cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/60a7784acef3038d3c8a16776a5b5746
title: Experimental microcosm incubations assessing the effect of hypoxia on aqueous iron and organic carbon, pH, sediment organic carbon, and sediment iron-bound organic carbon

description: To assess the effect of changing oxygen concentrations on coupled carbon and iron cycling in freshwater ecosystems, we performed 6-week microcosm incubations. Incubations were inoculated with sediment and water from Falling Creek Reservoir, Vinton, VA, USA. We started the experiment with 102 microcosms split evenly into oxic and hypoxic treatments. After two weeks, we switched the treatment of approximately half of the remaining microcosms, generating a total of four oxygen regimes: hypoxic, oxic, hypoxic to oxic, and oxic to hypoxic. We sampled the microcosms destructively approximately twice per week, collecting aqueous samples for total and dissolved carbon and iron, as well as sediment samples for organic carbon and iron-bound organic carbon analysis. Iron-bound organic carbon was determined using citrate-bicarbonate-dithionite extractions.
DOI: 10.6084/m9.figshare.21947897
title: Supplementary Material for: Xpert MTB/RIF in the Diagnosis of Mediastinal Tuberculous Lymphadenitis by Endoscopic Ultrasound-Guided Needle Aspiration Techniques: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Lymphadenopathy is one of the most prevalent clinical manifestations of extrapulmonary tuberculosis. Endosonography is the recommended technique in the diagnostic work-up of mediastinal lymphadenopathies. Xpert MTB/RIF assay is a self-contained cartridge-based fully automated DNA testing platform which can accurately detect both tuberculosis and mycobacterial resistance to rifampicin. A few studies assessed its accuracy for mediastinal lymph node aspirates collected using endosonography. A systematic review of observational studies was performed to provide a pooled estimate of sensitivity and specificity of Xpert MTB/RIF in the diagnosis of mediastinal tuberculous lymphadenitis using endoscopic ultrasound-guided needle aspiration techniques. <b><i>Methods:</i></b> A search of the scientific evidence was carried out using PubMed, Embase, and Scopus. Articles describing observational studies on Xpert MTB/RIF in the diagnosis of mediastinal tuberculous lymphadenitis using endoscopic ultrasound-guided needle aspiration techniques were selected. <b><i>Results:</i></b> Eight studies met the inclusion criteria. The overall pooled sensitivity was 61% (95% CI = 55–68%; <i>I</i><sup>2</sup> = 66.3%; <i>p</i> = 0.004), overall pooled specificity was 89% (95% CI = 85–91%; <i>I</i><sup>2</sup> = 90.1%; <i>p</i> &lt; 0.0001). Area under the sROC curve was 0.68. Only one study reported data on rifampin resistance detection and showed a sensitivity of 83.3% and a specificity of 16%. <b><i>Conclusions:</i></b> Xpert MTB/RIF shows a good accuracy in the diagnosis of mediastinal mycobacterial lymphadenitis by endosonographic needle aspiration techniques. It should be always recommended for suspected mediastinal tuberculosis.
DOI: 10.3886/icpsr01200
title: Using the Gravity Model to Estimate the Costs of Protection
title: Archival Version

description: Economists' estimates of the actual burden that trade protectionism imposes on the economy have been surprisingly small. In this article, the author presents a method that captures some of the effects and distortions of trade protection that have not been captured by existing methods. He finds that during 1996, worldwide protectionism reduced United States exports by 26.2 percent. Likewise, United States protectionism decreased United States imports from non-NAFTA countries by 15.4 percent. He calculates further that the welfare cost of United States protectionism amounted to about 1.45 percent of United States national income, which is much higher than previous estimates.
description: Datasets: 
 
 DS1: Dataset
description: (1) The file submitted is 9901hw.xls, which contains the data for the regressions in the article. (2) These data are part of ICPSR's Publication-Related Archive and are distributed exactly as they arrived from the data depositor. ICPSR has not checked or processed this material. Users should consult the investigator(s) if further information is desired.
DOI: 10.6073/pasta/a1d49c266b57465daa863cde4b1d4b4e
title: Total organic carbon, total nitrogen, and iron-bound organic carbon in surficial sediment and settling particulate material from Falling Creek and Beaverdam Reservoirs in 2019 and 2021

description: This dataset includes measurements of sediment properties (total organic carbon, total nitrogen, and iron-bound organic carbon) in surficial sediment and sedimenting material from two reservoirs: Falling Creek and Beaverdam Reservoirs, both located in Vinton, VA, USA. To measure surficial sediment properties, sediment cores were collected at the deepest site in each reservoir using a gravity corer, and the top 1 cm was frozen then lyophilized. Sediment cores were collected approximately once per month in both reservoirs throughout the stratified period (May–November) in 2019 and 2021, though sampling frequency and duration varied by reservoir and year. Sedimenting material was sampled using sediment traps suspended approximately 1 m above the sediment in both reservoirs. Iron-bound organic carbon was measured using the citrate-bicarbonate-dithionite method, and we used a CN analyzer (Elementar VarioMax, Ronkonkoma, NY, USA) to determine the amount of OC per unit mass of sediment.
DOI: 10.6084/m9.figshare.21760439
title: Microbial Dynamics

description: The data on <strong>microbial dynamics of three types of metata ayib</strong> (counted colonies along the fermentation period within 4 days interval for each); <strong>Sensory evaluation of traditional metata ayib varieties; </strong> <strong>Growth potential of pathogens in metata ayib (prefered through the sensory eavluation) within 24hrs </strong>are saved within SPSS version 16.0 <br>
DOI: 10.5255/ukda-sn-852575
title: Oral histories of homes and daily lives in Stocksbridge and Stevenage
DOI: 10.5258/soton/d2459
title: Data supporting the publication "Controlled generation of picosecond-pulsed higher-order Poincare sphere beams from an ytterbium-doped multicore fiber amplifier".

description: This dataset supports the publication: Controlled generation of picosecond-pulsed higher-order Poincare sphere beams from an ytterbium-doped multicore fiber amplifier, by K Ji, D Lin, I Davidson, S Wang, J Carpenter, Y Amma, Y Jung, M Guasoni and D J. Richardson in Photonics Research. This dataset contains all originally measured and calculated data for plotting figures within the journal paper.
DOI: 10.5281/zenodo.7013227
title: Parametric Study of FRP-confined RC columns

description: Results of numerical parametric study on the transverse steel confinement effects on the structural behavior of FRP-confined RC columns
description: {"references": ["Zignago, D., and Barbato, M. 2021. \"Effects of transverse steel on the axial-compression strength of FRP-confined reinforced concrete columns based on a numerical parametric study.\" J. Compos. Constr., 25(4), 04021024."]}
DOI: 10.18112/openneuro.ds004441.v1.0.1
title: Rat_diffusion_STZ
DOI: 10.6084/m9.figshare.21733048.v1
title: High levels of HDAC expression correlate with microglial aging

description: Cellular damage gradually accumulates with aging, promoting a time-dependent functional decline of the brain. Microglia play an essential regulatory role in maintaining cognitive activity by phagocytosing cell debris and apoptotic cells during neurogenesis. The activities of different histone deacetylases (HDACs) regulate microglial function during development and neurodegeneration. However, no studies have described the role of HDACs in microglia during physiological aging. HDAC and microglial marker levels were examined in microglial cells after inducing senescence <i>in vitro</i> and in mouse and human hippocampal biopsies <i>in vivo</i>, using quantitative real-time PCR. Publicly available datasets were used to determine HDAC expression in different brain areas during physiological aging. HDAC expression increased upon the induction of senescence with bleomycin or serial passage in microglial cultures. High levels of HDACs were detected in mice and aged human brain samples. Human hippocampal samples showed a positive correlation between the expression of <i>HDAC1, 3</i>, and <i>7</i> and microglial and senescence markers. <i>HDAC1</i> and <i>3</i> levels are enriched in the purified aged microglial population. Several HDACs, particularly HDAC1, are elevated in microglia upon senescence induction <i>in vitro</i> and with aging <i>in</i> <i>vivo</i>, and correlate with microglial and senescence biomarkers.
DOI: 10.6084/m9.figshare.21733048
title: High levels of HDAC expression correlate with microglial aging

description: Cellular damage gradually accumulates with aging, promoting a time-dependent functional decline of the brain. Microglia play an essential regulatory role in maintaining cognitive activity by phagocytosing cell debris and apoptotic cells during neurogenesis. The activities of different histone deacetylases (HDACs) regulate microglial function during development and neurodegeneration. However, no studies have described the role of HDACs in microglia during physiological aging. HDAC and microglial marker levels were examined in microglial cells after inducing senescence <i>in vitro</i> and in mouse and human hippocampal biopsies <i>in vivo</i>, using quantitative real-time PCR. Publicly available datasets were used to determine HDAC expression in different brain areas during physiological aging. HDAC expression increased upon the induction of senescence with bleomycin or serial passage in microglial cultures. High levels of HDACs were detected in mice and aged human brain samples. Human hippocampal samples showed a positive correlation between the expression of <i>HDAC1, 3</i>, and <i>7</i> and microglial and senescence markers. <i>HDAC1</i> and <i>3</i> levels are enriched in the purified aged microglial population. Several HDACs, particularly HDAC1, are elevated in microglia upon senescence induction <i>in vitro</i> and with aging <i>in</i> <i>vivo</i>, and correlate with microglial and senescence biomarkers.
DOI: 10.17632/7zbznd9x7x.2
title: Stable Isotopes signals from 78 marine species during the winter and summer from the Cananéia, São Paulo, Brazil.

description: This data show the stable isotope analysis (IS) for δ13C and δ15N  from 78 species sampled with a commercial trawl fisheries, during the winter 2018 and summer 2019, in the sea of Cananéia, São Paulo, Brazil. This data was used for construct a image of the complex trophic web that they are involved.
DOI: 10.5281/zenodo.7567762
title: Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques

description: Mazzaccaro D, Dolci M, Perego F, Delbue S, Giannetta M, Cardani R, Valentina Renna L, Costa E, Corsi-Romanelli MM, Galli C, Pariani E, Nano G, Clemente C, Basilico N. Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques. Ann Vasc Surg. 2022 May;82:325-333. doi: 10.1016/j.avsg.2021.10.070. Epub 2021 Dec 11. PMID: 34902464. Abstract <strong>Background: </strong>To investigate the presence of genetic material of viral agents and the serum level of inflammatory cytokines in patients submitted to carotid endarterectomy having vulnerable versus stable atherosclerotic plaques. <strong>Methods: </strong>Data of patients consecutively submitted to carotid endarterectomy for a significant stenosis from July 2019 to December 2019 were prospectively collected. The genetic material of Epstein-Barr (EBV), CitoMegalo (CMV), Herpes Simplex (HSV), Varicella-Zoster (VZV) and Influenza (IV) Viruses was searched in the patient's plaques, both in the "mid" of the plaque and in an adjacent lateral portion of no-plaque area. The serum levels of TNF-α, IL-1β, IL-6, IL10 and CCL5 were determined. The obtained results were then correlated to the histologic vulnerability of the removed carotid plaque. P values &lt; 0.05 were considered statistically significant. <strong>Results: </strong>Data of 50 patients were analyzed. A vulnerable plaque was found in 31 patients (62%). The genome of CMV, HSV, VZV and IV was not found in any of the vascular samples, while the EBV genome was found in the "mid" of 2 vulnerable plaques, but not in their respective control area. Eighty-two percent of patients who did not receive anti-IV vaccination (23/28) had vulnerable carotid plaque, compared with 36% of vaccinated patients (8/22, P = 0.001). Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque (73.6 ± 238.2 vs. 3.9 ± 13.1 pg/ml, P= 0.01, and 45.9 ± 103.6 vs. 10.1 ± 25.3 pg/ml, P= 0.01, respectively), independent of comorbidities, viral exposure or flu vaccination. <strong>Conclusions: </strong>The EBV genome was found in the "core" of 2 vulnerable carotid plaques, but not in their respective adjacent control. Influenza vaccination was associated with a lower incidence of carotid plaque vulnerability. Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque.
DOI: 10.5281/zenodo.7567761
title: Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques

description: Mazzaccaro D, Dolci M, Perego F, Delbue S, Giannetta M, Cardani R, Valentina Renna L, Costa E, Corsi-Romanelli MM, Galli C, Pariani E, Nano G, Clemente C, Basilico N. Viral Agents and Systemic Levels of Inflammatory Cytokines in Vulnerable and Stable Atherosclerotic Carotid Plaques. Ann Vasc Surg. 2022 May;82:325-333. doi: 10.1016/j.avsg.2021.10.070. Epub 2021 Dec 11. PMID: 34902464. Abstract <strong>Background: </strong>To investigate the presence of genetic material of viral agents and the serum level of inflammatory cytokines in patients submitted to carotid endarterectomy having vulnerable versus stable atherosclerotic plaques. <strong>Methods: </strong>Data of patients consecutively submitted to carotid endarterectomy for a significant stenosis from July 2019 to December 2019 were prospectively collected. The genetic material of Epstein-Barr (EBV), CitoMegalo (CMV), Herpes Simplex (HSV), Varicella-Zoster (VZV) and Influenza (IV) Viruses was searched in the patient's plaques, both in the "mid" of the plaque and in an adjacent lateral portion of no-plaque area. The serum levels of TNF-α, IL-1β, IL-6, IL10 and CCL5 were determined. The obtained results were then correlated to the histologic vulnerability of the removed carotid plaque. P values &lt; 0.05 were considered statistically significant. <strong>Results: </strong>Data of 50 patients were analyzed. A vulnerable plaque was found in 31 patients (62%). The genome of CMV, HSV, VZV and IV was not found in any of the vascular samples, while the EBV genome was found in the "mid" of 2 vulnerable plaques, but not in their respective control area. Eighty-two percent of patients who did not receive anti-IV vaccination (23/28) had vulnerable carotid plaque, compared with 36% of vaccinated patients (8/22, P = 0.001). Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque (73.6 ± 238.2 vs. 3.9 ± 13.1 pg/ml, P= 0.01, and 45.9 ± 103.6 vs. 10.1 ± 25.3 pg/ml, P= 0.01, respectively), independent of comorbidities, viral exposure or flu vaccination. <strong>Conclusions: </strong>The EBV genome was found in the "core" of 2 vulnerable carotid plaques, but not in their respective adjacent control. Influenza vaccination was associated with a lower incidence of carotid plaque vulnerability. Serum levels of TNF-α and IL-6 were higher in patients with a vulnerable plaque compared to patients with a stable plaque.
DOI: 10.6084/m9.figshare.21175042
title: Supplementary Material for: The mitochondrial genome of Isognomon nucleus and mitophylogenomics (Bivalvia: Autobranchia)

description: <strong>Appendix S1: </strong>Expanded Materials and Methods <strong>Appendix S2: </strong>Sequencing depth analysis <strong>Appendix S3: </strong>Lack of a convincing <em>ATP8</em> gene <strong>Appendix S4: </strong>Potential long novel transmembrane domain containing ORFs in <em>I. nucleus </em>and <em>P. fucata martensii</em> <strong>Fig. S1. </strong>Length versus base quality plot of ONT reads (within Appendix S1) <strong>Fig. S2. </strong>Evidence for a small gap in the <em>I. nucleus </em>mitogenome from ONT-only assembly (within Appendix S1) <strong>Fig. S3. </strong>Distribution of observed and theoretical protein sizes from ORFs found in the unannotated portion of the <em>I. nucleus </em>mitogenome (within Appendix S4) <strong>Table S1:</strong> Structural features of the standard mitochondrial genes in the <em>Isognomon nucleus </em>mitogenome <strong>Table S2:</strong> Summary statistics for ONT reads via NanoStat (within Appendix S1) <strong>Table S3:</strong> List of species, accession numbers and mitogenome sizes used in this study (within Appendix S1) <br> <strong>Data S1. </strong>Sequences of the 4 long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were included in the official annotation of the mitogenome) <strong>Data S2.</strong> Transmembrane domain identification for the <em>I. nucleus </em>predicted proteins by DeepTMHMM (gff output format) <strong>Data S3.</strong> Sequences of the 5 long <em>Pinctada fucata martensii</em> proteins with multiple predicted transmembrane domains <strong>Data S4.</strong> Transmembrane domain identification for the <em>P. fucata martensii</em> predicted proteins by DeepTMHMM (gff output format) <strong>Sup. Data 5.</strong> <em>(Not in this file; available at Figshare)</em> Contains the curated, GBLOCKS-alignment, all files from the IQTREE run and pdf exports of the estimated ML tree from FigTree. [https://figshare.com/projects/Isognomon_mitogenomes_Supplementary_Data_Files_tables/129485] <strong>Sup. Data 6.</strong> Sequences of the 3 additional long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were not included in the official mitogenome annotation)
DOI: 10.6084/m9.figshare.21175042.v2
title: Supplementary Material for: The mitochondrial genome of Isognomon nucleus and mitophylogenomics (Bivalvia: Autobranchia)

description: <strong>Appendix S1: </strong>Expanded Materials and Methods <strong>Appendix S2: </strong>Sequencing depth analysis <strong>Appendix S3: </strong>Lack of a convincing <em>ATP8</em> gene <strong>Appendix S4: </strong>Potential long novel transmembrane domain containing ORFs in <em>I. nucleus </em>and <em>P. fucata martensii</em> <strong>Fig. S1. </strong>Length versus base quality plot of ONT reads (within Appendix S1) <strong>Fig. S2. </strong>Evidence for a small gap in the <em>I. nucleus </em>mitogenome from ONT-only assembly (within Appendix S1) <strong>Fig. S3. </strong>Distribution of observed and theoretical protein sizes from ORFs found in the unannotated portion of the <em>I. nucleus </em>mitogenome (within Appendix S4) <strong>Table S1:</strong> Structural features of the standard mitochondrial genes in the <em>Isognomon nucleus </em>mitogenome <strong>Table S2:</strong> Summary statistics for ONT reads via NanoStat (within Appendix S1) <strong>Table S3:</strong> List of species, accession numbers and mitogenome sizes used in this study (within Appendix S1) <br> <strong>Data S1. </strong>Sequences of the 4 long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were included in the official annotation of the mitogenome) <strong>Data S2.</strong> Transmembrane domain identification for the <em>I. nucleus </em>predicted proteins by DeepTMHMM (gff output format) <strong>Data S3.</strong> Sequences of the 5 long <em>Pinctada fucata martensii</em> proteins with multiple predicted transmembrane domains <strong>Data S4.</strong> Transmembrane domain identification for the <em>P. fucata martensii</em> predicted proteins by DeepTMHMM (gff output format) <strong>Sup. Data 5.</strong> <em>(Not in this file; available at Figshare)</em> Contains the curated, GBLOCKS-alignment, all files from the IQTREE run and pdf exports of the estimated ML tree from FigTree. [https://figshare.com/projects/Isognomon_mitogenomes_Supplementary_Data_Files_tables/129485] <strong>Sup. Data 6.</strong> Sequences of the 3 additional long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were not included in the official mitogenome annotation)
DOI: 10.6084/m9.figshare.21799793.v2
title: Precision Oncology-Based Targeting of Signaling Pathways Toward a Holistic Approach to Cancer Therapeutics

description: The mutational changes occurring in the regulatory genes responsible for the maintenance of optimal cell growth and proliferation gradually lead to cancer progression and metastasis. The specific roles played by some of the molecules associated with cell signaling and others in the cell microenvironment that often induce oncogenesis have been understood in detail in the past decades based on findings of the human genome project and other related initiatives undertaken afterward to thoroughly understand the molecular basis of cancer cell behaviors. It is to rely upon the genomic study of cancer cells to get a clear idea of the prognosis and pathways involved in disease progression and to look for the means to selectively target them for a cure. Furthermore, patients with the same cancer types often respond differently to different cancer therapies, indicating the need for a patient-specific treatment regimen for the disease. To this end, precision oncology is the new field of cancer research that relies on molecular profiling of individual's tumor to identify targetable alterations for custom-tailored personalized treatment of the disease. Furthermore, the emerging field of single cell technology has now enabled scientists study genomics, proteomics and related interactions at the level of a single cell in a bulk population of cells which can be successfully exploited to decipher tissue heterogeneity associated with cancer development. This article intends to briefly explain the foundations and frontiers of precision oncology in the context of recent advances in cancer genomics and single-cell technologies for assessing its scope and importance in the realization of a proper cure for cancer.