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Article ; Online: Timely adaptation of a Pediatric Unit to COVID-19 emergency in Northern Italy: the experience of Fondazione IRCCS Policlinico San Matteo in Pavia.

Novelli, Viola / Cutti, Sara / Muzzi, Alba / Marena, Carlo / Grugnetti, Giuseppina / Triarico, Antonio / Nicora, Carlo / Venturi, Alessandro / Licari, Amelia / Marseglia, Gian Luigi / Bossi, Grazia / Brambilla, Ilaria / Caimmi, Silvia / Castagnoli, Riccardo / De Filippo, Maria / Delle Piane, Luciana / Iozzi, Lucia / Montagna, Daniela / Votto, Martina

Acta bio-medica : Atenei Parmensis

2020 Volume 91, Issue 11-S, Page(s) e2020004

Abstract: ... region in Italy. In this context, Fondazione IRCCS Policlinico San Matteo in Pavia, one of the largest ...

Abstract	Italy is one of the most exposed countries worldwide to COVID-19, and Lombardy is the most affected region in Italy. In this context, Fondazione IRCCS Policlinico San Matteo in Pavia, one of the largest University hospitals in the region, has been involved in the management of the outbreak since its inception. Immediately after the communication of the first Italian COVID-19+ patient, the Pediatric Unit has been completely reorganized to face the approaching outbreak. The optimization of the Pediatric Unit resources for COVID-19 emergency is reported as an example to safely preserve health activity during the pandemic.
MeSH term(s)	Betacoronavirus ; COVID-19 ; Child ; Coronavirus Infections/epidemiology ; Coronavirus Infections/therapy ; Disease Management ; Emergency Service, Hospital/organization & administration ; Humans ; Intensive Care Units, Pediatric/organization & administration ; Italy/epidemiology ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/therapy ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-09-15
Publishing country	Italy
Document type	Journal Article ; Review
ZDB-ID	2114240-3
ISSN	2531-6745 ; 0392-4203
ISSN (online)	2531-6745
ISSN	0392-4203
DOI	10.23750/abm.v91i11-S.10300
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Article ; Online: Reply to: Antonio Andrea Grosso, Agostino Tuccio, Matteo Salvi, Daniele Paganelli, Andrea Minervini, and Fabrizio Di Maida's Letter to the Editor re: Paolo Capogrosso, Eugenio Ventimiglia, Giuseppe Fallara, et al. Holmium Laser Enucleation of the Prostate Is Associated with Complications and Sequelae Even in the Hands of an Experienced Surgeon Following Completion of the Learning Curve. Eur Urol Focus. In press. https://doi.org/10.1016/j.euf.2023.03.018.

Capogrosso, Paolo / Ventimiglia, Eugenio / Fallara, Giuseppe / Schifano, Nicolò / Costa, Antonio / Candela, Luigi / Pellegrino, Francesco / Colandrea, Gianmarco / Cignoli, Daniele / De Angelis, Mario / Belladelli, Federico / Longoni, Mattia / Avesani, Giulio / Lanzaro, Francesco / Scattoni, Vincenzo / Dehò, Federico / Salonia, Andrea / Briganti, Alberto / Montorsi, Francesco

European urology focus

2023 Volume 10, Issue 1, Page(s) 207–208

MeSH term(s)	Male ; Humans ; Prostate ; Learning Curve ; Lasers, Solid-State ; Prostatic Neoplasms/surgery ; Surgeons
Language	English
Publishing date	2023-07-11
Publishing country	Netherlands
Document type	Letter
ISSN	2405-4569
ISSN (online)	2405-4569
DOI	10.1016/j.euf.2023.06.008
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Article ; Online: Double- vs single-blind peer review effect on acceptance rates: a systematic review and meta-analysis of randomized trials.

Ucci, Matteo Antonio / D'Antonio, Francesco / Berghella, Vincenzo

American journal of obstetrics & gynecology MFM

2022 Volume 4, Issue 4, Page(s) 100645

Abstract: Objective: This study aimed to assess the changes in the acceptance rates between double- and single-blind peer review systems.: Data sources: The search was conducted using Medline, Embase, and ClinicalTrials.gov databases as electronic databases ... ...

Abstract	Objective: This study aimed to assess the changes in the acceptance rates between double- and single-blind peer review systems. Data sources: The search was conducted using Medline, Embase, and ClinicalTrials.gov databases as electronic databases from the inception of each database to June 2021. No restriction for language or geographic location was applied. Study eligibility criteria: The selection criteria included randomized controlled trials comparing the double-blind peer review process vs the single-blind peer review process. Methods: The primary outcome was manuscripts acceptance rates. The summary measures were reported as relative risk with 95% confidence intervals using the random-effects model meta-analyses. Between-study heterogeneity was explored using the I Results: A total of 11 randomized controlled trials, including 3477 reviewers and 3784 manuscripts, were identified. The manuscript acceptance rates were significantly lower in the double-blind (200/1413 [14.2%]) peer review processes than in the single-blind (194/1019 [19.0%]) peer review processes (relative risk, 0.82; 95% confidence interval, 0.70-0.97; n=5 randomized controlled trials). Only 1 randomized controlled trial assessed the authors' and/or institutions' prestige on acceptance rates with results not statistically significant. Only 2 randomized controlled trials assessed the manuscript origin (US or non-US) effect on acceptance rates with results not statistically significant. Gender of the manuscript authors was assessed by only 1 randomized controlled trial, and although blinding or not female author names made no statistical difference, blinding of male author names was associated with a significant decrease in acceptance rate (139/1266 [11.0%] vs 190/1266 [15.0%]; relative risk, 0.73; 95% confidence interval, 0.59-0.90). Double-blind peer review was deemed successful by reviewers in only approximately 52% of the cases (n=5 randomized controlled trials). Conclusion: The double-blind peer review process seemed to be associated with an 18% lower manuscript acceptance rate than the single-blind peer review process. However, given the large heterogeneity among the included studies, more research is needed to confirm these findings and elucidate those factors that can affect the acceptance rate in double- and single-blind peer reviews.
MeSH term(s)	Double-Blind Method ; Humans ; Male ; Peer Review ; Randomized Controlled Trials as Topic ; Single-Blind Method
Language	English
Publishing date	2022-04-14
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Review ; Systematic Review
ISSN	2589-9333
ISSN (online)	2589-9333
DOI	10.1016/j.ajogmf.2022.100645
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Article ; Online: Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease.

D'Antonio, Matteo / Nguyen, Jennifer P / Arthur, Timothy D / Matsui, Hiroko / D'Antonio-Chronowska, Agnieszka / Frazer, Kelly A

Nature communications

2023 Volume 14, Issue 1, Page(s) 4370

Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40048-9
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Article ; Online: Haptools: a toolkit for admixture and haplotype analysis.

Massarat, Arya R / Lamkin, Michael / Reeve, Ciara / Williams, Amy L / D'Antonio, Matteo / Gymrek, Melissa

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 3

Abstract: Summary: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, ... ...

Abstract	Summary: Leveraging local ancestry and haplotype information in genome-wide association studies and downstream analyses can improve the utility of genomics for individuals from diverse and recently admixed ancestries. However, most existing simulation, visualization and variant analysis frameworks are based on variant-level analysis and do not automatically handle these features. We present haptools, an open-source toolkit for performing local ancestry aware and haplotype-based analysis of complex traits. Haptools supports fast simulation of admixed genomes, visualization of admixture tracks, simulation of haplotype- and local ancestry-specific phenotype effects and a variety of file operations and statistics computed in a haplotype-aware manner. Availability and implementation: Haptools is freely available at https://github.com/cast-genomics/haptools. Documentation: Detailed documentation is available at https://haptools.readthedocs.io. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Haplotypes ; Software ; Genome-Wide Association Study ; Genomics ; Genome
Language	English
Publishing date	2023-02-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad104
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Article ; Online: Scapulohumeral rhythm in shoulders with reverse shoulder arthroplasty measured with a new portable three-dimensional scapular kinematics assessment system.

Reina, Micaela / Fiumana, Gabriele / Mantovani, Matteo / D'Antonio, Lucio / Porcellini, Giuseppe

Journal of shoulder and elbow surgery

2023 Volume 32, Issue 4, Page(s) 729–737

Abstract: Background: Reverse shoulder arthroplasty (RSA) is a valid and increasingly popular treatment option in eccentric arthrosis and cuff arthropathy. We know that the deltoid is the motor of RSA. However, the role of scapular motion has been poorly ... ...

Abstract	Background: Reverse shoulder arthroplasty (RSA) is a valid and increasingly popular treatment option in eccentric arthrosis and cuff arthropathy. We know that the deltoid is the motor of RSA. However, the role of scapular motion has been poorly documented in the literature. The aim of our study is to analyze and quantify the role of the scapular contribution in the functional outcome of patients undergoing RSA. Materials and methods: Fourteen patients who underwent primary RSA were included in the study. In all cases, a reverse prosthesis with lateralizing stem was implanted. All patients underwent clinical examination, video recording, and motion analysis. X-ray and postoperative CT examinations were collected to evaluate positioning and any loosening. ShowMotion (NCS Lab srl, Modena, Italy) 3D kinematic tracking system was used to evaluate and measure the scapular motion in 3 planes. Results: All patients show substantial amount of posterior tilting and lateral rotation starting at 30° in forward elevation. A further difference is the anticipation of the retraction during the range of motion in the RSA side. The contribution of scapular motion in the RSA shoulder was greater than in the healthy shoulder. In patients with bilateral RSA, the contribution of scapular motion was higher in tilting and lateral rotation in the worse shoulder side in terms of range of motion. This means that to compensate for the loss of glenohumeral motion in RSA, more scapula-thoracic motion is needed to obtain the same thoraco-humeral elevation angle. Conclusions: In the light of what has been measured, the post-RSA scapular kinematics has typical characteristics that must be achieved in order to obtain a good functional outcome. We can conclude that on the RSA side, the patients anticipate upward rotation both in flexion and abduction. The contribution of the upward rotation to elevation in the RSA group is therefore more significant. In addition to this, to facilitate elevation movements, there is an anticipation of the scapular retraction and a more prominent tilt resulting in different scapular kinematics. The analysis of scapular motion could be useful in the postoperative follow-up of patients undergoing RSA surgery and improve adaptative physiotherapy protocols. It potentially can even be included in future arthroplasty planning systems.
MeSH term(s)	Humans ; Shoulder/surgery ; Arthroplasty, Replacement, Shoulder ; Biomechanical Phenomena ; Shoulder Joint/diagnostic imaging ; Shoulder Joint/surgery ; Scapula/diagnostic imaging ; Scapula/surgery ; Arthroplasty ; Range of Motion, Articular
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1170782-3
ISSN	1532-6500 ; 1058-2746
ISSN (online)	1532-6500
ISSN	1058-2746
DOI	10.1016/j.jse.2022.12.007
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Article ; Online: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease.

D'Antonio, Matteo / Nguyen, Jennifer P / Arthur, Timothy D / Matsui, Hiroko / D'Antonio-Chronowska, Agnieszka / Frazer, Kelly A

Nature communications

2023 Volume 14, Issue 1, Page(s) 1132

Abstract: The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting ...

Abstract	The causal variants and genes underlying thousands of cardiac GWAS signals have yet to be identified. Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. We identify 2,578 eQTLs associated with a specific developmental stage-, tissue- and/or cell type. Colocalization between eQTL and GWAS signals of five cardiac traits identified variants with high posterior probabilities for being causal in 210 GWAS loci. Pulse pressure GWAS loci are enriched for colocalization with fetal- and smooth muscle- eQTLs; pulse rate with adult- and cardiac muscle- eQTLs; and atrial fibrillation with cardiac muscle- eQTLs. Fine mapping identifies 79 credible sets with five or fewer SNPs, of which 15 were associated with spatiotemporal eQTLs. Our study shows that many cardiac GWAS variants impact traits and disease in a developmental stage-, tissue- and/or cell type-specific fashion.
MeSH term(s)	Humans ; Heart ; Myocardium ; Atrial Fibrillation/genetics ; Blood Pressure ; Fetus
Language	English
Publishing date	2023-02-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36638-2
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Article ; Online: Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.

Arthur, Timothy D / Nguyen, Jennifer P / D'Antonio-Chronowska, Agnieszka / Matsui, Hiroko / Silva, Nayara S / Joshua, Isaac N / Luchessi, André D / Greenwald, William W Young / D'Antonio, Matteo / Pera, Martin F / Frazer, Kelly A

Nature communications

2024 Volume 15, Issue 1, Page(s) 1664

Abstract: Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene ... ...

Abstract	Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells/metabolism ; Gene Regulatory Networks ; Chromatin/genetics ; Cell Differentiation/genetics ; Octamer Transcription Factor-3/genetics
Chemical Substances	Chromatin ; Octamer Transcription Factor-3
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45506-6
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Article: Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci.

Arthur, Timothy D / Nguyen, Jennifer P / D'Antonio-Chronowska, Agnieszka / Jaureguy, Jeffrey / Silva, Nayara / Henson, Benjamin / Panopoulos, Athanasia D / Belmonte, Juan Carlos Izpisua / D'Antonio, Matteo / McVicker, Graham / Frazer, Kelly A

bioRxiv : the preprint server for biology

2024

Abstract: Most GWAS loci are presumed to affect gene regulation, however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we identify eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation ... ...

Abstract	Most GWAS loci are presumed to affect gene regulation, however, only ∼43% colocalize with expression quantitative trait loci (eQTLs). To address this colocalization gap, we identify eQTLs, chromatin accessibility QTLs (caQTLs), and histone acetylation QTLs (haQTLs) using molecular samples from three early developmental (EDev) tissues. Through colocalization, we annotate 586 GWAS loci for 17 traits by QTL complexity, QTL phenotype, and QTL temporal specificity. We show that GWAS loci are highly enriched for colocalization with complex QTL modules that affect multiple elements (genes and/or peaks). We also demonstrate that caQTLs and haQTLs capture regulatory variations not associated with eQTLs and explain ∼49% of the functionally annotated GWAS loci. Additionally, we show that EDev-unique QTLs are strongly depleted for colocalizing with GWAS loci. By conducting one of the largest multi-omic QTL studies to date, we demonstrate that many GWAS loci exhibit phenotypic complexity and therefore, are missed by traditional eQTL analyses.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.10.588874
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Article ; Online: SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues.

D'Antonio, Matteo / Nguyen, Jennifer P / Arthur, Timothy D / Matsui, Hiroko / D'Antonio-Chronowska, Agnieszka / Frazer, Kelly A

Cell reports

2022 Volume 39, Issue 11, Page(s) 110968

Language	English
Publishing date	2022-06-07
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110968
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