cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25217840
title: Lapsed El Niño impact on Atlantic and Northwest Pacific tropical cyclone activity in 2023

description: The El Niño-Southern Oscillation (ENSO) is a major factor modulating interannual variability of tropical cyclone (TC) activity, typically resulting in the suppressed TC genesis frequency (TCGF) over the North Atlantic (NA) and a distinct northwest-southeast dipole pattern in TCGF anomaly over the western North Pacific (WNP) during El Niño years. However, the TC season of 2023, a year of strong El Niño, presented an intriguing departure from this norm, as the NA experienced an unexpectedly active season with 20 TCs, while the WNP witnessed a decrease in the basin count with only 13 TCs.
DOI: 10.18465/a97dfa46-4a1a-40fa-8c83-31366da85d25
title: MNT Nantes 2015

description: Modèle Numérique de Terrain obtenu par LiDAR sur la ville de Nantes
DOI: 10.6084/m9.figshare.23282921.v1
title: An exquisitely preserved skeleton of <i>Eoarctos vorax</i> (nov. gen. et sp.) from Fitterer Ranch, North Dakota (early Oligocene) and systematics and phylogeny of North American early arctoids (Carnivora, Caniformia)

description: An exquisitely preserved male skeleton of an early arctoid, <i>Eoarctos vorax</i> new genus and species, provides a unique window into the origin and early divergence of Carnivora. Recovered from the Fitterer Ranch locality in the early Oligocene (Orellan to Whitneyan North American Land Mammal ages) Brule Formation of southwestern North Dakota (∼32 Ma), the new arctoid offers an opportunity to evaluate the fundamental relationships of the caniform (dog-like) carnivorans. <i>Eoarctos vorax</i> possesses a suite of plesiomorphic characters inherited from its miacid ancestors, making it an ideal model for ancestral arctoids. We present a comprehensive treatment of <i>E. vorax</i>, combining traditional description with photographic documentation, microCT, laser scans, and photogrammetry. Showing its plesiomorphic morphology, <i>Eoarctos vorax</i> is scansorial, somewhat like a modern raccoon, retaining the ability to climb trees and lacking cursorial adaptations present in the early canid <i>Hesperocyon</i>. However, <i>E. vorax</i> shows clear signs of durophagous cranio-dental morphology, presumably for an obligatory diet of mollusks, with frequent damage to shell-crushing premolars, plus associated dental infections. We review several other key North American early arctoids and present total-evidence (nuclear DNA and discrete morphological characters) Bayesian and parsimony analyses of Caniformia phylogeny, including extinct stem taxa plus a living member of all modern families. We recognize an endemic North American ursoid clade, Subparictidae, which includes <i>Eoarctos vorax</i>. We demonstrate the importance of North America as an early cradle of evolution for caniform carnivorans, including early precursors of Canidae, Amphicyonidae, Ursidae, and Pinnipedia.
DOI: 10.6084/m9.figshare.25217885
title: Supplementary Material for: Duodenal papillary metastasis of lung cancer with bleeding controlled by endoscopic treatment and systemic osimertinib therapy: Case report

description: Introduction: Solid organ malignancies rarely metastasize to the duodenal papilla. We describe a case of primary lung cancer with duodenal papillary metastasis in a patient who presented with melena. To the best of our knowledge, this is only the second report of duodenal papillary metastasis from lung cancer.
Case Presentation: A 65-year-old woman presented with complaints of anorexia, weight loss, and black stool. Imaging studies led to a clinical diagnosis of stage IVB lung cancer, and anticoagulants were initiated to treat pulmonary artery thrombosis. However, endoscopic hemostasis was challenging because of bleeding from a duodenal papillary tumor. Fortunately, the patient was positive for the plasma epidermal growth factor receptor (EGFR) gene mutation, and osimertinib, an EGFR tyrosine kinase inhibitor, was administered, successfully achieving hemostasis. Subsequently, endoscopic ultrasonography-guided transbronchial needle aspiration of an enlarged mediastinal lymph node and duodenal papillary tumor biopsy confirmed duodenal papillary metastasis of the primary lung adenocarcinoma. 
Conclusion: Although duodenal papillary metastasis is extremely rare, a good clinical outcome was achieved in this case by considering duodenal papillary metastasis from lung cancer as the differential diagnosis and administering systemic osimertinib therapy.
DOI: 10.6084/m9.figshare.8080661
title: Additional file 6: of Knockdown of HMGA2 regulates the level of autophagy via interactions between MSI2 and Beclin1 to inhibit NF1-associated malignant peripheral nerve sheath tumour growth

description: Table S4. ChIP-Seq data. (XLSX 664 kb)
DOI: 10.6084/m9.figshare.8080661.v1
title: Additional file 6: of Knockdown of HMGA2 regulates the level of autophagy via interactions between MSI2 and Beclin1 to inhibit NF1-associated malignant peripheral nerve sheath tumour growth

description: Table S4. ChIP-Seq data. (XLSX 664 kb)
DOI: 10.6084/m9.figshare.25040621
title: Dataset for the "Comparison of Clinical Characteristics and Outcomes between COVID-19 Survivors and Non Survivors: A Retrospective Observational Study"

description: The aim of this study was to compare the clinical characteristics and outcomes of COVID-19 survivors and non-survivors who were transferred from general wards to critical care units in four tertiary hospitals in Nepal. The study employed a retrospective observational design, utilizing data from the ICU registry managed by the Nepal Intensive Care Research Foundation (NICRF) which utilized Case Report Forms that contained comprehensive information on patients admitted to the ICU. Demographic data, clinical characteristics, laboratory parameters, treatments, and outcomes were analyzed. The statistical analysis involved the use of the Mann-Whitney U test for continuous variables and Pearson's chi-squared test for categorical variables. Fisher's exact test was applied when expected frequencies were less than 5. IBM Statistical Package for the Social Sciences (SPSS) software, version 25, was used for analysis. Ethical clearance for the study was obtained from the Nepal Health Research Council on January 23, 2023 (Ref No. 1698/2022). The study received exemption from the review of secondary data, as the information was de-identified and did not involve direct patient participation. The ethical approval ensured compliance with ethical standards and protected the rights and confidentiality of the study participants.<br><br>
DOI: 10.6084/m9.figshare.25040621.v2
title: Dataset for the "Comparison of Clinical Characteristics and Outcomes between COVID-19 Survivors and Non Survivors: A Retrospective Observational Study"

description: This study aimed to compare the clinical characteristics of COVID-19 survivors and non-survivors who were transferred from general wards to the critical care units in four tertiary hospitals of Nepal.
DOI: 10.6084/m9.figshare.23282921
title: An exquisitely preserved skeleton of <i>Eoarctos vorax</i> (nov. gen. et sp.) from Fitterer Ranch, North Dakota (early Oligocene) and systematics and phylogeny of North American early arctoids (Carnivora, Caniformia)

description: An exquisitely preserved male skeleton of an early arctoid, <i>Eoarctos vorax</i> new genus and species, provides a unique window into the origin and early divergence of Carnivora. Recovered from the Fitterer Ranch locality in the early Oligocene (Orellan to Whitneyan North American Land Mammal ages) Brule Formation of southwestern North Dakota (∼32 Ma), the new arctoid offers an opportunity to evaluate the fundamental relationships of the caniform (dog-like) carnivorans. <i>Eoarctos vorax</i> possesses a suite of plesiomorphic characters inherited from its miacid ancestors, making it an ideal model for ancestral arctoids. We present a comprehensive treatment of <i>E. vorax</i>, combining traditional description with photographic documentation, microCT, laser scans, and photogrammetry. Showing its plesiomorphic morphology, <i>Eoarctos vorax</i> is scansorial, somewhat like a modern raccoon, retaining the ability to climb trees and lacking cursorial adaptations present in the early canid <i>Hesperocyon</i>. However, <i>E. vorax</i> shows clear signs of durophagous cranio-dental morphology, presumably for an obligatory diet of mollusks, with frequent damage to shell-crushing premolars, plus associated dental infections. We review several other key North American early arctoids and present total-evidence (nuclear DNA and discrete morphological characters) Bayesian and parsimony analyses of Caniformia phylogeny, including extinct stem taxa plus a living member of all modern families. We recognize an endemic North American ursoid clade, Subparictidae, which includes <i>Eoarctos vorax</i>. We demonstrate the importance of North America as an early cradle of evolution for caniform carnivorans, including early precursors of Canidae, Amphicyonidae, Ursidae, and Pinnipedia.
DOI: 10.6084/m9.figshare.21185654.v1
title: Additional file 10 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 10: Supplementary Table 5. Specific marker genes of BM tumor microenvironment cells in patients with NDMM and RRMM.
DOI: 10.6084/m9.figshare.21185043
title: Additional file 2 of Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity

description: Additional file 2: Supplemental Table 2. Metrics obtained for each brain extract. (A) Quantifying Aβ, tau, and effect size in the neurite integrity and/or MEA assay for each brain extract. (B) Proteomic measurements of TBS-soluble brain tissue extracts tested in MEA and/or neurite integrity assay.
DOI: 10.6084/m9.figshare.8078708
title: drawing of partial figures from The efficiency of migration and profile control with emulsion systems in class Ⅲ reservoirs

description: Tingting Zhu_figures_ESM.xlsx
DOI: 10.6084/m9.figshare.21185046.v1
title: Additional file 3 of Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity

description: Additional file 3: Supplemental Table 3. Relevant results of linear modeling of effect size in neurite integrity and MEA assays.
DOI: 10.6084/m9.figshare.21185684
title: Additional file 7 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 7: Supplementary Table 2. The known marker genes used for annotating cell clusters.
DOI: 10.6084/m9.figshare.21185690
title: Additional file 9 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 9: Supplementary Table 4. Specific marker genes of malignant plasma cell subclones in NDMM and RRMM patients. NDMM, newly diagnosed multiple myeloma; RRMM, relapsed and/or refractory MM.
DOI: 10.6084/m9.figshare.21185040.v1
title: Additional file 1 of Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity

description: Additional file 1: Supplemental Table 1. Differentially expressed proteins in the soluble AD brain proteome. TBS-soluble extracts were prepared from brain tissue described in Table 1, and mass spectrometry used to quantify proteins. Differential expression of individual proteins was analyzed between AD vs. LP-NCI (A) and AD vs. HP-NCI (B). Many more proteins were differentially expressed in the LP-NCI vs. AD comparison than in the HP-NCI vs. AD comparison. Unpaired t-test with Welch correction, two-stage step-up, FDR &lt; 0.05.
DOI: 10.6084/m9.figshare.21185687.v1
title: Additional file 8 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 8: Supplementary Table 3. Specific marker genes of control donor BM cells. BM, bone marrow.
DOI: 10.6084/m9.figshare.21185690.v1
title: Additional file 9 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 9: Supplementary Table 4. Specific marker genes of malignant plasma cell subclones in NDMM and RRMM patients. NDMM, newly diagnosed multiple myeloma; RRMM, relapsed and/or refractory MM.
DOI: 10.6084/m9.figshare.8078708.v1
title: drawing of partial figures from The efficiency of migration and profile control with emulsion systems in class Ⅲ reservoirs

description: Tingting Zhu_figures_ESM.xlsx
DOI: 10.6084/m9.figshare.21185043.v1
title: Additional file 2 of Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity

description: Additional file 2: Supplemental Table 2. Metrics obtained for each brain extract. (A) Quantifying Aβ, tau, and effect size in the neurite integrity and/or MEA assay for each brain extract. (B) Proteomic measurements of TBS-soluble brain tissue extracts tested in MEA and/or neurite integrity assay.
DOI: 10.6084/m9.figshare.5457409
title: Sparsity Oriented Importance Learning for High-Dimensional Linear Regression

description: With now well-recognized nonnegligible model selection uncertainty, data analysts should no longer be satisfied with the output of a single final model from a model selection process, regardless of its sophistication. To improve reliability and reproducibility in model choice, one constructive approach is to make good use of a sound variable importance measure. Although interesting importance measures are available and increasingly used in data analysis, little theoretical justification has been done. In this article, we propose a new variable importance measure, sparsity oriented importance learning (SOIL), for high-dimensional regression from a sparse linear modeling perspective by taking into account the variable selection uncertainty via the use of a sensible model weighting. The SOIL method is theoretically shown to have the inclusion/exclusion property: When the model weights are properly around the true model, the SOIL importance can well separate the variables in the true model from the rest. In particular, even if the signal is weak, SOIL rarely gives variables not in the true model significantly higher important values than those in the true model. Extensive simulations in several illustrative settings and real-data examples with guided simulations show desirable properties of the SOIL importance in contrast to other importance measures. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21185681.v1
title: Additional file 6 of Malignant clonal evolution drives multiple myeloma cellular ecological diversity and microenvironment reprogramming

description: Additional file 6: Supplementary Table 1. Demographic, clinical, molecular, and diagnostic information of all patients in this study.
DOI: 10.6084/m9.figshare.6505901.v3
title: Melatonin promotes Cashmere goat (<i>Capra hircus</i>) secondary hair follicle growth: a view from integrated analysis of long non-coding and coding RNAs

description: The role of melatonin in promoting the yield of Cashmere goat wool has been demonstrated for decades though there remains a lack of knowledge regarding melatonin mediated hair follicle growth. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are widely transcribed in the genome and play ubiquitous roles in regulating biological processes. However, the role of lncRNAs in regulating melatonin mediated hair follicle growth remains unclear. In this study, we established an <i>in vitro</i> Cashmere goat secondary hair follicle culture system, and demonstrated that 500 ng/L melatonin exposure promoted hair follicle fiber growth. Based on long intergenic RNA sequencing, we demonstrated that melatonin promoted hair follicle elongation via regulating genes involved in focal adhesion and extracellular matrix receptor pathways and further cis predicting of lncRNAs targeted genes indicated that melatonin mediated lncRNAs mainly targeted vascular smooth muscle contraction and signaling pathways regulating the pluripotency of stem cells. We proposed that melatonin exposure not only perturbed key signals secreted from hair follicle stem cells to regulate hair follicle development, but also mediated lncRNAs mainly targeted to pathways involved in the microvascular system and extracellular matrix, which constitute the highly orchestrated microenvironment for hair follicle stem cell. Taken together, our findings here provide a profound view of lncRNAs in regulating Cashmere goat hair follicle circadian rhythms and broaden our knowledge on melatonin mediated hair follicle morphological changes.
DOI: 10.6084/m9.figshare.6505910.v1
title: Small RNA-induced INTS6 gene up-regulation suppresses castration-resistant prostate cancer cells by regulating β-catenin signaling

description: Small RNAs play an important role in gene regulatory networks. The gene suppressive effect of small RNAs was previously the dominant focus of studies, but during the recent decade, small RNA-induced gene activation has been reported and has become a notable gene manipulation technique. In this study, a putative tumor suppressor, <i>INTS6</i>, was activated by introducing a promoter-targeted small RNA (dsRNA-915) into castration-resistant prostate cancer (CRPC) cells. Unique dynamics associated with the gene upregulation phenomenon was observed. Following gene activation, cell proliferation and motility were suppressed in vitro. Downregulation of <i>Wnt</i>/β-catenin signaling was observed during the activation period, and the impairment of β-catenin degradation reversed the tumor suppressor effects of <i>INTS6</i>. These results suggest the potential application of small activating RNAs in targeted gene therapy for CRPC.
DOI: 10.6084/m9.figshare.5457412
title: A Bayesian Phase I/II Trial Design for Immunotherapy

description: Immunotherapy is an innovative treatment approach that stimulates a patient’s immune system to fight cancer. It demonstrates characteristics distinct from conventional chemotherapy and stands to revolutionize cancer treatment. We propose a Bayesian phase I/II dose-finding design that incorporates the unique features of immunotherapy by simultaneously considering three outcomes: immune response, toxicity, and efficacy. The objective is to identify the biologically optimal dose, defined as the dose with the highest desirability in the risk–benefit tradeoff. An Emax model is utilized to describe the marginal distribution of the immune response. Conditional on the immune response, we jointly model toxicity and efficacy using a latent variable approach. Using the accumulating data, we adaptively randomize patients to experimental doses based on the continuously updated model estimates. A simulation study shows that our proposed design has good operating characteristics in terms of selecting the target dose and allocating patients to the target dose. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6505901.v1
title: Melatonin promotes Cashmere goat (<i>Capra hircus</i>) secondary hair follicle growth: A view from integrated analysis of long non-coding and coding RNAs

description: The role of melatonin in promoting the yield of Cashmere goat wool has been demonstrated for decades though there remains a lack of knowledge regarding melatonin mediated hair follicle growth. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are widely transcribed in the genome and play ubiquitous roles in regulating biological processes. However, the role of lncRNAs in regulating melatonin mediated hair follicle growth remains unclear. In this study, we established an in vitro Cashmere goat secondary hair follicle culture system, and demonstrated that 500 ng/L melatonin exposure promoted hair follicle fiber growth. Based on long intergenic RNA sequencing, we demonstrated that melatonin promoted hair follicle elongation via regulating genes involved in focal adhesion and extracellular matrix receptor pathways and further cis predicting of lncRNAs targeted genes indicated that melatonin mediated lncRNAs mainly targeted vascular smooth muscle contraction and signaling pathways regulating the pluripotency of stem cells. We proposed that melatonin exposure not only perturbed key signals secreted from hair follicle stem cells to regulate hair follicle development, but also mediated lncRNAs mainly targeted to pathways involved in the microvascular system and extracellular matrix, which constitute the highly orchestrated microenvironment for hair follicle stem cell. Taken together, our findings here provide a profound view of lncRNAs in regulating Cashmere goat hair follicle circadian rhythms and broaden our knowledge on melatonin mediated hair follicle morphological changes.
DOI: 10.6084/m9.figshare.6505901.v2
title: Melatonin promotes Cashmere goat (<i>Capra hircus</i>) secondary hair follicle growth: a view from integrated analysis of long non-coding and coding RNAs

description: The role of melatonin in promoting the yield of Cashmere goat wool has been demonstrated for decades though there remains a lack of knowledge regarding melatonin mediated hair follicle growth. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are widely transcribed in the genome and play ubiquitous roles in regulating biological processes. However, the role of lncRNAs in regulating melatonin mediated hair follicle growth remains unclear. In this study, we established an <i>in vitro</i> Cashmere goat secondary hair follicle culture system, and demonstrated that 500 ng/L melatonin exposure promoted hair follicle fiber growth. Based on long intergenic RNA sequencing, we demonstrated that melatonin promoted hair follicle elongation via regulating genes involved in focal adhesion and extracellular matrix receptor pathways and further cis predicting of lncRNAs targeted genes indicated that melatonin mediated lncRNAs mainly targeted vascular smooth muscle contraction and signaling pathways regulating the pluripotency of stem cells. We proposed that melatonin exposure not only perturbed key signals secreted from hair follicle stem cells to regulate hair follicle development, but also mediated lncRNAs mainly targeted to pathways involved in the microvascular system and extracellular matrix, which constitute the highly orchestrated microenvironment for hair follicle stem cell. Taken together, our findings here provide a profound view of lncRNAs in regulating Cashmere goat hair follicle circadian rhythms and broaden our knowledge on melatonin mediated hair follicle morphological changes.
DOI: 10.6084/m9.figshare.21185046
title: Additional file 3 of Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity

description: Additional file 3: Supplemental Table 3. Relevant results of linear modeling of effect size in neurite integrity and MEA assays.
DOI: 10.6084/m9.figshare.21185189.v1
title: Additional file 10 of Unraveling axonal mechanisms of traumatic brain injury

description: Additional file 10: Table S1. Proteomics original and processed data for both discovery and confirmatory experiments.