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R code and patient data for 'Bacterial Transmission Dynamics Revealed by Prophage Barcoding'
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Data Set_Urinary Albumin-to-Creatinine Ratio as an Independent Predictor of Long-term Mortality in Atherosclerotic Cardiovascular Disease Patients: A Propensity Score-Matched Study
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The association between body mass index and fibromyalgia severity: data from a cross-sectional survey of 2339 patients
<p>The association between body mass index and fibromyalgia severity: data from a cross-sectional survey of 2339 patients</p> <p>Objective Various studies have shown that overweight and obesity are central features of FM, but<br> the real impact of a high BMI on clinical severity in patients with FM is still controversial. The aim of<br> this study was to analyse the relationships between BMI categories and measures of symptom severity<br> and functional impairment using data from a Web-based registry of patients with FM.<br> Methods Adult patients with an ACR 2010/2011 diagnosis of FM underwent a complete physical examination<br> and laboratory tests and were asked to complete a package of questionnaires covering their<br> sociodemographic and treatment details, in addition to the following disease-specific questionnaires:<br> the revised Fibromyalgia Impact Questionnaire (FIQR), the modified Fibromyalgia Assessment Status<br> questionnaire (ModFAS) and the Polysymptomatic Distress Scale (PDS).<br> Results A total of 2339 patients were recruited and divided into two weight categories, underweight/<br> normal (U/N, n¼1127, 48.2%) and overweight/obese (O/O, n¼1212, 51.8%). The total and subscales significantly higher in the O/O patients, as were all the mean scores of the individual FIQR items<br> (P<0.001 for all).<br> Conclusion Our findings demonstrate that O/O patients with FM are significantly more impaired than<br> U/N patients in all the symptomatological and functional domains as measured using the FIQR,<br> ModFAS and PDS, thus suggesting that being O/O has an additional effect on symptoms and<br> function.</p>
Dataset related to article "Prognostic Value of Metabolic Imaging Data of 11 C-choline PET/CT in Patients Undergoing Hepatectomy for Hepatocellular Carcinoma "
<p>This record contains raw data related to article “Prognostic Value of Metabolic Imaging Data of <sup>11</sup> C-choline PET/CT in Patients Undergoing Hepatectomy for Hepatocellular Carcinoma"</p> <p><sup>11</sup>C-choline positron emission tomography/computed tomography (PET/CT) has been used for patients with some types of tumors, but few data are available for hepatocellular carcinoma (HCC). We queried our prospective database for patients with HCC staged with <sup>11</sup>C-choline PET/CT to assess the clinical impact of this imaging modality. Seven parameters were recorded: maximum standardized uptake value (SUVmax), mean standardized uptake value (SUVmean), liver standardized uptake value (SUVliver), metabolic tumor volume (MTV), photopenic area, metabolic tumor burden (MTB = MTVxSUVmean), and SUVratio (SUVmax/SUVliver). Analysis was performed to identify parameters that could be predictors of overall survival (OS). Sixty patients were analyzed: fourteen (23%) were in stage 0-A, 37 (62%) in stage B, and 9 (15%) in stage C of the Barcelona classification. The Cox regression for OS showed that Barcelona stages (HR = 2.94; 95%CI = 1.41-4.51; <em>p</em> = 0.003) and MTV (HR = 2.11; 95%CI = 1.51-3.45; <em>p</em> = 0.026) were the only factors independently associated with OS. Receiver operating characteristics curve analysis revealed MTV ability in discriminating survival (area under the curve (AUC) = 0.77; 95%CI = 0.57-097; <em>p</em> < 0.001: patients with MTV ≥ 380 had worse OS (<em>p</em> = 0.015)). The use of <sup>11</sup>C-choline PET/CT allows for better prognostic refinement in patients undergoing hepatectomy for HCC. Incorporation of such modality into HCC staging system should be considered.</p>
Data related to article "Histone Deacetylase Inhibitors Ameliorate Morphological Defects and Hypoexcitability of iPSC-Neurons from Rubinstein-Taybi Patients"
<p>THE DATASET CONTAINS RAW DATA UNDERLYING ARTICLE FIG N.6</p>
data set from the article De Marco F, Casenghi M, Spagnolo P, Popolo Rubbio A, Brambilla N, Testa L, Bedogni F. A patient-specific algorithm to achieve commissural alignment with Acurate Neo: The sextant technique. Catheter Cardiovasc Interv. 2021 Nov 15;98(6):E847-E854. doi: 10.1002/ccd.29737. Epub 2021 May 7. PMID: 33960624.
<p>data set from the article De Marco F, Casenghi M, Spagnolo P, Popolo Rubbio A, Brambilla N, Testa L, Bedogni F. A patient-specific algorithm to achieve commissural alignment with Acurate Neo: The sextant technique. Catheter Cardiovasc Interv. 2021 Nov 15;98(6):E847-E854. doi: 10.1002/ccd.29737. Epub 2021 May 7. PMID: 33960624</p> <p>abstract:</p> <p><strong>Aims: </strong>The aim of this proof-of-concept study was to investigate safety and efficacy of a CT-scan based patient-specific algorithm to maximize coronary clearance and secondarily to achieve anatomically correct commissural alignment with the Acurate Neo device.</p> <p><strong>Method and results: </strong>A total of 45 consecutive patients undergoing TAVR with the Acurate Neo THV were prospectively enrolled in the study. Mean age was 81.6 ± 5.5 years, mean STS score was 6.1 ± 3.7. Device success rate was 100%. Aim of the technique was to rotationally deploy the TAVR device with a commissure lying on the bisector between the coronary ostia as calculated on the pre-procedural CT-scan. At post-TAVR CT-scan, coronary clearance was achieved in 98% of patients with no cases of severe coronary artery overlap. In 42 out of 45 patients, THV was aligned or, at most, mildly misaligned; there were 2 cases of moderate misalignment without any case of severe misalignment. Post-TAVR selective coronary artery engagement was attempted and succeeded in all patients (100%).</p> <p><strong>Conclusion: </strong>Our CT-scan based patient-specific algorithm is safe and proven to be effective in avoiding coronary artery overlap and providing commissural alignment with Acurate Neo in all treated patients.</p>
Dataset related to article "Different Personality Profiles In Patients With Chronic Cluster Headache: A Data-Driven Approach"
<p>dataset contains clinical information on patient involved in the study described at article at title</p>
Raw Data_Inflammation-based Glasgow Prognostic Score level and mortality in patients with cardiovascular disease: the National and Health Nutrition Examination Survey 1999-2010
<p>The raw data supporting the results of this study (Inflammation-based Glasgow Prognostic Score level and mortality in patients with cardiovascular disease: the National and Health Nutrition Examination Survey 1999-2010)</p>
Data used for the scientific work "Effectiveness of Cognitive Behavioral Therapy in naturalistic settings for patients with and without personality disorders: a comparative study of the English IAPT and the Italian inTHERAPY programs on anxiety and depression symptoms"
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Data set for "Hemoglobin, albumin, lymphocyte, and platelet score: A risk prediction tool for incidence and mortality in diabetic kidney disease patients with type 2 diabetes "
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Raw data: Role of cardiopulmonary exercise test in the prediction of hemodynamic impairment in patients with pulmonary arterial hypertension
<p>Periodic repetition of right heart catheterization (RHC) in pulmonary arterial hypertension (PAH) can be challenging. We evaluated the correlation between RHC and cardiopulmonary exercise test (CPET) aiming at CPET use as a potential noninvasive tool for hemodynamic burden evaluation. One hundred and forty‐four retrospective PAH patients who had performed CPET and RHC within 2 months were enrolled. The following analyses were performed: (a) CPET parameters in hemodynamic variables tertiles; (b) position of hemodynamic parameters in the peak end‐tidal carbon dioxide pressure (P<sub>ET</sub>CO<sub>2</sub>) versus ventilation/carbon dioxide output (VE/VCO<sub>2</sub>) slope scatterplot, which is a specific hallmark of exercise respiratory abnormalities in PAH; (c) association between CPET and a hemodynamic burden score developed including mean pulmonary arterial pressure (mPAP), pulmonary vascular resistance (PVR), cardiac index, and right atrial pressure. VE/VCO<sub>2</sub> slope and peak P<sub>ET</sub>CO<sub>2</sub> significantly varied in mPAP and PVR tertiles, while peak oxygen uptake (peak VO<sub>2</sub>) and O<sub>2</sub> pulse varied in the tertiles of all hemodynamic parameters. P<sub>ET</sub>CO<sub>2</sub> versus VE/VCO<sub>2</sub> slope showed a strong hyperbolic relationship (<em>R</em> <sup>2</sup> =&thinsp;0.7627). Patients with peak P<sub>ET</sub>CO<sub>2</sub> > median (26 mmHg) and VE/VCO<sub>2</sub> slope < median (44) presented lower mPAP and PVR (p < 0.005) than patients with peak P<sub>ET</sub>CO<sub>2</sub> < median and VE/VCO<sub>2</sub> slope > median. Multivariate analysis individuated peak VO<sub>2</sub> (<em>p</em> =&thinsp;0.0158) and peak P<sub>ET</sub>CO<sub>2</sub> (<em>p</em> =&thinsp;0.0089) as hemodynamic score independent predictors; the formula 11.584 − 0.0925 × peak VO<sub>2</sub> − 0.0811 × peak P<sub>ET</sub>CO<sub>2</sub> best predicts the hemodynamic score value from CPET data. A significant correlation was found between estimated and calculated scores (<em>p</em> < 0.0001), with a precise match for patients with mild‐to‐moderate hemodynamic burden (76% of cases). The results of the present study suggest that CPET could allow to estimate the hemodynamic burden in PAH patients.</p> <p> </p>
Data set related to the article: "Gender Differences Associated with the Prognostic Value of BPIFB4 in COVID-19 Patients: A Single-Center Preliminary Study."
<p><strong>Abstract:</strong> In the ongoing global COVID-19 pandemic, male sex is a risk factor for severe disease and death, and the reasons for these clinical discrepancies are largely unknown. The aim of this work is to study the influence of sex on the course of infection and the differences in prognostic markers between genders in COVID-19 patients. Our cohort consisted of 64 adult patients (n = 34 men and n = 30 women) with PCR-proven SARS-CoV-2 infection. Further, a group of patients was characterized by a different severity degree (n = 8 high- and n = 8 low-grade individuals for both male and female patients). As expected, the serum concentrations of LDH, fibrinogen, CRP, and leucocyte count in men were significantly higher than in females. When serum concentrations of the inflammatory cytokines, including IL-6, IL-2, IP-10 and IL-4 and chemokines like MCP-1, were measured with multiplex ELISA, no significant differences between male and female patients were found. In COVID-19 patients, we recently attributed a new prognostic value to BPIFB4, a natural defensin against dysregulation of the immune responses. Here, we clarify that BPIFB4 is inversely related to the disease degree in men but not in women. Indeed, higher levels of BPIFB4 characterized low-grade male patients compared to high-grade ones. On the contrary, no significant difference was reported between low-grade female patients and high-grade ones. In conclusion, the identification of BPIFB4 as a biomarker of mild/moderate disease and its sex-specific activity would open an interesting field for research to underpin gender-related susceptibility to the disease.</p>
Data set related to the article "Predictors of Prognosis in Patients With Secondary Mitral Regurgitation Undergoing Mitral Valve Transcatheter Edge-to-Edge Repair"
<p>This record contains raw data related to the article <em>Predictors of Prognosis in Patients With Secondary Mitral Regurgitation Undergoing Mitral Valve Transcatheter Edge-to-Edge Repair</em></p>
Data set related to the article: "The Longevity-Associated Variant of BPIFB4 Reduces Senescence in Glioma Cells and in Patients' Lymphocytes Favoring Chemotherapy Efficacy"
<p>Abstract: Glioblastoma (GBM) is the most common primary brain cancer with the median age at diagnosis around 64 years, thus pointing to aging as an important risk factor. Indeed, aging, by increasing the senescence burden, is configured as a negative prognostic factor for GBM stage. Furthermore, several anti-GBM therapies exist, such as temozolomide (TMZ) and etoposide (ETP), that unfortunately trigger senescence and the secretion of proinflammatory senescence-associated secretory phenotype (SASP) factors that are responsible for the improper burst of (i) tumorigenesis, (ii) cancer metastasis, (iii) immunosuppression, and (iv) tissue dysfunction. Thus, adjuvant therapies that limit senescence are urgently needed. The longevity-associated variant (LAV) of the bactericidal/permeability-increasing fold-containing family B member 4 (BPIFB4) gene previously demonstrated a modulatory activity in restoring age-related immune dysfunction and in balancing the low-grade inflammatory status of elderly people. Based on the above findings, we tested LAV- BPIFB4 senotherapeutic effects on senescent glioblastoma U87-MG cells and on T cells from GBM patients. We interrogated SA-β-gal and HLA-E senescence markers, SASP factors, and proliferation and apoptosis assays. The results highlighted a LAV-BPIFB4 remodeling of the senescent phenotype of GBM cells, enhancement of their sensitivity to temozolomide and a selective reduction of the T cells’ senescence from GBM patients. Overall, these findings candidate LAV-BPIFB4 as an adjuvant therapy for GBM.</p>
Supplementary material for the article: Analysis of transcriptomics data from COVID-19 patients: pilot re-search
<p><strong>Supplementary table 1:</strong> <strong>Genes affected by COVID-19 infection.</strong> Differentially expressed genes analysis by DESeq2 statistical test – whole result table. Comparison of gene expressions between 72 samples from COVID-19 positive patients and 24 samples from healthy donors. Significance was judged by adjusted p-vlaue, with threshold set on 0.1. </p> <p><strong>Supplementary table 2:</strong> <strong>Genes affected by severity of COVID-19.</strong> Differentially expressed genes analysis by DESeq2 statistical test – whole result table. Comparison of gene expressions between 23 samples from COVID-19 positive patients with severe symptoms and 25 with mild symptoms. Significance was judged by adjusted p-vlaue, with threshold set on 0.1. </p>
Data related to article EFFICACY OF MINDFULNESS ADDED TO TREATMENT AS USUAL IN PATIENTS WITH CHRONIC MIGRAINE AND MEDICATION OVERUSE HEADACHE: A PHASE-III SINGLE-BLIND RANDOMIZED-CONTROLLED TRIAL (THE MIND-CM STUDY) - submitted
<p>DATA ON PATIENTS INCLUDED IN THE MIND-CM STUDY. TWO ARMS (TAU AND TAU+MIND), AND FOUR EVALUATIONS: BASELINE, 3-MONTHS, 6-MONTHS AND 12-MONTS FOLLOW-UP.</p>
Raw data for "Effects of sacubitril/valsartan on exercise capacity: a prognostic improvement that starts during uptitration. Eur J Clin Pharmacol. 2023;79:1173-1184." and "Looking into the Kinetics of NT-proBNP and sST2 Changes in Patients with Heart Failure Treated with Sacubitril/Valsartan: A Hint to Different Therapeutic Pathways;Drugs R D. 2023 Sep 13. doi: 10.1007/s40268-023-00438-2."
<p><strong>Looking into the Kinetics of NT-proBNP and sST2 Changes in Patients with Heart Failure Treated with Sacubitril/Valsartan: A Hint to Different Therapeutic Pathways:</strong></p> <p><strong>Background and objective: </strong>N-terminal pro-B-type natriuretic peptide (NT-proBNP) and soluble interleukin 1 receptor-like 1 ST2 (sST2) are biomarkers used to grade heart failure with reduced ejection fraction (HFrEF) severity. Both are potential targets of HFrEF treatment, but the first is associated with the patient's hemodynamic status, while the second is more indicative of the inflammatory status and of myocardial fibrosis. The aim of this study was to assess the kinetics of these biomarkers after treatment with sacubitril/valsartan in HFrEF.</p> <p><strong>Methods: </strong>We analyzed blood samples of patients with HFrEF at baseline (before sacubitril/valsartan treatment), after 1, 2, and 3 months (respectively, after a month taking the 24/26 - 49/51 - 97/103 mg twice daily, or b.i.d., doses), and 6 months after the maximum-tolerated dose was reached (end study).</p> <p><strong>Results: </strong>We obtained samples from 72 patients with HFrEF (age 64.0 ± 10.5 years, 83% males). NT-proBNP and sST2 values progressively and significantly reduced to 37% and 16%, respectively, with a greater reduction for NT-proBNP (p < 0.001). Specifically, NT-proBNP reduced from 1144 [593-2586] pg/mL to 743 [358-1524] pg/mL and sST2 from 27.3 [20.5-35.0] ng/mL to 23.1 [15.9-30.7] ng/mL, p for trend < 0.001 in both cases. The reduction of the two biomarkers over time occurred with statistically significant different kinetics: deferred for sST2 and faster for NT-proBNP. No significant changes in renal function and potassium levels were recorded.</p> <p><strong>Conclusion: </strong>These findings suggest that, in patients with HF, sacubitril/valsartan effects on the cardiovascular system share a double pathway: a first, hemodynamic, faster pathway and a second, non-hemodynamic anti-fibrotic, delayed one. Both likely contribute to the sacubitril/valsartan benefits in HFrEF.</p> <p> </p> <p><strong>Effects of sacubitril/valsartan on exercise capacity: a prognostic improvement that starts during uptitration</strong></p> <p><strong>Purpose: </strong>Sacubitril/valsartan is a mainstay of the treatment of heart failure with reduced ejection fraction (HFrEF); however, its effects on exercise performance yielded conflicting results. Aim of our study was to evaluate the impact of sacubitril/valsartan on exercise parameters and echocardiographic and biomarker changes at different drug doses.</p> <p><strong>Methods: </strong>We prospectively enrolled consecutive HFrEF outpatients eligible to start sacubitril/valsartan. Patients underwent clinical assessment, cardiopulmonary exercise test (CPET), blood sampling, echocardiography, and completed the Kansas City Cardiomyopathy Questionnaire (KCCQ-12). Sacubitril/valsartan was introduced at 24/26 mg b.i.d. dose and progressively uptitrated in a standard monthly-based fashion to 97/103 mg b.i.d. or maximum tolerated dose. Study procedures were repeated at each titration visit and 6 months after reaching the maximum tolerated dose.</p> <p><strong>Results: </strong>Ninety-six patients completed the study, 73 (75%) reached maximum sacubitril/valsartan dose. We observed a significant improvement in functional capacity across all study steps: oxygen intake increased, at peak exercise (from 15.6 ± 4.5 to 16.5 ± 4.9 mL/min/kg; p trend = 0.001), while minute ventilation/carbon dioxide production relationship reduced in patients with an abnormal value at baseline. Sacubitril/valsartan induced positive left ventricle reverse remodeling (EF from 31 ± 5 to 37 ± 8%; p trend < 0.001), while NT-proBNP reduced from 1179 [610-2757] to 780 [372-1344] pg/ml (p trend < 0.0001). NYHA functional class and the subjective perception of limitation in daily life at KCCQ-12 significantly improved. The Metabolic Exercise Cardiac Kidney Index (MECKI) score progressively improved from 4.35 [2.42-7.71] to 2.35% [1.24-4.96], p = 0.003.</p> <p><strong>Conclusions: </strong>A holistic and progressive HF improvement was observed with sacubitril/valsartan in parallel with quality of life. Likewise, a prognostic enhancement was observed.</p>
Raw data for "The importance of re-evaluating the risk score in heart failure patients: An analysis from the Metabolic Exercise Cardiac Kidney Indexes (MECKI) score database" 2023 Int J Cardiol
<p>Abstract</p> <p><strong>Background: </strong>The role of risk scores in heart failure (HF) management has been highlighted by international guidelines. In contrast with HF, which is intrinsically a dynamic and unstable syndrome, all its prognostic studies have been based on a single evaluation. We investigated whether time-related changes of a well-recognized risk score, the MECKI score, added prognostic value. MECKI score is based on peak VO<sub>2</sub>, VE/VCO<sub>2</sub> slope, Na<sup>+</sup>, LVEF, MDRD and Hb.</p> <p><strong>Methods: </strong>A multi-centre retrospective study was conducted involving 660 patients who performed MECKI re-evaluation at least 6 months apart. Based on the difference between II and I evaluation of MECKI values (MECKI II - MECKI I = ∆ MECKI) the study population was divided in 2 groups: those presenting a score reduction (∆ MECKI <0, i.e. clinical improvement), vs. patients presenting an increase (∆ MECKI >0, clinical deterioration).</p> <p><strong>Results: </strong>The prognostic value of MECKI score is confirmed also when re-assessed during follow-up. The group with improved MECKI (366 patients) showed a better prognosis compared to patients with worsened MECKI (294 patients) (p < 0.0001). At 1st evaluation, the two groups differentiated by LVEF, V<sub>E</sub>/VCO<sub>2</sub> slope and blood Na<sup>+</sup> concentration, while at 2nd evaluation they differentiated in all 6 parameters considered in the score. The patients who improved MECKI score, improved in all components of the score but hemoglobin, while patients who worsened the score, worsened all parameters.</p> <p><strong>Conclusions: </strong>This study shows that re-assessment of MECKI score identifies HF subjects at higher risk and that score improvement or deterioration regards several MECKI score generating parameters confirming the holistic background of HF.</p>
Expression data from lesions and non-lesions before and after treatment in patients with atopic dermatitis
GEO Series GSE309828. Homo sapiens. 24 samples. Type: Expression profiling by array.
Affymetrix CytoScan HD array data for patient with Intellectual Disabilities
GEO Series GSE58694. Homo sapiens. 1 samples. Type: Genome variation profiling by genome tiling array; Genome variation profiling by SNP array.
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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.