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15,733 results for “article”
Raw data for the article "N-terminal selective C-H azidation of proline-containing peptides: a platform for late-stage diversification"
<p>Raw NMR, IR and MS data for the article "N-terminal selective C-H azidation of proline-containing peptides: a platform for late-stage diversification" published in Chemistry- A European Journal, DOI: </p> <p><a href="http://dx.doi.org/10.1002/chem.202200368">http://dx.doi.org/10.1002/chem.202200368</a>.</p> <p>The number of the folders correspond to compounds numbers in the article. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Data for the journal article "Brown Carbon from Biomass Burning Imposes Strong Circum-Arctic Warming"
<p>The data for the 3 figures in the journal article "Brown Carbon from Biomass Burning Imposes Strong Circum-Arctic Warming"</p>
raw data for the article "Synthesis of Polycyclic Aminal Heterocycles via Decarboxylative Cyclisation of Dipeptide Derivatives"
<p>Raw NMR, IR and MS data for the article "Synthesis of Polycyclic Aminal Heterocycles via Decarboxylative Cyclisation of Dipeptide Derivatives" published in Chemical Communications, DOI: </p> <p><a href="https://doi.org/10.1039/D2CC00167E">https://doi.org/10.1039/D2CC00167E</a></p> <p>The number of the folders correspond to compounds numbers in the article. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Data for the article "Solution of the Thirring model in thimble regularization"
<p>Data set for the paper "Solution of the Thirring model in thimble regularization", arXiv:2109.02511 [hep-lat]. It includes the data required to generate the figures in the article.</p> <p> </p>
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</p>
Raw Data for the article: A Radioactive-Free Method for the Thorough Analysis of the Kinetics of Cell Cytotoxicity
<p>The cytotoxic activity of T cells and Natural Killer cells is usually measured with the chromium release assay (CRA), which involves the use of 51Chromium (<sup>51</sup>Cr), a radioactive substance dangerous to the operator and expensive to handle and dismiss. The accuracy of the measurements depends on how well the target cells incorporate <sup>51</sup>Cr during labelling which, in turn, depends on cellular division. Due to bystander metabolism, the target cells spontaneously release <sup>51</sup>Cr, producing a high background noise. Alternative radioactive-free methods have been developed. Here, we compare a bioluminescence (BLI)-based and a carboxyfluorescein succinimidyl ester (CFSE)-based cytotoxicity assay to the standard radioactive CRA. In the first assay, the target cells stably express the enzyme luciferase, and vitality is measured by photon emission upon the addition of the substrate d-luciferin. In the second one, the target cells are labelled with CFSE, and the signal is detected by Flow Cytometry. We used these two protocols to measure cytotoxicity induced by treatment with NK cells. The cytotoxicity of NK cells was determined by adding increasing doses of human NK cells. The results obtained with the BLI method were consistent with those obtained with the CRA- or CFSE-based assays 4 hours after adding the NK cells. Most importantly, with the BLI assay, the kinetic of NK cells' killing was thoroughly traced with multiple time point measurements, in contrast with the single time point measurement the other two methods allow, which unveiled additional information on NK cell killing pathways.</p>
Raw Data for the article: Post-crisis debriefing: A tool for improving quality in the medical emergency team system
<p><strong>Objectives: </strong>To examine clinicians' perception of quality of technical and non-technical response to emergencies and application of post crisis debriefing.</p> <p><strong>Design: </strong>Descriptive, anonymous, self-reporting survey on the needs and perception of a post-crisis debriefing implementation.</p> <p><strong>Setting: </strong>Multi-specialist medical institute in Italy focused on solid organ transplantation and organ failure support.</p> <p><strong>Main outcomes: </strong>Perception of application of guidelines and evaluation of debriefing implementation during in-hospital emergencies.</p> <p><strong>Results: </strong>Response rate to the survey was 25% (148 health care workers). Of all respondents, 86% were employed >10 years, 75% were involved in ≤5 emergencies over the previous year. Resuscitation guidelines were considered fully applied by 55%; 64% of respondents considered the teaching programme as sufficient. Of all participants, 97% were aware of the importance of teamwork dynamics, 79% were aware of the importance of the personal performance, and 52% considered emergencies as valid opportunities for professional growth. Leadership was considered important by 45% of respondents; debriefing implemented by 41%, and considered a potentially useful tool by 85%.</p> <p><strong>Conclusion: </strong>Post-crisis debriefing is a way to diffuse self-reflective and life-long learning culture; it is perceived as a powerful tool for improving quality of the rapid response system by the vast majority of those surveyed.</p> <p><strong>Keywords: </strong>Communication; Crisis resource management; Emergency; ICU; Intensive care medicine; Leadership; Patient safety; Teamwork.</p>
Raw Data for the article: miRNA expression analysis in the human heart: Undifferentiated progenitors vs. bioptic tissues-Implications for proliferation and ageing
<p>In developed countries, cardiovascular diseases are currently the first cause of death. Cardiospheres (CSs) and cardiosphere-derived cells (CDCs) have been found to have the ability to regenerate the myocardium after myocardial infarction (MI). In recent years, much effort has been made to gain insight into the human heart repair mechanisms, in which miRNAs have been shown to play an important role. In this regard, to elucidate the involvement of miRNAs, we evaluated the miRNA expression profile across human heart biopsy, CSs and CDCs using microarray and next-generation sequencing (NGS) technologies. We identified several miRNAs more represented in the progenitors, where some of them can be responsible for the proliferation or the maintenance of an undifferentiated state, while others have been found to be downregulated in the undifferentiated progenitors compared with the biopsies. Moreover, we also found a correlation between downregulated miRNAs in CSs/CDCs and patient age (eg miR-490) and an inverse correlation among miRNAs upregulated in CSs/CDCs (eg miR-31).</p>
Raw Data for the article: HCV Interplay With Mir34a: Implications in Hepatocellular Carcinoma
<p>Since its identification, HCV has been considered one of the main causes of hepatitis and liver cancer. Currently, the molecular mechanisms of HCC development induced by HCV infection have not been sufficiently clarified. The recent discovery of novel treatments that inhibit HCV replication gave rise to new questions concerning HCC mechanisms. In particular, the HCV eradication mediated by new direct-acting antiviral (DAAs) drugs does not exclude the possibility of <em>de novo</em> HCC development; this finding opened more questions on the interplay between liver cells and the virus. Different groups have investigated the pathways leading to cancer recurrence in patients treated with DAAs. For this reason, we tried to gain molecular insights into the changes induced by HCV infection in the target liver cells. In particular, we observed an increase in microRNA34a (miR34a) expression following HCV infection of HCC cell line Huh7.5. In addition, Huh7.5 treated with extracellular vesicles (EVs) from the previously HCV-infected Huh7.5 underwent apoptosis. Since miR34 expression was increased in Huh7.5 EVs, we hypothesized a paracrine mechanism of viral infection mediated by miR34a cargo of EVs. The balance between viral infection and cell transformation may raise some questions on the possible use of antiviral drugs in association with antineoplastic treatment.</p>
Raw data for the article: Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome
<p>Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.</p>
Raw Data for the article: Atrial Septostomy for Left Ventricular Unloading During Extracorporeal Membrane Oxygenation for Cardiogenic Shock: Animal Model
<p><strong>Objectives: </strong>The aim of this study was to quantify and understand the unloading effect of percutaneous balloon atrial septostomy (BAS) in acute cardiogenic shock (CS) treated with venoarterial (VA) extracorporeal membranous oxygenation (ECMO).</p> <p><strong>Background: </strong>In CS treated with VA ECMO, increased left ventricular (LV) afterload is observed that commonly interferes with myocardial recovery or even promotes further LV deterioration. Several techniques for LV unloading exist, but the optimal strategy and the actual extent of such procedures have not been fully disclosed.</p> <p><strong>Methods: </strong>In a porcine model (n = 11; weight 56 kg [53-58 kg]), CS was induced by coronary artery balloon occlusion (57 minutes [53-64 minutes]). Then, a step-up VA ECMO protocol (40-80 mL/kg/min) was run before and after percutaneous BAS was performed. LV pressure-volume loops and multiple hemoglobin saturation data were evaluated. The Wilcoxon rank sum test was used to assess individual variable differences.</p> <p><strong>Results: </strong>Immediately after BAS while on VA ECMO support, LV work decreased significantly: pressure-volume area, end-diastolic pressure, and stroke volume to ∼78% and end-systolic pressure to ∼86%, while superior vena cava and tissue oximetry did not change. During elevating VA ECMO support (40-80 mL/kg/min) with BAS vs without BAS, we observed 1) significantly less mechanical work increase (122% vs 172%); 2) no end-diastolic volume increase (100% vs 111%); and 3) a considerable increase in end-systolic pressure (134% vs 144%).</p> <p><strong>Conclusions: </strong>In acute CS supported by VA ECMO, atrial septostomy is an effective LV unloading tool. LV pressure is a key component of LV work load, so whenever LV work reduction is a priority, arterial pressure should carefully be titrated low while maintaining organ perfusion.</p>
Raw Data for the article: Patient-Specific Analysis of Ascending Thoracic Aortic Aneurysm with the Living Heart Human Model
<p>In ascending thoracic aortic aneurysms (ATAAs), aneurysm kinematics are driven by ventricular traction occurring every heartbeat, increasing the stress level of dilated aortic wall. Aortic elongation due to heart motion and aortic length are emerging as potential indicators of adverse events in ATAAs; however, simulation of ATAA that takes into account the cardiac mechanics is technically challenging. The objective of this study was to adapt the realistic Living Heart Human Model (LHHM) to the anatomy and physiology of a patient with ATAA to assess the role of cardiac motion on aortic wall stress distribution. Patient-specific segmentation and material parameter estimation were done using preoperative computed tomography angiography (CTA) and ex vivo biaxial testing of the harvested tissue collected during surgery. The lumped-parameter model of systemic circulation implemented in the LHHM was refined using clinical and echocardiographic data. The results showed that the longitudinal stress was highest in the major curvature of the aneurysm, with specific aortic quadrants having stress levels change from tensile to compressive in a transmural direction. This study revealed the key role of heart motion that stretches the aortic root and increases ATAA wall tension. The ATAA LHHM is a realistic cardiovascular platform where patient-specific information can be easily integrated to assess the aneurysm biomechanics and potentially support the clinical management of patients with ATAAs.</p>
Data set for the article 'Temporal scaling in C. elegans larval development'
<p>This directory contains all analyzed data and data analysis scripts to create all figures for the article<br> Filina et al., Temporal scaling in C. elegans larval development, PNAS 2022 119:e2123110119</p>
Raw Data for the article: Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo
<p>Currently, <em>Klebsiella pneumoniae</em> is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During <em>K. pneumoniae</em> infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant <em>K. pneumoniae</em> strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from <em>K. pneumoniae</em> strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant <em>K. pneumoniae</em> expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium.</p>
Raw Data for the article: Impaired anti-SARS-CoV-2 humoral and cellular immune response induced by Pfizer-BioNTech BNT162b2 mRNA vaccine in solid organ transplanted patients
<p>SARS‐CoV‐2 vaccine is considered the primary health strategy able to end the current COVID‐19 pandemic. This viral infection impacts more severely solid organ transplant recipients (SOTRs) than general population, but the effect of vaccination in this subgroup of immunosuppressed patients is not known due to their exclusion from vaccination trials. Preliminary reports suggest a lower antibody production after BNT162b2 Pfizer/BioNTech mRNA‐vaccine,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0001"> 1 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0002">2 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0003">3 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0004">4 </a>but no data are currently available on the elicited virus‐specific T cell responses.</p>
Raw Data for the article: Clinical and Molecular-Based Approach in the Evaluation of Hepatocellular Carcinoma Recurrence after Radical Liver Resection
<p><strong>Background: </strong>Hepatic resection remains the treatment of choice for patients with early-stage HCC with preserved liver function. Unfortunately, however, the majority of patients develop tumor recurrence. While several clinical factors were found to be associated with tumor recurrence, HCC pathogenesis is a complex process of accumulation of somatic genomic alterations, which leads to a huge molecular heterogeneity that has not been completely understood. The aim of this study is to complement potentially predictive clinical and pathological factors with next-generation sequencing genomic profiling and loss of heterozygosity analysis.</p> <p><strong>Methods: </strong>124 HCC patients, who underwent a primary hepatic resection from January 2016 to December 2019, were recruited for this study. Next-generation sequencing (NGS) analysis and allelic imbalance assessment in a case-control subgroup analysis were performed. A time-to-recurrence analysis was performed as well by means of Kaplan-Meier estimators.</p> <p><strong>Results: </strong>Cumulative number of HCC recurrences were 26 (21%) and 32 (26%), respectively, one and two years after surgery. Kaplan-Meier estimates for the probability of recurrence amounted to 37% (95% C.I.: 24-47) and to 51% (95% C.I.: 35-62), after one and two years, respectively. Multivariable analysis identified as independent predictors of HCC recurrence: hepatitis C virus (HCV) infection (HR: 1.96, 95%C.I.: 0.91-4.24, <em>p</em> = 0.085), serum bilirubin levels (HR: 5.32, 95%C.I.: 2.07-13.69, <em>p</em> = 0.001), number of nodules (HR: 1.63, 95%C.I.: 1.12-2.38, <em>p</em> = 0.011) and size of the larger nodule (HR: 1.11, 95%C.I.: 1.03-1.18, <em>p</em> = 0.004). Time-to-recurrence analysis showed that loss of heterozygosity in the <em>PTEN</em> loci (involved in the PI3K/AKT/mTOR signaling pathway) was significantly associated with a lower risk of HCC recurrence (HR: 0.35, 95%C.I.: 0.13-0.93, <em>p</em> = 0.036).</p> <p><strong>Conclusions: </strong>multiple alterations of cancer genes are associated with HCC progression. In particular, the evidence of a specific AI mutation presented in 20 patients seemed to have a protective effect on the risk of HCC recurrence.</p>
Raw Data for the article: Liver Transplantation for Unresectable Intrahepatic Cholangiocarcinoma: The Role of Sequencing Genetic Profiling
<p>Intrahepatic cholangiocarcinoma (iCCA) is a rare and aggressive primary liver tumor, characterized by a range of different clinical manifestations and by increasing incidence and mortality rates even after curative treatment with radical resection. In recent years, growing attention has been devoted to this disease and some evidence supports liver transplantation (LT) as an appropriate treatment for intrahepatic cholangiocarcinoma; evolving work has also provided a framework for better understanding the genetic basis of this cancer. The aim of this study was to provide a clinical description of our series of patients complemented with Next-Generation Sequencing genomic profiling. From 1999 to 2021, 12 patients who underwent LT with either iCCA or a combined hepatocellular and cholangiocellular carcinoma (HCC-iCCA) were included in this study. Mutations were observed in gene activating signaling pathways known to be involved with iCCA tumorigenesis (KRAS/MAPK, P53, PI3K-Akt/mTOR, cAMP, WNT, epigenetic regulation and chromatin remodeling). Among several others, a strong association was observed between the Notch pathway and tumor size (point-biserial <em>rho<sub>pb</sub></em> = 0.93). Our results are suggestive of the benefit potentially derived from molecular analysis to improve our diagnostic capabilities and to devise new treatment protocols, and eventually ameliorate long-term survival of patients affected by iCCA or HCC-iCCA.</p>
Raw Data for the article: Liver transplantation for unresectable intrahepatic cholangiocarcinoma: an Italian experience
<p>Intrahepatic cholangiocarcinoma (iCCA) is an aggressive form of primary liver cancer treated exclusively with surgery.</p> <p>Its incidence in the western world is growing lately [<a href="https://link.springer.com/article/10.1007/s13304-021-01064-w#ref-CR1">1</a>] and the overall 5-year survival is poor due to late diagnosis, since patients rarely present a jaundice differently from patients affected by perihilar cholangiocarcinoma. Ideally liver resection and regional lymphadenectomy are the best treatments; however, these are unfortunately connotated by a 75% recurrence rate 5 years after surgery. Systemic chemotherapy offers a minimal response, as well as loco-regional therapy such as selective internal radiotherapy (SIRT), with a survival varying from 11 to 15 months between the two therapies</p>
Raw Data for the article: Extracellular Vesicle-Derived microRNAs of Human Wharton's Jelly Mesenchymal Stromal Cells May Activate Endogenous VEGF-A to Promote Angiogenesis
<p>Despite low levels of vascular endothelial growth factor (VEGF)-A, the secretome of human Wharton's jelly (WJ) mesenchymal stromal cells (MSCs) effectively promoted proangiogenic responses in vitro, which were impaired upon the depletion of small (~140 nm) extracellular vesicles (EVs). The isolated EVs shared the low VEGF-A profile of the secretome and expressed five microRNAs, which were upregulated compared to fetal dermal MSC-derived EVs. These upregulated microRNAs exclusively targeted the <em>VEGF-A</em> gene within 54 Gene Ontology (GO) biological processes, 18 of which are associated with angiogenesis. Moreover, 15 microRNAs of WJ-MSC-derived EVs were highly expressed (Ct value ≤ 26) and exclusively targeted the thrombospondin 1 (<em>THBS1</em>) gene within 75 GO biological processes, 30 of which are associated with the regulation of tissue repair. The relationship between predicted microRNA target genes and WJ-MSC-derived EVs was shown by treating human umbilical-vein endothelial cells (HUVECs) with appropriate doses of EVs. The exposure of HUVECs to EVs for 72 h significantly enhanced the release of VEGF-A and THBS1 protein expression compared to untreated control cells. Finally, WJ-MSC-derived EVs stimulated in vitro tube formation along with the migration and proliferation of HUVECs. Our findings can contribute to a better understanding of the molecular mechanisms underlying the proangiogenic responses induced by human umbilical cord-derived MSCs, suggesting a key regulatory role for microRNAs delivered by EVs.</p>
Raw Data for the article: Apneic Tracheostomy in COVID-19 Patients on Veno-Venous Extracorporeal Membrane Oxygenation
<p>COVID-19 creates an impressive burden for intensive care units in terms of need for advanced respiratory care, with a huge number of acute respiratory distress syndromes (ARDS) requiring prolonged mechanical ventilation. In some cases, this proves to be insufficient, with a refractory respiratory failure calling for an extracorporeal approach (veno-venous ECMO). In this scenario, most of these patients need an early tracheostomy procedure to be carried out, which creates the risk of distribution of aerosol particles, possibly leading to personnel infection. The use of apneic tracheostomy has been proposed for COVID-19 patients, but in case of ECMO it may produce lung derecruitment, severe hypoxemia, and sudden worsening of respiratory mechanics. We developed an apneic tracheostomy technique and applied it in over 32 patients supported by veno-venous ECMO. We present data showing the safety and feasibility of this technique in terms of patient care and personnel protection. Gas exchange and pH did not show statistically significant changes after the tracheostomy, nor did respiratory mechanics data or the need for inspiratory pressure and FiO<sub>2</sub>. The use of apneic tracheostomy was a safe option for patient care during ECMO and reduced the possibility of virus spreading.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.