cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12581309
title: Supplementary Material for: Implementation of PD-L1 22C3 IHC pharmDx<sup>TM</sup> in Cell Block Preparations of Lung Cancer: Concordance with Surgical Resections and Technical Validation of CytoLyt® Prefixation

description: <b><i>Background:</i></b> Programmed death ligand-1 (PD-L1) assessed by immunohistochemistry (IHC) is used as biomarker for pembrolizumab therapy in advanced stage lung cancer patients. However, data permitting direct performance comparison between cytology and surgical specimen types are limited since both specimens from a single tumor site are infrequently available. In addition, alcohol fixation used with cytology specimens requires technical validation of the PD-L1 IHC assay before clinical use. We here report our experience with implementation of the PD-L1 22C3 IHC pharmDx<sup>TM</sup> assay for cytologic samples at a large tertiary cancer center. <b><i>Study Design:</i></b> Archival formalin-fixed (FF), paraffin-embedded cell blocks (CBs) and subsequent lung tumor resections (LTRs) from the same anatomical site were used for a direct comparison of PD-L1 tumor proportion scores (TPSs). TPS values were independently determined by one surgical lung pathologist and two cytopathologists blinded to the specimen pairs. An interim analysis was performed to facilitate the pooling of expertise among observers. After PD-L1 22C3 IHC pharmDx<sup>TM</sup> implementation for FF cytology specimens, dual-processed samples were used for a prospective technical validation of CytoLyt® prefixation (CF). Digital image analysis was performed for a subset of dual-processed specimens. <b><i>Results:</i></b> Eighty-one CBs and LTRs were included for comparison of the specimen types. PD-L1 assessment in CBs had an accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of 88.9/72.8, 66.7/73.5, 95.2/72.3, 80.0/65.8, and 90.9/79.1% for the ≥50/≥1% cutoff, respectively. The intraclass correlation coefficient was 0.84 (95% confidence interval [CI]: 0.76, 0.90), and it improved after interim analysis (before: 0.79 and after: 0.92). The overall concordance between CF and FF for the categories defined by the ≥50/≥1% cutoff values was 90.4% (95% CI: 79.0, 96.8). Similar assay performance was confirmed by digital analysis. <b><i>Conclusions:</i></b> PD-L1 22C3 IHC pharmDx<sup>TM</sup> shows good reliability if used with CB preparations. CF does not impact assay results significantly. Clinical validation with outcome data is needed, and digital methods of assessment should be further investigated.
DOI: 10.6084/m9.figshare.12581306
title: Soil Global Blindspots - coverage analysis

description: Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil biodiversity and ecosystem functioning data across soil macroecological studies and &gt;17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
DOI: 10.6084/m9.figshare.12581306.v1
title: Soil Global Blindspots - coverage analysis

description: Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil biodiversity and ecosystem functioning data across soil macroecological studies and &gt;17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
DOI: 10.6084/m9.figshare.12581261
title: RT-PCR all data

description: All amplification results shown in table 2
DOI: 10.6084/m9.figshare.12581237
title: blindspots_datasets

description: Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil biodiversity and ecosystem functioning data across soil macroecological studies and &gt;17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
DOI: 10.6084/m9.figshare.12581261.v1
title: RT-PCR all data

description: All amplification results shown in table 2
DOI: 10.6084/m9.figshare.12581237.v1
title: blindspots_datasets

description: Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil biodiversity and ecosystem functioning data across soil macroecological studies and &gt;17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.
DOI: 10.6084/m9.figshare.12581303.v1
title: Raw data - N forms

description: Raw data of N forms:-Nitrate-Ammonium-Total-N-Organic-N<br>including ABS values for each N form
DOI: 10.6084/m9.figshare.12581228
title: Supplementary S3. Comparison of Various Machine Learning Models with ANNs:extraTree_and_Logistic_Regression.tar.gz

description: The files present the output for the extra tree classifier and the logistic regression used for the classification of ADR for two drugs in combination.<br>
DOI: 10.6084/m9.figshare.12581303.v3
title: Supporting data - N forms and Humus% in Sand soil, Nyírség

description: Raw data of N forms:-Nitrate-Ammonium-Total-N-Organic-N-pH-KA (textrure Arany type)<br>including ABS values for each N form and Humus% in 3 repetitions
DOI: 10.6084/m9.figshare.12581213
title: Supplementary Material for: Small Symptomatic Unilateral Choroidal Osteoma Diagnosed with Enhanced-Depth Imaging Optical Coherence Tomography and Thin-Slice Computed Tomography: 2 Clinical Cases

description: <b><i>Background:</i></b> Choroidal osteoma is a rare, benign, ossifying intraocular tumor of unknown etiology. While patients with choroidal osteoma usually show distinct large yellowish subretinal lesions, some could have small lesions, making the differential diagnosis difficult. We experienced 2 cases of small symptomatic unilateral osteoma approximately 1.0-mm disc diameter in size. <b><i>Methods:</i></b> Retrospective medical charts of 2 patients with small symptomatic unilateral osteoma were reviewed. Fundus examination, spectral domain enhanced-depth optical coherence tomography (EDI-OCT), fluorescein angiography, indocyanine green angiography, B-scan ultrasonography (USG), and X-ray computed tomography (CT) were performed. <b><i>Results:</i></b> Case 1: a case of a 41-year-old male. Fundus examination revealed a yellowish-white lesion of 1.0-mm disc diameter in size. EDI-OCT of the lesion shows sub-RPE elevation. B-scan USG was not definite for diagnosis. Thin-slice (2 mm) CT scan revealed a choroidal osteoma. Case 2: a case of a 70-year-old male. Fundus examination revealed a yellowish-white lesion of 0.9-mm disc diameter. EDI-OCT showed sub-RPE elevation without serous retinal detachment and horizontal lamellar-like structure within the lesion. B-scan USG suggested acoustic shadowing, but it was unclear. The thin-slice CT scan confirmed bony tissue at the lesion. <b><i>Conclusions:</i></b> We report 2 cases of small choroidal osteoma. Diagnosis of small yellowish subretinal lesions is sometimes difficult. Characteristic findings with EDI-OCT may sometimes suggest this disease, and thin-slice CT could help to diagnose choroidal osteoma.
DOI: 10.6084/m9.figshare.12581228.v1
title: Supplementary S3. Comparison of Various Machine Learning Models with ANNs:extraTree_and_Logistic_Regression.tar.gz

description: The files present the output for the extra tree classifier and the logistic regression used for the classification of ADR for two drugs in combination.<br>
DOI: 10.6084/m9.figshare.12581186
title: NSCLC_GEM.tar.gz

description: single-cell RNA-Seq of 28 NSCLC patients
DOI: 10.6084/m9.figshare.12581303.v2
title: Supporting data - N forms and Humus% in Sand soil, Nyírség

description: Raw data of N forms:-Nitrate-Ammonium-Total-N-Organic-N<br>including ABS values for each N form and Humus% in 3 repetitions
DOI: 10.6084/m9.figshare.12581168
title: Obstructs-equipped Apparatus Reduced Cannibalism and Improved High Density Larval Rearing of the Natural Enemy, Harmonia axyridis

description: The development parameters of Harmonia axyridis in obstructs-equipped containers
DOI: 10.6084/m9.figshare.12581186.v1
title: NSCLC_GEM.tar.gz

description: single-cell RNA-Seq of 28 NSCLC patients
DOI: 10.6084/m9.figshare.12581147
title: A utility-aware multi-task scheduling method in cloud manufacturing using extended NSGA-II embedded with game theory

description: This is the experimental data of the manuscript entitled "A utility-aware multi-task scheduling method in cloud manufacturing using extended NSGA-II embedded with game theory". All data are generated through computer simulation and saved in the file with csv format. The data are the simulation of the real-world case. There are nine instances for these experiments, which cover multiple scales. Three attributes including time, cost, and reliability of services for achieving corresponding subtasks are shown in datasets.
DOI: 10.6084/m9.figshare.12581132
title: Bacteria_raw_data

description: <b>Soil texture primarily affects diversity of bacteria, but organic carbon shapes community composition in paddy soils having different parent materials and fertility levels</b>
DOI: 10.6084/m9.figshare.12581168.v2
title: Obstructs-equipped Apparatus Reduced Cannibalism and Improved High Density Larval Rearing of the Natural Enemy, Harmonia axyridis

description: The development parameters of Harmonia axyridis in obstructs-equipped containers
DOI: 10.6084/m9.figshare.12581126
title: Supplementary Material for: Clinical and Operative Determinants of Acute Kidney Injury after Cardiac Surgery

description: <b><i>Introduction:</i></b> Cardiac surgery-associated acute kidney injury (CSA-AKI) is associated with increased morbidity and mortality. <b><i>Objectives:</i></b> We aimed to identify potentially modifiable risk factors for CSA-AKI. <b><i>Methods:</i></b> This was a<b><i></i></b>single-center retrospective cohort study of 495 adult patients undergoing cardiac surgery. AKI was diagnosed and staged using full KDIGO criteria incorporating baseline serum creatinine (SC) levels and correction of postoperative SC levels for fluid balance. We examined the association of routinely available clinical and laboratory data with AKI using multivariate logistic regression modeling. <b><i>Results:</i></b> A total of 103 (20.8%) patients developed AKI: 16 (15.5%) patients were diagnosed with AKI upon hospital admission, and 87 (84.5%) patients were diagnosed with CSA-AKI. Correction of SC levels for fluid balance increased the number of AKI cases to 104 (21.0%), with 6 patients categorized to different AKI stages. Univariate logistic regression analysis identified five preoperative (age, sex, diabetes mellitus, preoperative systolic pulmonary arterial pressure [PSPAP], acute decompensated heart failure) and five intraoperative predictors of AKI (age, sex, red blood cell [RBC] volume transfused, use of minimally invasive surgery, duration of cardiopulmonary bypass). When all preoperative and intraoperative variables were incorporated into one model, six predictors remained significant (age, sex, use of minimally invasive surgery, RBC volume transfused, PSPAP, duration of cardiopulmonary bypass). Model discrimination performance showed an area under the curve of 0.69 for the model including only preoperative variables, 0.76 for the model including only intraoperative variables, and 0.77 for the model including all preoperative and intraoperative variables. <b><i>Conclusions:</i></b> Use of minimally invasive surgery and therapies mitigating PSPAP and intraoperative blood loss may offer protection against CSA-AKI.
DOI: 10.6084/m9.figshare.12581168.v1
title: High density larval rearing is viable for a cannibalistic ladybird beetle, Harmonia axyridis in obstructs-equipped container

description: The development parameters of Harmonia axyridis in obstructs-equipped containers
DOI: 10.6084/m9.figshare.12581084
title: Supplementary Material for: A Compound Heterozygosis of Two Novel Mutations Causes Factor X Deficiency in a Chinese Pedigree

description: <b><i>Background:</i></b> Mutations in the <i>F10</i>-coding gene can cause factor X (FX) deficiency, leading to abnormal coagulation activity and severe tendency for hemorrhage. Therefore, identifying mutations in <i>F10</i> is important for diagnosing congenital FX deficiency. <b><i>Methods:</i></b> We studied a 63-year-old male patient with FX deficiency and 10 of his family members. Clotting and immunological methods were used to determine activated partial thromboplastin time (aPTT), prothrombin time (PT), thrombin time (TT), fibrinogen levels, FX activity, and FX antigen levels. The platelet count was determined. A mixing study was performed to eliminate the presence of coagulation factor inhibitors and lupus anticoagulant. Mutations were searched using whole-exome sequencing and certified by Sanger sequencing. <b><i>Results:</i></b> Genetic analysis of the proband identified two single-base substitutions: c.1085G&gt;A (p.Ser362Asn) and c.1152C&gt;A (p.Tyr384Ter, termination codon, caused by the DNA sequence TAA). His FX activity and antigen levels were 1.7% and 408.53 pg/mL, respectively; aPTT and PT were 52.3 and 48.0 s, respectively. One brother had the same compound heterozygous mutations, and his FX activity and antigen levels were 1.3% and 465.47 pg/mL, respectively; his aPTT and PT were 65.2 and 54.5 s, respectively. His mother, another brother, and one sister were heterozygous for c.1085G&gt;A (p.Ser362Asn), and his daughter and grandson (6 years old) were heterozygous for c.1152C&gt;A (p.Tyr384Ter). <b><i>Conclusion:</i></b> The heterozygous variants p.Ser362Asn or p.Tyr384Ter indicate mild FX deficiency, but the compound heterozygous mutation of the two causes severe congenital FX deficiency and bleeding. Genetic analysis of these two mutations may help characterize the bleeding tendency and confirm congenital FX deficiency.
DOI: 10.6084/m9.figshare.12581084.v1
title: Supplementary Material for: A Compound Heterozygosis of Two Novel Mutations Causes Factor X Deficiency in a Chinese Pedigree

description: <b><i>Background:</i></b> Mutations in the <i>F10</i>-coding gene can cause factor X (FX) deficiency, leading to abnormal coagulation activity and severe tendency for hemorrhage. Therefore, identifying mutations in <i>F10</i> is important for diagnosing congenital FX deficiency. <b><i>Methods:</i></b> We studied a 63-year-old male patient with FX deficiency and 10 of his family members. Clotting and immunological methods were used to determine activated partial thromboplastin time (aPTT), prothrombin time (PT), thrombin time (TT), fibrinogen levels, FX activity, and FX antigen levels. The platelet count was determined. A mixing study was performed to eliminate the presence of coagulation factor inhibitors and lupus anticoagulant. Mutations were searched using whole-exome sequencing and certified by Sanger sequencing. <b><i>Results:</i></b> Genetic analysis of the proband identified two single-base substitutions: c.1085G&gt;A (p.Ser362Asn) and c.1152C&gt;A (p.Tyr384Ter, termination codon, caused by the DNA sequence TAA). His FX activity and antigen levels were 1.7% and 408.53 pg/mL, respectively; aPTT and PT were 52.3 and 48.0 s, respectively. One brother had the same compound heterozygous mutations, and his FX activity and antigen levels were 1.3% and 465.47 pg/mL, respectively; his aPTT and PT were 65.2 and 54.5 s, respectively. His mother, another brother, and one sister were heterozygous for c.1085G&gt;A (p.Ser362Asn), and his daughter and grandson (6 years old) were heterozygous for c.1152C&gt;A (p.Tyr384Ter). <b><i>Conclusion:</i></b> The heterozygous variants p.Ser362Asn or p.Tyr384Ter indicate mild FX deficiency, but the compound heterozygous mutation of the two causes severe congenital FX deficiency and bleeding. Genetic analysis of these two mutations may help characterize the bleeding tendency and confirm congenital FX deficiency.
DOI: 10.6084/m9.figshare.12581081
title: Seasonal variations of hydraulic exchange between canal water and groundwater in an alluvial plain setting using 222Rn

description: Date for analyzing the interaction between groundwater and surface water and rainfall events<br>
DOI: 10.6084/m9.figshare.12581048
title: GWAS datasets of HQLA-HB AIL population

description: These files contains the phenotypes and genotypes of HQLA-HB AIL chicken individuals.<br>
DOI: 10.6084/m9.figshare.12581063
title: Genotype of HQLA-HB population

description: This file contains the genotypes of chicken HQLA-HB AIL individuals using GBS method.
DOI: 10.6084/m9.figshare.12581063.v1
title: Genotype of HQLA-HB population

description: This file contains the genotypes of chicken HQLA-HB AIL individuals using GBS method.
DOI: 10.6084/m9.figshare.12581081.v2
title: Seasonal variations of hydraulic exchange between canal water and groundwater in an alluvial plain setting using 222Rn

description: Date for analyzing the interaction between groundwater and surface water and rainfall events<br>
DOI: 10.6084/m9.figshare.12581072.v1
title: 510 Ma S-Hg-C data

description: Tables 1-2, Tables s1-s4
DOI: 10.6084/m9.figshare.12581081.v1
title: Seasonal variations of hydraulic exchange between canal water and groundwater in an alluvial plain setting using 222Rn

description: Date for analyzing the interaction between groundwater and surface water and rainfall events<br>
DOI: 10.6084/m9.figshare.12580970
title: Anexo_1_Registros_análisis_estudios_incluidos_Figshare2020.pdf

description: Registros de análisis e interpretación de estudios tratados en seis aspectos (Moher et al.,2009): <i>a)</i> tipo y tópico de intervención; <i>b </i><i>)</i> descripción de la evidencia (método: diseño, fases, técnicas de recolección de datos, grupos de comparación, línea base, escenario o contexto); <i>c)</i> participantes; <i>d)</i> detenciones (grupos, número, duración, secuencia, características); <i>e </i><i>)</i> resultados cuali-cuantitativos; <i>f </i><i>)</i> <i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i>anotaciones: sobre tipo de intervención multi-componente, información adicional sobre sesgos, y equivalencias de reacciones.
DOI: 10.6084/m9.figshare.12580970.v2
title: Anexo_1_Registros_análisis_estudios_incluidos_Figshare2020.pdf

description: Registros de análisis e interpretación de estudios tratados en seis aspectos (Moher et al.,2009): <i>a)</i> tipo y tópico de intervención; <i>b </i><i>)</i> descripción de la evidencia (método: diseño, fases, técnicas de recolección de datos, grupos de comparación, línea base, escenario o contexto); <i>c)</i> participantes; <i>d)</i> detenciones (grupos, número, duración, secuencia, características); <i>e </i><i>)</i> resultados cuali-cuantitativos; <i>f </i><i>)</i> <i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i>anotaciones: sobre tipo de intervención multi-componente, información adicional sobre sesgos, y equivalencias de reacciones.
DOI: 10.6084/m9.figshare.12580970.v1
title: ANEX_1_REGISTROS_ANALIS_ESTUD_INCLUIDOS_Figshare2020.pdf

description: Registros de análisis e interpretación de estudios tratados en seis aspectos (Moher et al.,2009): <i>a)</i> tipo y tópico de intervención; <i>b </i><i>)</i> descripción de la evidencia (método: diseño, fases, técnicas de recolección de datos, grupos de comparación, línea base, escenario o contexto); <i>c)</i> participantes; <i>d)</i> detenciones (grupos, número, duración, secuencia, características); <i>e </i><i>)</i> resultados cuali-cuantitativos; <i>f </i><i>)</i> <i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i><i></i>anotaciones: sobre tipo de intervención multi-componente, información adicional sobre sesgos, y equivalencias de reacciones.
DOI: 10.6084/m9.figshare.12580907
title: Additional file 9 of Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

description: Additional file 9: Table S8. Complete list of CTCF and TF binding motifs that show significant correlations between allelic PWM scores and magnitude of ASM.
DOI: 10.6084/m9.figshare.12580904
title: Additional file 8 of Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

description: Additional file 8: Table S7. Complete list of polymorphic CTCF and TF binding motifs found to be significantly enriched among ASM loci, requiring that the motif be disrupted by the ASM index SNP.