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Article ; Online: Re: Stephen B. Williams, Marcus G.K. Cumberbatch, Ashish M. Kamat, et al. Reporting Radical Cystectomy Outcomes Following Implementation of Enhanced Recovery After Surgery Protocols: A Systematic Review and Individual Patient Data Meta-analysis. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.06.039.

Giannarini, Gianluca / Ficarra, Vincenzo / Valotto, Claudio

2020 Volume 78, Issue 5, Page(s) e188–e189

MeSH term(s)	Cystectomy/adverse effects ; Enhanced Recovery After Surgery ; Humans ; Male ; Prostatic Neoplasms/surgery ; Urinary Bladder
Language	English
Publishing date	2020-08-14
Publishing country	Switzerland
Document type	Letter ; Comment
ZDB-ID	193790-x
ISSN	1873-7560 ; 1421-993X ; 0302-2838
ISSN (online)	1873-7560 ; 1421-993X
ISSN	0302-2838
DOI	10.1016/j.eururo.2020.07.037
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Zs.A 1247: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 294: Show issues

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Article ; Online: Re: Andrea Minervini, Marco Carini, Robert G. Uzzo, Riccardo Campi, Marc C. Smaldone, Alexander Kutikov. Standardized reporting of resection technique during nephron-sparing surgery: the surface-intermediate-base margin score. Eur Urol 2014;66:803-5.

Ficarra, Vincenzo / Palumbo, Vito / Kungulli, Afrovita / Giannarini, Gianluca

European urology

2015 Volume 67, Issue 3, Page(s) e45–7

MeSH term(s)	Humans ; Kidney Neoplasms/surgery ; Nephrectomy/standards ; Nephrons/surgery ; Organ Sparing Treatments/standards ; Research Design/standards ; Terminology as Topic
Language	English
Publishing date	2015-03
Publishing country	Switzerland
Document type	Comment ; Letter
ZDB-ID	193790-x
ISSN	1873-7560 ; 1421-993X ; 0302-2838
ISSN (online)	1873-7560 ; 1421-993X
ISSN	0302-2838
DOI	10.1016/j.eururo.2014.10.047
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Zs.A 1247: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 294: Show issues

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Article ; Online: Reply to Robert P. Myers' letter to the editor re: Francesco Montorsi, Timothy G. Wilson, Raymond C. Rosen, et al. best practices in robot-assisted radical prostatectomy: recommendations of the Pasadena consensus panel. Eur Urol 2012;62:368-81.

Ficarra, Vincenzo / Novara, Giacomo / Mottrie, Alexandre / Wilson, Timothy G / Montorsi, Francesco

European urology

2013 Volume 63, Issue 3, Page(s) e42–3

MeSH term(s)	Benchmarking/standards ; Humans ; Laparoscopy/standards ; Male ; Prostatectomy/standards ; Prostatic Neoplasms/surgery ; Robotics/standards ; Surgery, Computer-Assisted/standards
Language	English
Publishing date	2013-03
Publishing country	Switzerland
Document type	Comment ; Letter
ZDB-ID	193790-x
ISSN	1873-7560 ; 1421-993X ; 0302-2838
ISSN (online)	1873-7560 ; 1421-993X
ISSN	0302-2838
DOI	10.1016/j.eururo.2012.11.036
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Zs.A 1247: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: A Graph-Based Multi-Scale Approach With Knowledge Distillation for WSI Classification.

Bontempo, Gianpaolo / Bolelli, Federico / Porrello, Angelo / Calderara, Simone / Ficarra, Elisa

IEEE transactions on medical imaging

2024 Volume 43, Issue 4, Page(s) 1412–1421

Abstract: The usage of Multi Instance Learning (MIL) for classifying Whole Slide Images (WSIs) has recently increased. Due to their gigapixel size, the pixel-level annotation of such data is extremely expensive and time-consuming, practically unfeasible. For this ... ...

Abstract	The usage of Multi Instance Learning (MIL) for classifying Whole Slide Images (WSIs) has recently increased. Due to their gigapixel size, the pixel-level annotation of such data is extremely expensive and time-consuming, practically unfeasible. For this reason, multiple automatic approaches have been raised in the last years to support clinical practice and diagnosis. Unfortunately, most state-of-the-art proposals apply attention mechanisms without considering the spatial instance correlation and usually work on a single-scale resolution. To leverage the full potential of pyramidal structured WSI, we propose a graph-based multi-scale MIL approach, DAS-MIL. Our model comprises three modules: i) a self-supervised feature extractor, ii) a graph-based architecture that precedes the MIL mechanism and aims at creating a more contextualized representation of the WSI structure by considering the mutual (spatial) instance correlation both inter and intra-scale. Finally, iii) a (self) distillation loss between resolutions is introduced to compensate for their informative gap and significantly improve the final prediction. The effectiveness of the proposed framework is demonstrated on two well-known datasets, where we outperform SOTA on WSI classification, gaining a +2.7% AUC and +3.7% accuracy on the popular Camelyon16 benchmark.
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	622531-7
ISSN	1558-254X ; 0278-0062
ISSN (online)	1558-254X
ISSN	0278-0062
DOI	10.1109/TMI.2023.3337549
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Zs.A 2546: Show issues

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Article ; Online: MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge.

Pianfetti, Elena / Lovino, Marta / Ficarra, Elisa / Martignetti, Loredana

BMC bioinformatics

2023 Volume 24, Issue 1, Page(s) 443

Abstract: ... levels from the DNA sequence, exploiting the DNA sequence and gene features (e.g., number of exons ... TFs) and small RNAs (e.g., microRNAs - miRNAs). Recently, a convolutional neural network (CNN) model ...

Abstract	Messenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for understanding gene regulation, and various models (statistical and neural network-based) have been developed for this purpose. A few models predict mRNA expression levels from the DNA sequence, exploiting the DNA sequence and gene features (e.g., number of exons/introns, gene length). Other models include information about long-range interaction molecules (i.e., enhancers/silencers) and transcriptional regulators as predictive features, such as transcription factors (TFs) and small RNAs (e.g., microRNAs - miRNAs). Recently, a convolutional neural network (CNN) model, called Xpresso, has been proposed for mRNA expression level prediction leveraging the promoter sequence and mRNAs' half-life features (gene features). To push forward the mRNA level prediction, we present miREx, a CNN-based tool that includes information about miRNA targets and expression levels in the model. Indeed, each miRNA can target specific genes, and the model exploits this information to guide the learning process. In detail, not all miRNAs are included, only a selected subset with the highest impact on the model. MiREx has been evaluated on four cancer primary sites from the genomics data commons (GDC) database: lung, kidney, breast, and corpus uteri. Results show that mRNA level prediction benefits from selected miRNA targets and expression information. Future model developments could include other transcriptional regulators or be trained with proteomics data to infer protein levels.
MeSH term(s)	MicroRNAs/genetics ; RNA, Messenger/genetics ; Mirex ; Gene Expression Regulation ; Transcription Factors/genetics ; Gene Expression Profiling
Chemical Substances	MicroRNAs ; RNA, Messenger ; Mirex (Z917AN264P) ; Transcription Factors
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-023-05560-1
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Article ; Online: Predicting gene and protein expression levels from DNA and protein sequences with Perceiver.

Stefanini, Matteo / Lovino, Marta / Cucchiara, Rita / Ficarra, Elisa

Computer methods and programs in biomedicine

2023 Volume 234, Page(s) 107504

Abstract: ... The State-of-the-art models (e.g., Xpresso and Basenjii) predict mRNA levels exploiting Convolutional (CNN ...

Abstract	Background and objective: The functions of an organism and its biological processes result from the expression of genes and proteins. Therefore quantifying and predicting mRNA and protein levels is a crucial aspect of scientific research. Concerning the prediction of mRNA levels, the available approaches use the sequence upstream and downstream of the Transcription Start Site (TSS) as input to neural networks. The State-of-the-art models (e.g., Xpresso and Basenjii) predict mRNA levels exploiting Convolutional (CNN) or Long Short Term Memory (LSTM) Networks. However, CNN prediction depends on convolutional kernel size, and LSTM suffers from capturing long-range dependencies in the sequence. Concerning the prediction of protein levels, as far as we know, there is no model for predicting protein levels by exploiting the gene or protein sequences. Methods: Here, we exploit a new model type (called Perceiver) for mRNA and protein level prediction, exploiting a Transformer-based architecture with an attention module to attend to long-range interactions in the sequences. In addition, the Perceiver model overcomes the quadratic complexity of the standard Transformer architectures. This work's contributions are 1. DNAPerceiver model to predict mRNA levels from the sequence upstream and downstream of the TSS; 2. ProteinPerceiver model to predict protein levels from the protein sequence; 3. Protein&DNAPerceiver model to predict protein levels from TSS and protein sequences. Results: The models are evaluated on cell lines, mice, glioblastoma, and lung cancer tissues. The results show the effectiveness of the Perceiver-type models in predicting mRNA and protein levels. Conclusions: This paper presents a Perceiver architecture for mRNA and protein level prediction. In the future, inserting regulatory and epigenetic information into the model could improve mRNA and protein level predictions. The source code is freely available at https://github.com/MatteoStefanini/DNAPerceiver.
MeSH term(s)	Animals ; Mice ; DNA ; Neural Networks, Computer ; Algorithms ; Proteins/genetics ; RNA, Messenger/genetics
Chemical Substances	DNA (9007-49-2) ; Proteins ; RNA, Messenger
Language	English
Publishing date	2023-03-22
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2023.107504
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Zs.B 521: Show issues

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Article ; Online: LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.

Winkler, Jörg / Urgese, Gianvito / Ficarra, Elisa / Reinert, Knut

BMC bioinformatics

2022 Volume 23, Issue 1, Page(s) 18

Abstract: Background: The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson-Crick interactions between nucleotides. Hence, modern RNA alignment algorithms ... ...

Abstract	Background: The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson-Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results: We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions: With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.
MeSH term(s)	Algorithms ; Base Sequence ; Humans ; Nucleic Acid Conformation ; RNA/genetics ; Sequence Alignment ; Sequence Analysis, RNA ; Software
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-01-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04532-7
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Article ; Online: Incidence of Rectal Injury After Radical Prostatectomy: A Systematic Review and Meta-analysis.

Romito, Ilaria / Giannarini, Gianluca / Rossanese, Marta / Mucciardi, Giuseppe / Simonato, Alchiede / Ficarra, Vincenzo

European urology open science

2023 Volume 52, Page(s) 85–99

Abstract: Context: Rectal injury (RI) is a dreaded complication after radical prostatectomy (RP), increasing the risk of early postoperative complications, such as bleeding and severe infection/sepsis, and late sequelae, such as a rectourethral fistula (RUF). ... ...

Abstract	Context: Rectal injury (RI) is a dreaded complication after radical prostatectomy (RP), increasing the risk of early postoperative complications, such as bleeding and severe infection/sepsis, and late sequelae, such as a rectourethral fistula (RUF). Considering its traditionally low incidence, uncertainty remains as to predisposing risk factors and management. Objective: To examine the incidence of RI after RP in contemporary series and to propose a pragmatic algorithm for its management. Evidence acquisition: A systematic literature search was performed using the Medline and Scopus databases. Studies reporting data on RI incidence were selected. Subgroup analyses were conducted to assess the differential incidence by age, surgical approach, salvage RP after radiation therapy, and previous benign prostatic hyperplasia (BPH)-related surgery. Evidence synthesis: Eighty-eight, mostly retrospective noncomparative, studies were selected. The meta-analysis obtained a pooled RI incidence of 0.58% (95% confidence interval [CI] 0.46-0.73) in contemporary series with significant across-study heterogeneity (I Conclusions: RI is a rare, but potentially devastating, complication following RP. RI incidence was higher in patients ≥60 yr of age, and in those who underwent open/laparoscopic approach or salvage RP after radiation therapy. Intraoperative RI detection and repair apparently constitute the single most critical step to significantly decrease the risk of major postoperative complications and subsequent RUF formation. Conversely, intraoperatively undetected RI can lead more often to severe infective complications and RUF, the management of which remains poorly standardised and requires complex procedures. Patient summary: Accidental rectum tear is a rare, but potentially devastating, complication in men undergoing prostate removal for cancer. It occurs more often in patients aged 60 yr or older as well as in those who underwent prostate removal via an open/laparoscopic approach and/or prostate removal after radiation therapy for recurrent disease. Prompt identification and repair of this condition during the initial operation are the key to reduce further complications such as the formation of an abnormal opening between the rectum and the urinary tract.
Language	English
Publishing date	2023-05-04
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	3040546-4
ISSN	2666-1683 ; 2058-4881
ISSN (online)	2666-1683
ISSN	2058-4881
DOI	10.1016/j.euros.2023.03.017
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Article ; Online: A "test in-train out" program versus a "go home and walk" intervention for home-based exercise therapy in patients with peripheral artery disease: A randomized controlled trial.

Manfredini, Fabio / Traina, Luca / Ficarra, Valentina / Gandolfi, Giorgio / Argentoni, Antonio / Straudi, Sofia / Gasbarro, Vincenzo / Lamberti, Nicola

Scandinavian journal of medicine & science in sports

2024 Volume 34, Issue 2, Page(s) e14584

Abstract: Objective: In this single-blinded randomized controlled trial, we compared the "Test in-Train Out" structured home-based exercise program (TiTo-SHB) with the traditional "go home and walk" exercise intervention in people with peripheral artery disease ( ... ...

Abstract	Objective: In this single-blinded randomized controlled trial, we compared the "Test in-Train Out" structured home-based exercise program (TiTo-SHB) with the traditional "go home and walk" exercise intervention in people with peripheral artery disease (PAD). Methods: Peripheral artery disease patients at Leriche-Fontaine's stage II were randomized to receive TiTo-SHB or walking advice (C-WA). The TiTo-SHB group performed two daily 8-min sessions of pain-free interval walking at progressive low-to-moderate speed maintained with a metronome. The C-WA group was recommended to walk for 30 min at least three times per week and to endure claudication pain. Outcomes collected at baseline and at the end of the program (6 months) included: 6-min and pain-free walking distance (6MWD, PFWD), ankle-brachial index (ABI), 5-time sit-to-stand test (5STS), and health-related quality of life (HRQoL) by the VascuQoL-6 questionnaire. Results: A total of 68 patients were randomized (males n = 50; aged 73 ± 9; TiTo-SHB n = 34). At the end of the program, patients in the TiTo-SHB group compared with the C-WA group had significantly improved 6MWD (Δ + 60 ± 32 m vs. Δ - 5 ± 37 m; p < 0.001) and PFWD (Δ + 140 ± 92 m vs. Δ - 7 ± 87 m; p < 0.001). A significant between-group difference in favor of the TiTo-SHB group was also recorded for all the secondary outcomes, including 5STS (Δ - 2.6 ± 1.8 s vs. Δ + 0.8 ± 2.6 s; p < 0.001), ABI of the more impaired limb (Δ + 0.10 ± 0.11 vs. Δ + 0.02 ± 0.08; p = 0.003), and VascuQoL-6 score (Δ +2 ± 2 vs. -1 ± 4; p < 0.001). Conclusion: In PAD patients with claudication, the pain-free in-home TiTo-SHB program was more effective in improving exercise capacity and HRQoL than the traditional walking advice recommendation.
MeSH term(s)	Male ; Humans ; Female ; Quality of Life ; Peripheral Arterial Disease/therapy ; Intermittent Claudication/therapy ; Walking ; Exercise Therapy ; Treatment Outcome ; Walk Test
Language	English
Publishing date	2024-02-22
Publishing country	Denmark
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	1077418-x
ISSN	1600-0838 ; 0905-7188
ISSN (online)	1600-0838
ISSN	0905-7188
DOI	10.1111/sms.14584
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Zs.A 3247: Show issues

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Article ; Online: Implication of COVID-19 on Erythrocytes Functionality: Red Blood Cell Biochemical Implications and Morpho-Functional Aspects.

Russo, Annamaria / Tellone, Ester / Barreca, Davide / Ficarra, Silvana / Laganà, Giuseppina

International journal of molecular sciences

2022 Volume 23, Issue 4

Abstract: Several diseases (such as diabetes, cancer, and neurodegenerative disorders) affect the morpho-functional aspects of red blood cells, sometimes altering their normal metabolism. In this review, the hematological changes are evaluated, with particular ... ...

Abstract	Several diseases (such as diabetes, cancer, and neurodegenerative disorders) affect the morpho-functional aspects of red blood cells, sometimes altering their normal metabolism. In this review, the hematological changes are evaluated, with particular focus on the morphology and metabolic aspects of erythrocytes. Changes in the functionality of such cells may, in fact, help provide important information about disease severity and progression. The viral infection causes significant damage to the blood cells that are altered in size, rigidity, and distribution width. Lower levels of hemoglobin and anemia have been reported in several studies, and an alteration in the concentration of antioxidant enzymes has been shown to promote a dangerous state of oxidative stress in red blood cells. Patients with severe COVID-19 showed an increase in hematological changes, indicating a progressive worsening as COVID-19 severity progressed. Therefore, monitored hematological alterations in patients with COVID-19 may play an important role in the management of the disease and prevent the risk of a severe course of the disease. Finally, monitored changes in erythrocytes and blood, in general, may be one of the causes of the condition known as Long COVID.
MeSH term(s)	Anemia/virology ; Antiviral Agents/pharmacology ; COVID-19/blood ; COVID-19/complications ; COVID-19/diet therapy ; COVID-19/etiology ; COVID-19/metabolism ; Erythrocytes/metabolism ; Erythrocytes/pathology ; Erythrocytes/virology ; Hemoglobins/metabolism ; Hemolysis ; Humans ; Oxidative Stress
Chemical Substances	Antiviral Agents ; Hemoglobins
Language	English
Publishing date	2022-02-16
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23042171
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