 years at Deep Sea Drilling Project Site 594 off Southeastern New Zealand, Southwest Pacific Ocean. Paleoceanography, 8(4): 435-458.
Niebler H.-S. 1995. Reconstruction of paleo-environmental parameters using stable isotopes and faunal assemblages of planktonic foraminifera in the South Atlantic Ocean. Reports on Polar Research, 167: 1-198.
Paillard D., Labeyrie L. & Yiou P. 1996. Macintosh program performs time-series analysis. Eos, 77: 379.
Pahnke K., et al. 2003. 340,000-Year Centennial-Scale Marine Record of Southern Hemisphere Climatic Oscillation. Science, 301: 948-952.
Pichon J.J., et al. 1992. Surface Water Temperature Changes in the High Latitudes of the Southern Hemisphere over the Last Glacial-Interglacial Cycle. Paleoceanography, 7(3): 289-318.
DOI: 10.6084/m9.figshare.21118915.v3
title: Feline environmental variables data

description: Data used in the article "Fearfulness associates with problematic behaviours and poor socialization in cats".* Mikkola S, Salonen M, Hakanen E, Lohi H. Fearfulness associates with problematic behaviours and poor socialization in cats. <em>iScience </em>(2022). <em>doi: 10.1016/j.isci.2022.105265</em>
DOI: 10.6084/m9.figshare.26323627.v1
title: Supplementary Material for: Infected inclusion cyst of a conjunctival nevus treated with a mini-incision: A case report.

description: Introduction
Conjunctival cysts are usually asymptomatic but they can cause foreign body sensation and contribute to dry eye disease. The purpose of this case report is to describe the presentation and treatment of an infected inclusion cyst of a conjunctival nevus in a healthy 36-year-old patient.
Case Presentation
A healthy 36-year-old-man presented to the emergency department for a redness and pain in his left eye for 1 day. Slit lamp examination revealed a conjunctival hyperemia and conjunctival nevus with 4 inclusion cysts, one of which was filled with a purulent material. Fluoresceine staining of the conjunctival epithelium was negative. Α mini-incision of the white cyst was performed using a 30 G needle, followed by a bimanual drainage and topical treatment with tobramycin and moxifloxacin drops every 3 hours for a week. A swab of the purulent drainage was positive for Gram+ flora. One week after the drainage of the cyst, the patient was asymptomatic and on slit lamp examination, the 4 inclusion cysts were filled with a transparent liquid, there was not any vessel dilation and staining with fluorescein was negative. 
Conclusion
Conjunctival inclusion cysts, although considered benign, can become infected and form a conjunctival abscess. A mini-incision on the slit-lamp combined with bimanual drainage and followed by topical antibiotic drops seems to be a safe and effective treatment.
DOI: 10.6084/m9.figshare.5128135.v1
title: Supplementary Material for: The RoPE Score and Right-to-Left Shunt Severity by Transcranial Doppler in the CODICIA Study

description: <b><i>Background:</i></b> For patients with cryptogenic stroke (CS) and patent foramen ovale (PFO), it is unknown whether the magnitude of right-to-left shunt (RLSh) measured by contrast transcranial Doppler (c-TCD) is correlated with the likelihood an identified PFO is related to CS as determined by the Risk of Paradoxical Embolism (RoPE) score. Additionally, for patients with CS, it is unknown whether PFO assessment by c-TCD is more sensitive for identifying RLSh compared with transesophageal echocardiography (TEE). Our aim was to determine the significance of RLSh grade by c-TCD in patients with PFO and CS. <b><i>Methods:</i></b> We evaluated patients with CS who had RLSh quantified by c-TCD in the Multicenter Study into RLSh in Cryptogenic Stroke (CODICIA) to determine whether there is an association between c-TCD shunt grade and the RoPE Score. For patients who underwent c-TCD and TEE, we determined whether there is agreement in identifying and grading RLSh between these two modalities. <b><i>Results:</i></b> The RoPE score predicted the presence versus the absence of RLSh documented by c-TCD (c-statistic = 0.66). For patients with documented RLSh by c-TCD, shunt severity was correlated with increasing RoPE score (rank correlation (r) = 0.15, p = 0.01). Among 293 patients who had both c-TCD and TEE performed, c-TCD was more sensitive (98.7%) for detecting RLSh. Of the 97 patients with no PFO identified on TEE, 28 (29%) had a large amount of RLSh seen on c-TCD. <b><i>Conclusions:</i></b> For patients with CS, severity of RLSh by c-TCD is positively correlated with the RoPE score, indicating that this technique for shunt grading identifies patients more likely to have pathogenic rather than incidental PFOs. c-TCD is also more sensitive in detecting RLSh than TEE. These findings suggest an important role for c-TCD in the evaluation of PFO in the setting of CS.
DOI: 10.17632/bswvsp24nk
title: Data for: Suboptimal and conflict-free control of a fleet of AGVs to serve online requests

description: see README.txt
DOI: 10.17632/xjvsp3dhzf
title: Single cortical neurons as deep artificial neural networks

description: This dataset is related to the work "Single cortical neurons as deep artificial neural networks" (bioRxiv: https://www.biorxiv.org/content/10.1101/613141v2, SSRN: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3717773) Code, data and pretrained networks of the work can be found at following links below: Live Notebook with main result replicated: https://www.kaggle.com/selfishgene/single-neuron-as-deep-net-replicating-key-result Dataset and pretrained networks: https://www.kaggle.com/selfishgene/single-neurons-as-deep-nets-nmda-test-data Live Notebook exploring the dataset: https://www.kaggle.com/selfishgene/exploring-a-single-cortical-neuron Full Github repo: https://github.com/SelfishGene/neuron_as_deep_net The specific csv file in this dataset holds the full test evaluation details (network hyperparameters, various evaluation metrics) for 174 deep networks fitted on 3 different types of biophysical models {AMPA + NMDA synapses, AMPA only synapses, AMPA only synapses w/o somatic SK ion channel} All other files related to the dataset are in the kaggle dataset linked above (doi: 10.34740/KAGGLE/DS/417817)
DOI: 10.6084/m9.figshare.7982183.v1
title: Supplementary Material for: Turkish Ectodermal Dysplasia Cohort: From Phenotype to Genotype in 17 Families

description: Hypohidrotic or anhidrotic ectodermal dysplasia (HED/EDA) is characterized by impaired development of the hair, teeth, or sweat glands. HED/EDA is inherited in an X-linked, autosomal dominant, or autosomal recessive pattern and caused by the pathogenic variants in 4 genes: <i>EDA</i>, <i>EDAR</i>, <i>EDARADD</i>, and <i>WNT10A</i>. The aim of the present study was to perform molecular screening of these 4 genes in a cohort of Turkish individuals diagnosed with HED/EDA. We screened for pathogenic variants of <i>WNT10A</i>, <i>EDA</i>, <i>EDAR</i>, and <i>EDARADD</i> through Sanger sequencing. We further assessed the clinical profiles of the affected individuals in order to establish phenotype-genotype correlation. In 17 (63%) out of 27 families, 17 pathogenic variants, 8 being novel, were detected in the 4 well-known ectodermal dysplasia genes. <i>EDAR</i> and <i>EDA</i> variants were identified in 6 families each, <i>WNT10A</i> variants in 4, and an <i>EDARADD</i> variant in 1, accounting for 35.3, 35.3, 23.5, and 5.9% of mutation-positive families, respectively. The low mutation detection rate of the cohort and the number of the <i>EDAR</i> pathogenic variants being as high as the <i>EDA</i> ones were the most noteworthy findings which could be attributed to the high consanguinity rate.