cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7052606
title: Additional file 4: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: R notebook for microbe-microbe correlation analyses at genus and species level. (HTML 1518 kb)
DOI: 10.6084/m9.figshare.7052603
title: Additional file 15: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S15. The RNA-Seq analysis of DEGs associated with the functional category â Ribosomal proteinâ . (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.7052606.v1
title: Additional file 4: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: R notebook for microbe-microbe correlation analyses at genus and species level. (HTML 1518 kb)
DOI: 10.6084/m9.figshare.7052600
title: Additional file 14: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S14. The RNA-Seq analysis of DEGs associated with the functional category â Proteasomeâ . (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7052603.v1
title: Additional file 15: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S15. The RNA-Seq analysis of DEGs associated with the functional category â Ribosomal proteinâ . (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.7052600.v1
title: Additional file 14: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S14. The RNA-Seq analysis of DEGs associated with the functional category â Proteasomeâ . (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.7052594
title: Additional file 3: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: Output of GraphPad Prism for statistics of heterogeneity of microbial communities isolated from skin associated with different disease state. (XML 18 kb)
DOI: 10.6084/m9.figshare.7052591
title: Additional file 13: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S13. The RNA-Seq analysis of DEGs associated with the functional category â Neurogenesisâ . (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7052594.v1
title: Additional file 3: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: Output of GraphPad Prism for statistics of heterogeneity of microbial communities isolated from skin associated with different disease state. (XML 18 kb)
DOI: 10.6084/m9.figshare.7052591.v1
title: Additional file 13: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S13. The RNA-Seq analysis of DEGs associated with the functional category â Neurogenesisâ . (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.7052582
title: Additional file 2: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: R notebook for applying linear mixed effects model to test the significance of difference in microbial diversity among psoriatic lesional, psoriatic unaffected, and healthy skin. (HTML 772 kb)
DOI: 10.6084/m9.figshare.7052579
title: Additional file 12: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S12. The RNA-Seq analysis of DEGs associated with the functional category â Ion channelâ . (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.7052582.v1
title: Additional file 2: of Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

description: R notebook for applying linear mixed effects model to test the significance of difference in microbial diversity among psoriatic lesional, psoriatic unaffected, and healthy skin. (HTML 772 kb)
DOI: 10.6084/m9.figshare.7052579.v1
title: Additional file 12: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S12. The RNA-Seq analysis of DEGs associated with the functional category â Ion channelâ . (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.7052555
title: Additional file 11: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S11. The RNA-Seq analysis of DEGs associated with the functional category â Innate immunityâ . (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.7052555.v1
title: Additional file 11: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S11. The RNA-Seq analysis of DEGs associated with the functional category â Innate immunityâ . (XLSX 34Â kb)
DOI: 10.6084/m9.figshare.7052537
title: Additional file 10: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S10. The RNA-Seq analysis of DEGs associated with the functional category â Inflammatory responseâ . (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7052537.v1
title: Additional file 10: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

description: Table S10. The RNA-Seq analysis of DEGs associated with the functional category â Inflammatory responseâ . (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7052360
title: MOESM1 of SOX2OT knockdown derived changes in mitotic regulatory gene network of cancer cells

description: Additional file 1: Figure S1. The most associated cancers with the SOX2OT long non-coding RNA. The GENEVESTIGATOR tool was used to find out the most related conditions reported in databases to be associated with SOX2OT expression changes. The top significant conditions are listed in left including two types of brain and lung cancers (A). The schematic presentation of the SOX2OT expression level in different tissues adopted from the MiTranscriptome (B). Figure S2. The most similar conditions to the DEGs in SOX2OT knocked down U87-MG cell line (log2 expression). Figure S3. The most similar conditions to the DEGs in SOX2OT knocked down A549 cell line (log2 expression). Figure S4. The heat map presentation of all the significant common DEGs in siRNA treated or control cell line, which red: high expression value, blue: low expression value and white: mean level of expression value. Figure S5. SOX2OT inhibition effect in apoptosis and cell cycle of cancer cell lines. (A) The apoptotic response of the SOX2OTknocked down U-87 MG was compared with control cells with annexin V/PI staining. As is shown, no annexinV-positive cells (FL1) were detected. (B) The flow cytometry evaluation of PI-stained (FL3) cell cycle progression in U-87 MG cell is illustrated in tables for control and SOX2OT knocked down cells. Table S1. The complete common DEGs (P value ≤ 0.05) in both cancer cell lines (A549 and U-87MG). Table S2. Functional gene enrichment results of the common DEGS carried out by Bingo or GeneCodis. Table S3. Functional enrichment of transcription associated genes.
DOI: 10.6084/m9.figshare.7052360.v1
title: MOESM1 of SOX2OT knockdown derived changes in mitotic regulatory gene network of cancer cells

description: Additional file 1: Figure S1. The most associated cancers with the SOX2OT long non-coding RNA. The GENEVESTIGATOR tool was used to find out the most related conditions reported in databases to be associated with SOX2OT expression changes. The top significant conditions are listed in left including two types of brain and lung cancers (A). The schematic presentation of the SOX2OT expression level in different tissues adopted from the MiTranscriptome (B). Figure S2. The most similar conditions to the DEGs in SOX2OT knocked down U87-MG cell line (log2 expression). Figure S3. The most similar conditions to the DEGs in SOX2OT knocked down A549 cell line (log2 expression). Figure S4. The heat map presentation of all the significant common DEGs in siRNA treated or control cell line, which red: high expression value, blue: low expression value and white: mean level of expression value. Figure S5. SOX2OT inhibition effect in apoptosis and cell cycle of cancer cell lines. (A) The apoptotic response of the SOX2OTknocked down U-87 MG was compared with control cells with annexin V/PI staining. As is shown, no annexinV-positive cells (FL1) were detected. (B) The flow cytometry evaluation of PI-stained (FL3) cell cycle progression in U-87 MG cell is illustrated in tables for control and SOX2OT knocked down cells. Table S1. The complete common DEGs (P value ≤ 0.05) in both cancer cell lines (A549 and U-87MG). Table S2. Functional gene enrichment results of the common DEGS carried out by Bingo or GeneCodis. Table S3. Functional enrichment of transcription associated genes.
DOI: 10.6084/m9.figshare.7052342
title: Additional file 3: of High-resolution ISR amplicon sequencing reveals personalized oral microbiome

description: All bioinformatic scripts, database, and tables used in data analysis for this study. (ZIP 9385 kb)
DOI: 10.6084/m9.figshare.7052342.v1
title: Additional file 3: of High-resolution ISR amplicon sequencing reveals personalized oral microbiome

description: All bioinformatic scripts, database, and tables used in data analysis for this study. (ZIP 9385 kb)
DOI: 10.6084/m9.figshare.7052264
title: Varieties of Elitism

description: Varieties of Elitism paper and PERL Simulation
DOI: 10.6084/m9.figshare.7052333
title: Additional file 1: of High-resolution ISR amplicon sequencing reveals personalized oral microbiome

description: Metadata for this study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7052333.v1
title: Additional file 1: of High-resolution ISR amplicon sequencing reveals personalized oral microbiome

description: Metadata for this study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7052264.v1
title: Varieties of Elitism

description: Varieties of Elitism paper and PERL Simulation
DOI: 10.6084/m9.figshare.7052162
title: Both fluid intelligence and visual object recognition ability relate to nodule detection in chest radiographs

description: Data from study "Both fluid intelligence and visual object recognition ability relate to nodule detection" published in Applied Cognitive Psychology. This is the data from a sample of radiologists and non-radiologists who completed measures of fluid intelligence, radiological ability, and novel object recognition ability. p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Helvetica; color: #393939}
DOI: 10.6084/m9.figshare.7052150
title: Amundsen Sea: Potential Temperature and Salinity

description: Potential temperature and salinity data at Station 6, 10, 19 collected during a cruise aboard the IBRV <i>Araon</i> in the Amundsen Sea, Antarctic.
DOI: 10.6084/m9.figshare.7052150.v1
title: amundsenDIC_temp_sal.xlsx

description: Temperature and salinity data at Station 6, 10, 19 collected during a cruise aboard the IBRV <i>Araon</i> in the Amundsen Sea
DOI: 10.6084/m9.figshare.7052150.v2
title: Amundsen Sea: Potential Temperature and Salinity

description: Potential temperature and salinity data at Station 6, 10, 19 collected during a cruise aboard the IBRV <i>Araon</i> in the Amundsen Sea, Antarctic.
DOI: 10.6084/m9.figshare.7052105
title: Eutrophication In Lake Rotorua. 2. Using ROTAN and OVERSEER to model historic, present and future nitrogen loads

description: OVERSEER is used in New Zealand to estimate nutrient losses from farmland, but does not quantify subsequent movement through the catchment, or attenuation. This paper uses the ROTAN model, based on the Scandinavian HBV-N model, to route nitrogen losses from 1900–2015 to Lake Rotorua where groundwater age ranges from 14 to 170 years. ROTAN conceptualises three delivery pathways (quickflow, groundwater and streamflow) with different attenuation. When calibrated to measured stream and groundwater concentrations, several combinations of attenuation gave equally good fits largely because of sparse and uncertain input and calibration data. Nevertheless, lake N loads were predicted for current land use (754 ± 39 t y<sup>−1</sup>) and with proposed N loss reductions (431 ± 26 t y<sup>−1</sup>). Probabilities were also calculated that the reductions are more (12%–18%) or less (82%–88%) than required to meet the target lake N load (405 t y<sup>−1</sup>). ROTAN shows promise for calculating nitrogen movement in catchments dominated by groundwater where there is limited data.
DOI: 10.6084/m9.figshare.7052102
title: 05 — Corridor — High Density Setting

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052105.v1
title: Eutrophication In Lake Rotorua. 2. Using ROTAN and OVERSEER to model historic, present and future nitrogen loads

description: OVERSEER is used in New Zealand to estimate nutrient losses from farmland, but does not quantify subsequent movement through the catchment, or attenuation. This paper uses the ROTAN model, based on the Scandinavian HBV-N model, to route nitrogen losses from 1900–2015 to Lake Rotorua where groundwater age ranges from 14 to 170 years. ROTAN conceptualises three delivery pathways (quickflow, groundwater and streamflow) with different attenuation. When calibrated to measured stream and groundwater concentrations, several combinations of attenuation gave equally good fits largely because of sparse and uncertain input and calibration data. Nevertheless, lake N loads were predicted for current land use (754 ± 39 t y<sup>−1</sup>) and with proposed N loss reductions (431 ± 26 t y<sup>−1</sup>). Probabilities were also calculated that the reductions are more (12%–18%) or less (82%–88%) than required to meet the target lake N load (405 t y<sup>−1</sup>). ROTAN shows promise for calculating nitrogen movement in catchments dominated by groundwater where there is limited data.
DOI: 10.6084/m9.figshare.7052102.v1
title: 05 — Corridor — High Density Setting

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052096
title: 04 — Bottleneck — Frictional Effects

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052099
title: 01 — Frontal Collision — C Decision Potential

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052099.v1
title: 01 — Frontal Collision — C Decision Potential

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052093
title: 03 — Large Crowd — Slow Walker

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052096.v1
title: 04 — Bottleneck — Frictional Effects

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052090
title: 02 — Large Crowd — Repulsion Effects

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052093.v1
title: 03 — Large Crowd — Slow Walker

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.6084/m9.figshare.7052090.v1
title: 02 — Large Crowd — Repulsion Effects

description: Simulations for the article https://arxiv.org/abs/1808.07426
DOI: 10.25373/ctsnet.7051925
title: Pulmonary Artery Pseudoaneurysm

description: A 68-year-old woman presented to the thoracic surgery clinic for evaluation of a large left lower lobe mass. Six months prior, she had undergone attempted right-heart-catheterization at an outside hospital, which was aborted due to an acute pulmonary hemorrhage. Physical examination revealed decreased breath sounds at the left lung base. Computed tomography revealed an enhancing 8.9 cm mass (Figure 1A, arrow) arising from the left lower lobe segmental pulmonary artery (Figure 1B, arrowhead), compatible with a pseudoaneurysm. Iatrogenic damage to the pulmonary artery and its branches is a known complication of percutaneous interventional procedures, such as Swan-Ganz catheterization (1). Small pseudoaneurysms can frequently be managed with a transcatheter approach utilizing coil-embolization or thrombin injection. However, larger lesions may require surgical intervention (2). The patient underwent left thoracotomy and left lower lobectomy. She was seen in the clinic following hospital discharge and was recovering well without complications (Figure 2). <b>References </b> 1. Shah MR, Hasselblad V, Stevenson LW, et al. Impact of the pulmonary artery catheter in critically ill patients: meta-analysis of randomized clinical trials. <i>JAMA. 2005;294(13):1664-1670</i>.<br> 2. Lafita V, Borge MA, Demos TC. Pulmonary artery pseudoaneurysm: etiology, presentation, diagnosis, and treatment. <i>Semin Intervent Radiol. 2007;24(1):119-123</i>.
DOI: 10.25373/ctsnet.7051925.v1
title: Pulmonary Artery Pseudoaneurysm

description: A 68-year-old woman presented to the thoracic surgery clinic for evaluation of a large left lower lobe mass. Six months prior, she had undergone attempted right-heart-catheterization at an outside hospital, which was aborted due to an acute pulmonary hemorrhage. Physical examination revealed decreased breath sounds at the left lung base. Computed tomography revealed an enhancing 8.9 cm mass (Figure 1A, arrow) arising from the left lower lobe segmental pulmonary artery (Figure 1B, arrowhead), compatible with a pseudoaneurysm. Iatrogenic damage to the pulmonary artery and its branches is a known complication of percutaneous interventional procedures, such as Swan-Ganz catheterization (1). Small pseudoaneurysms can frequently be managed with a transcatheter approach utilizing coil-embolization or thrombin injection. However, larger lesions may require surgical intervention (2). The patient underwent left thoracotomy and left lower lobectomy. She was seen in the clinic following hospital discharge and was recovering well without complications (Figure 2). <b>References </b> 1. Shah MR, Hasselblad V, Stevenson LW, et al. Impact of the pulmonary artery catheter in critically ill patients: meta-analysis of randomized clinical trials. <i>JAMA. 2005;294(13):1664-1670</i>.<br> 2. Lafita V, Borge MA, Demos TC. Pulmonary artery pseudoaneurysm: etiology, presentation, diagnosis, and treatment. <i>Semin Intervent Radiol. 2007;24(1):119-123</i>.
DOI: 10.23641/asha.7051616
title: Clinical progression of PPAOS (Utianski et al., 2018)

description: <b>Purpose: </b>This case series details the clinical progression of patients with primary progressive apraxia of speech (PPAOS) to illustrate, using several methods and supplemental material examples, the changes that occur in speech and language functioning in this patient population.<b>Method: </b>Four patients who presented with PPAOS were followed between 5 and 6 years. Two patients had predominant articulatory abnormalities (termed <i>phonetic PPAOS</i>), 1 had predominant prosodic abnormalities (prosodic PPAOS), and 1 had relatively equal articulatory and prosodic abnormalities (mixed PPAOS). Detailed speech (including acoustics), language, neurologic, and neuropsychological data were collected.<b>Results: </b>At initial exam, the patients ranged from 60 to 77 years old, with presenting disease duration of 1.5–10 years. Although all patients presented with an isolated apraxia of speech, all developed varying degrees of aphasia and dysarthria. Patients with phonetic PPAOS developed relatively more severe aphasia than the other 2 patients. All patients eventually had severe functional communication limitations and required alternative or augmentative means of communication, although at varying times postonset of their initial speech problem. Two patients developed dysphagia, 3 showed mild–moderate Parkinsonism, and 2 developed depression. For all patients, simple temporal acoustic measurements documented slowed speech rate over time.<b>Conclusions: </b>This case series demonstrates that patients who initially present with PPAOS may develop aphasia and dysarthria, cognitive and behavioral changes, and other neurologic signs. Whether these changes can be predicted by the perceptual characteristics of the apraxia of speech is yet to be determined. The detailed longitudinal profiles provide valuable clinical insight into the progression of disease in people with PPAOS.<br><b>Supplemental Materials S1–S4. </b>Brief videos of each patient repeating words of increasing length and complexity at each visit. <br><b>Supplemental Material S5. </b>Video commentary on Supplemental Materials S1–S4, including the articulatory and prosodic features of each patient during each visit.<b><br></b><b>Supplemental Material S6. </b>Participant scores from the Western Aphasia Battery subtests and Part II subtest.<br>Utianski, R. L., Duffy, J. R., Clark, H. M., Strand, E. A., Boland, S. M., Machulda, M. M., Whitwell, J. L., & Josephs, K. A. (2018). Clinical progression in four cases of primary progressive apraxia of speech. <i>American Journal of Speech-Language Pathology, 27, </i>1303–1318. https://doi.org/10.1044/2018_AJSLP-17-0227<br><br>
DOI: 10.23641/asha.7051616.v1
title: Clinical progression of PPAOS (Utianski et al., 2018)

description: <b>Purpose: </b>This case series details the clinical progression of patients with primary progressive apraxia of speech (PPAOS) to illustrate, using several methods and supplemental material examples, the changes that occur in speech and language functioning in this patient population.<b>Method: </b>Four patients who presented with PPAOS were followed between 5 and 6 years. Two patients had predominant articulatory abnormalities (termed <i>phonetic PPAOS</i>), 1 had predominant prosodic abnormalities (prosodic PPAOS), and 1 had relatively equal articulatory and prosodic abnormalities (mixed PPAOS). Detailed speech (including acoustics), language, neurologic, and neuropsychological data were collected.<b>Results: </b>At initial exam, the patients ranged from 60 to 77 years old, with presenting disease duration of 1.5–10 years. Although all patients presented with an isolated apraxia of speech, all developed varying degrees of aphasia and dysarthria. Patients with phonetic PPAOS developed relatively more severe aphasia than the other 2 patients. All patients eventually had severe functional communication limitations and required alternative or augmentative means of communication, although at varying times postonset of their initial speech problem. Two patients developed dysphagia, 3 showed mild–moderate Parkinsonism, and 2 developed depression. For all patients, simple temporal acoustic measurements documented slowed speech rate over time.<b>Conclusions: </b>This case series demonstrates that patients who initially present with PPAOS may develop aphasia and dysarthria, cognitive and behavioral changes, and other neurologic signs. Whether these changes can be predicted by the perceptual characteristics of the apraxia of speech is yet to be determined. The detailed longitudinal profiles provide valuable clinical insight into the progression of disease in people with PPAOS.<br><b>Supplemental Materials S1–S4. </b>Brief videos of each patient repeating words of increasing length and complexity at each visit. <br><b>Supplemental Material S5. </b>Video commentary on Supplemental Materials S1–S4, including the articulatory and prosodic features of each patient during each visit.<b><br></b><b>Supplemental Material S6. </b>Participant scores from the Western Aphasia Battery subtests and Part II subtest.<br>Utianski, R. L., Duffy, J. R., Clark, H. M., Strand, E. A., Boland, S. M., Machulda, M. M., Whitwell, J. L., & Josephs, K. A. (2018). Clinical progression in four cases of primary progressive apraxia of speech. <i>American Journal of Speech-Language Pathology, 27, </i>1303–1318. https://doi.org/10.1044/2018_AJSLP-17-0227<br><br>