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Article ; Online: Specific protein-RNA interactions are mostly preserved in biomolecular condensates.

de Vries, Tebbe / Novakovic, Mihajlo / Ni, Yinan / Smok, Izabela / Inghelram, Clara / Bikaki, Maria / Sarnowski, Chris P / Han, Yaning / Emmanouilidis, Leonidas / Padroni, Giacomo / Leitner, Alexander / Allain, Frédéric H-T

Science advances

2024 Volume 10, Issue 10, Page(s) eadm7435

Abstract: Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and ... ...

Abstract	Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
MeSH term(s)	Biomolecular Condensates ; Preservation, Biological ; Phase Separation ; RNA ; Ribonucleoproteins
Chemical Substances	RNA (63231-63-0) ; Ribonucleoproteins
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adm7435
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Book ; Online: Geo-didattiche per il futuro. La geografia alla prova delle competenze

Gilardi, Thomas / De Lucia, Rossella / Zanolin, Giacomo

2017

Abstract: This volume comes from the 4th National Workshop of the Italian Association of Geography Teachers (Milan, 26-27 August 2015) and proposes a reflection shared by scholars and teachers on the potentials and criticalities of teaching geography, facing the ... ...

Abstract	This volume comes from the 4th National Workshop of the Italian Association of Geography Teachers (Milan, 26-27 August 2015) and proposes a reflection shared by scholars and teachers on the potentials and criticalities of teaching geography, facing the present and the future of education
Keywords	Geography (General) ; Geology
Size	1 electronic resource ( p.)
Publisher	FrancoAngeli
Document type	Book ; Online
Note	Italian ; Open Access
HBZ-ID	HT020097905
ISBN	9788891756299 ; 8891756296
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Retrospective Investigation of Human Papillomavirus Cervical Infection and Lymphoma Incidence: A Clinical and Pathological Evaluation.

Gardella, Barbara / Dominoni, Mattia / Pasquali, Marianna Francesca / Gotti, Manuel / Fraticelli, Sara / Lucioni, Marco / Cesari, Stefania / Fiandrino, Giacomo / De Silvestri, Annalisa / Zerbi, Caterina / Lazic, Tanja / Arcaini, Luca / Paulli, Marco / Spinillo, Arsenio

Gynecologic and obstetric investigation

2024 Volume 89, Issue 2, Page(s) 95–102

Abstract: ... for neoplastic progression, and evidence suggests that regulatory T cells play an important role in the failure ... of viral elimination. Regulatory T cells may be involved in maintaining a microenvironment favourable ...

Abstract	Objective: Human papillomavirus (HPV) persistence is considered the main risk factor for neoplastic progression, and evidence suggests that regulatory T cells play an important role in the failure of viral elimination. Regulatory T cells may be involved in maintaining a microenvironment favourable for viral persistence and neoplasticity, through a deregulation of the local immune response. The association between altered immune function and the development of chronic infections, cancer (solid and haematological), and autoimmune diseases is documented in the literature. The purpose of this retrospective analysis was to evaluate the possible correlation between HPV cervical infection and lymphoma incidence in women attending colposcopy due to an abnormal Pap smear during a period of 15 years. Design: This is a cross-sectional study. Participants: We investigated retrospectively the incidence of haematological diseases in women aged 21-84 with an abnormal Pap smear who referred to our centre between 2004 and 2019. Setting: This study was conducted at the university hospital. Methods: In our analysis, we included women with diagnoses of HL and NHL after the detection of abnormal Pap smears and HPV infections. We excluded patients with a diagnosis of lymphoma preceding the date of the abnormal Pap smear and HPV test. Results: We divided the patients into two groups in order to analyse the standard incidence ratio (SIR): HL patients (19/7,064, 0.26%) and NHL patients (22/7,064, 0.31%). In our sample, we reported a significant risk of developing lymphoma compared to the general population, both for HL and NHL disease, at age <45 years. Regarding HL, the SIR of disease in women <45 years was 4.886 (95% CI 2.775-9.6029) and in women between 45 and 59 years was 2.612 (95% CI 0.96-7.108804). On the other hand, for NHL in women <45 years, we reported an SIR of about 3.007 (95%, CI 1.273-7.101575), in women aged 45-59 years, the SIR was 4.291 (95% CI 2.444-7.534399), and in women aged 60-74 years, the SIR was 3.283 (95% CI 1.054-10.22303). Limitations: This retrospective analysis was conducted in a single centre in Northern Italy and did not consider all interregional differences existing in the country in terms of HPV genotypes, ethnicity, and population characteristics. Regarding the analysis of SIR for HL and NHL, we did not divide the disease into subtypes because of the small sample of cases. Finally, we considered in our analysis only women with an abnormal Pap smear and not the general population. Conclusions: Women with chronic and persistent HPV infections may have a higher relative risk of developing lymphoma. This possible association may be caused by the deregulation of the immune system response against HPV and the failure of viral clearance, especially in younger women.
MeSH term(s)	Humans ; Female ; Middle Aged ; Papillomavirus Infections/complications ; Papillomavirus Infections/epidemiology ; Papillomavirus Infections/diagnosis ; Vaginal Smears ; Retrospective Studies ; Papanicolaou Test ; Uterine Cervical Neoplasms/pathology ; Cross-Sectional Studies ; Papillomaviridae/genetics ; Human Papillomavirus Viruses ; Lymphoma/epidemiology ; Uterine Cervical Dysplasia/pathology ; DNA, Viral/analysis ; Tumor Microenvironment
Chemical Substances	DNA, Viral
Language	English
Publishing date	2024-01-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	800003-7
ISSN	1423-002X ; 0378-7346
ISSN (online)	1423-002X
ISSN	0378-7346
DOI	10.1159/000535592
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Article ; Online: Postoperative Radiographic Outcomes Following Primary Open Coracoid Transfer (Bristow-Latarjet) Vary in Definition, Classification, and Imaging Modality: A Systematic Review.

DeClercq, Madeleine G / Martin, Maitland D / Whalen, Ryan J / Cote, Mark P / Midtgaard, Kaare S / Peebles, Liam A / Di Giacomo, Giovanni / Provencher, Matthew T

Arthroscopy : the journal of arthroscopic & related surgery : official publication of the Arthroscopy Association of North America and the International Arthroscopy Association

2023 Volume 40, Issue 4, Page(s) 1311–1324.e1

Abstract: Purpose: To analyze radiographic outcomes by conventional radiography, computed tomography (CT), or both and complication rates of open coracoid transfer at a minimum of 12-months follow-up.: Methods: A literature search was performed according to ... ...

Abstract	Purpose: To analyze radiographic outcomes by conventional radiography, computed tomography (CT), or both and complication rates of open coracoid transfer at a minimum of 12-months follow-up. Methods: A literature search was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, using PubMed, Medline (Ovid), and EMBASE library databases. Inclusion criteria were clinical studies reporting on open Latarjet as the primary surgical procedure(revision coracoid transfer after failed prior stabilization excluded) with postoperative radiographic outcomes at a minimum mean 1-year follow-up. Patient demographics, type of postoperative imaging modality, and radiographic outcomes and complications including graft union, osteoarthritis, and osteolysis were systematically reviewed. Data were summarized as ranges of reported values for each outcome metric. Each radiographic outcome was graphically represented in a Forest plot with point estimates of the incidence of radiographic outcomes with corresponding 95% confidence intervals and I Results: Thirty-three studies met inclusion criteria, with a total of 1,456 shoulders. The most common postoperative imaging modality was plain radiography only (n = 848 [58.2%]), both CT and radiography (n = 287 [19.7%]), and CT only (n = 321 [22.1%]). Overall, the reported graft union rate ranged from 75% to 100%, of which 79.8% (n = 395) were detected on plain radiography. The most common reported postoperative radiographic complications after the open coracoid transfer were osteoarthritis (range, 0%-100%, pooled mean 28%), graft osteolysis (range, 0%-100%, pooled mean 30%), nonunion (range, 0%-32%, pooled mean 5.1%), malpositioned graft (range, 0%-75%, pooled mean 14.75%), hardware issues (range, 0%-9.1%, pooled mean 5%), and bone block fracture (range, 0%-8%, pooled mean 2.1%). Graft healing was achieved in a majority of cases (range, 75%-100%). Conclusion: Postoperative radiographic outcomes after open coracoid transfer vary greatly in definition, classification, and imaging modality of choice. Greater consistency in postoperative radiographic outcomes is essential to evaluate graft healing, osteolysis, and nonunion. Level of evidence: Level IV, systematic review of Level III-IV studies.
MeSH term(s)	Humans ; Shoulder Joint/surgery ; Osteolysis ; Joint Instability/surgery ; Shoulder/surgery ; Shoulder Dislocation/surgery ; Osteoarthritis/diagnostic imaging ; Osteoarthritis/surgery ; Osteoarthritis/complications ; Fractures, Bone/complications ; Coracoid Process/surgery ; Coracoid Process/transplantation
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	632528-2
ISSN	1526-3231 ; 0749-8063
ISSN (online)	1526-3231
ISSN	0749-8063
DOI	10.1016/j.arthro.2023.09.032
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Article ; Online: Intraspecific variability of leaf form and function across habitat types.

Puglielli, Giacomo / Bricca, Alessandro / Chelli, Stefano / Petruzzellis, Francesco / Acosta, Alicia T R / Bacaro, Giovanni / Beccari, Eleonora / Bernardo, Liliana / Bonari, Gianmaria / Bolpagni, Rossano / Boscutti, Francesco / Calvia, Giacomo / Campetella, Giandiego / Cancellieri, Laura / Canullo, Roberto / Carbognani, Michele / Carboni, Marta / Carranza, Maria Laura / Castellani, Maria Beatrice /

Ciccarelli, Daniela / Coppi, Andrea / Cutini, Maurizio / Dalla Vecchia, Alice / Dalle Fratte, Michele / de Francesco, Maria Carla / De Frenne, Pieter / De Sanctis, Michele / de Simone, Leopoldo / Di Cecco, Valter / Fanelli, Giuliano / Farris, Emmanuele / Ferrara, Arianna / Fenu, Giuseppe / Filibeck, Goffredo / Gasperini, Cristina / Gargano, Domenico / Kindermann, Elisabeth / La Bella, Greta / Lastrucci, Lorenzo / Lazzaro, Lorenzo / Maccherini, Simona / Marignani, Michela / Mugnai, Michele / Naselli-Flores, Luigi / Passalacqua, Nicodemo Giuseppe / Pavanetto, Nicola / Petraglia, Alessandro / Rota, Francesco / Santoianni, Lucia Antonietta / Schettino, Aldo / Selvi, Federico / Stanisci, Angela / Trotta, Giacomo / Vangansbeke, Pieter / Varricchione, Marco / Vuerich, Marco / Wellstein, Camilla / Tordoni, Enrico

Ecology letters

2024 Volume 27, Issue 3, Page(s) e14396

Abstract: Trait-based ecology has already revealed main independent axes of trait variation defining trait spaces that summarize plant adaptive strategies, but often ignoring intraspecific trait variability (ITV). By using empirical ITV-level data for two ... ...

Abstract	Trait-based ecology has already revealed main independent axes of trait variation defining trait spaces that summarize plant adaptive strategies, but often ignoring intraspecific trait variability (ITV). By using empirical ITV-level data for two independent dimensions of leaf form and function and 167 species across five habitat types (coastal dunes, forests, grasslands, heathlands, wetlands) in the Italian peninsula, we found that ITV: (i) rotated the axes of trait variation that define the trait space; (ii) increased the variance explained by these axes and (iii) affected the functional structure of the target trait space. However, the magnitude of these effects was rather small and depended on the trait and habitat type. Our results reinforce the idea that ITV is context-dependent, calling for careful extrapolations of ITV patterns across traits and spatial scales. Importantly, our study provides a framework that can be used to start integrating ITV into trait space analyses.
MeSH term(s)	Ecosystem ; Forests ; Plant Leaves ; Phenotype ; Ecology
Language	English
Publishing date	2024-03-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1441608-6
ISSN	1461-0248 ; 1461-023X
ISSN (online)	1461-0248
ISSN	1461-023X
DOI	10.1111/ele.14396
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Article: Functionalization with Polyphenols of a Nano-Textured Ti Surface through a High-Amino Acid Medium: A Chemical-Physical and Biological Characterization.

Scannavino, Rafaella C P / Riccucci, Giacomo / Ferraris, Sara / Duarte, Gabriel L C / de Oliveira, Paulo T / Spriano, Silvia

Nanomaterials (Basel, Switzerland)

2022 Volume 12, Issue 17

Abstract: The study aimed to identify an effective mechanism of adsorption of polyphenols on a nano-textured Ti surface and to evaluate the osteogenic differentiation on it. The source of polyphenols was a natural extract from red grape pomace. A chemical etching ... ...

Abstract	The study aimed to identify an effective mechanism of adsorption of polyphenols on a nano-textured Ti surface and to evaluate the osteogenic differentiation on it. The source of polyphenols was a natural extract from red grape pomace. A chemical etching was used to form an oxide layer with a nanoscale texture on Ti; this layer is hydrophilic, but without hydroxyl groups with high acidic-basic chemical reactivity. The samples were characterized by electron and fluorescence microscopies, UV-Vis spectroscopy, contact angle measurements, zeta potential titration curves, and Folin-Ciocâlteu test. The presence of an adsorbed layer of polyphenols on the functionalized surface, maintaining redox ability, was confirmed by several tests. Consistent with the surface features, the adsorption was maximized by dissolving the extract in a high-amino acid medium, with respect to an inorganic solution, exploiting the high affinity of amino acids for polyphenols and for porous titanium surfaces. The osteogenic differentiation was assessed on an osteoblastic cell line by immunofluorescence, cell viability, expression of key osteoblast markers, and extracellular matrix mineralization. The surfaces functionalized with the extract diluted in the range 1 × 10
Language	English
Publishing date	2022-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano12172916
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Article ; Online: Early histologic findings of pulmonary SARS-CoV-2 infection detected in a surgical specimen.

Pernazza, Angelina / Mancini, Massimiliano / Rullo, Emma / Bassi, Massimiliano / De Giacomo, Tiziano / Rocca, Carlo Della / d'Amati, Giulia

Virchows Archiv : an international journal of pathology

2020 Volume 477, Issue 5, Page(s) 743–748

Abstract: ... within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T ...

Abstract	Despite the current pandemic season, reports on pathologic features of coronavirus disease 19 (Covid-19) are exceedingly rare at the present time. Here we describe the pathologic features of early lung involvement by Covid-19 in a surgical sample resected for carcinoma from a patient who developed SARS-CoV-2 infection soon after surgery. The main histologic findings observed were pneumocyte damage, alveolar hemorrhages with clustering of macrophages, prominent and diffuse neutrophilic margination within septal vessels, and interstitial inflammatory infiltrates, mainly represented by CD8+ T lymphocytes. These features are similar to those previously described in SARS-CoV-1 infection. Subtle histologic changes suggestive pulmonary involvement by Covid-19 may be accidentally encountered in routine pathology practice, especially when extensive sampling is performed for histology. These findings should be carefully interpreted in light of the clinical context of the patient and could prompt a pharyngeal swab PCR test to rule out the possibility of SARS-CoV-2 infection in asymptomatic patients.
MeSH term(s)	Adenocarcinoma/pathology ; Adenocarcinoma/surgery ; Adenocarcinoma/virology ; Betacoronavirus/isolation & purification ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Coronavirus Infections/diagnosis ; Coronavirus Infections/etiology ; Coronavirus Infections/pathology ; Humans ; Lung/pathology ; Lung/surgery ; Lung/virology ; Lung Neoplasms/pathology ; Lung Neoplasms/surgery ; Lung Neoplasms/virology ; Male ; Middle Aged ; Pandemics ; Pneumonectomy ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/etiology ; Pneumonia, Viral/pathology ; Postoperative Complications/diagnosis ; Postoperative Complications/pathology ; Postoperative Complications/virology ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-04-30
Publishing country	Germany
Document type	Case Reports ; Journal Article
ZDB-ID	1184867-4
ISSN	1432-2307 ; 0945-6317
ISSN (online)	1432-2307
ISSN	0945-6317
DOI	10.1007/s00428-020-02829-1
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Article ; Online: Functionalization with Polyphenols of a Nano-Textured Ti Surface through a High–Amino Acid Medium

Rafaella C. P. Scannavino / Giacomo Riccucci / Sara Ferraris / Gabriel L. C. Duarte / Paulo T. de Oliveira / Silvia Spriano

Nanomaterials, Vol 12, Iss 2916, p

A Chemical–Physical and Biological Characterization

2022 Volume 2916

Abstract	The study aimed to identify an effective mechanism of adsorption of polyphenols on a nano-textured Ti surface and to evaluate the osteogenic differentiation on it. The source of polyphenols was a natural extract from red grape pomace. A chemical etching was used to form an oxide layer with a nanoscale texture on Ti; this layer is hydrophilic, but without hydroxyl groups with high acidic–basic chemical reactivity. The samples were characterized by electron and fluorescence microscopies, UV–Vis spectroscopy, contact angle measurements, zeta potential titration curves, and Folin–Ciocâlteu test. The presence of an adsorbed layer of polyphenols on the functionalized surface, maintaining redox ability, was confirmed by several tests. Consistent with the surface features, the adsorption was maximized by dissolving the extract in a high–amino acid medium, with respect to an inorganic solution, exploiting the high affinity of amino acids for polyphenols and for porous titanium surfaces. The osteogenic differentiation was assessed on an osteoblastic cell line by immunofluorescence, cell viability, expression of key osteoblast markers, and extracellular matrix mineralization. The surfaces functionalized with the extract diluted in the range 1 × 10 −5 –1 mg/mL resulted in having a greater osteogenic activity for the highest concentration, with lower values of cell viability; higher expression of alkaline phosphatase, bone sialoprotein, and collagen; and lower levels of osteopontin. In conclusion, the functionalization of a nano-textured Ti surface with polyphenols can potentially favor the osteogenic activity of osseointegrated implants.
Keywords	titanium ; functionalization ; polyphenols ; implants ; Chemistry ; QD1-999
Subject code	500
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Adversarial robustness guarantees for random deep neural networks

De Palma, Giacomo / Kiani, Bobak T. / Lloyd, Seth

2020

Abstract: The reliability of most deep learning algorithms is fundamentally challenged by the existence of adversarial examples, which are incorrectly classified inputs that are extremely close to a correctly classified input. We study adversarial examples for ... ...

Abstract	The reliability of most deep learning algorithms is fundamentally challenged by the existence of adversarial examples, which are incorrectly classified inputs that are extremely close to a correctly classified input. We study adversarial examples for deep neural networks with random weights and biases and prove that the $\ell^1$ distance of any given input from the classification boundary scales at least as $\sqrt{n}$, where $n$ is the dimension of the input. We also extend our proof to cover all the $\ell^p$ norms. Our results constitute a fundamental advance in the study of adversarial examples, and encompass a wide variety of architectures, which include any combination of convolutional or fully connected layers with skipped connections and pooling. We validate our results with experiments on both random deep neural networks and deep neural networks trained on the MNIST and CIFAR10 datasets. Given the results of our experiments on MNIST and CIFAR10, we conjecture that the proof of our adversarial robustness guarantee can be extended to trained deep neural networks. This extension will open the way to a thorough theoretical study of neural network robustness by classifying the relation between network architecture and adversarial distance.
Keywords	Statistics - Machine Learning ; Condensed Matter - Disordered Systems and Neural Networks ; Computer Science - Machine Learning ; Mathematical Physics ; Quantum Physics
Subject code	006
Publishing date	2020-04-13
Publishing country	us
Document type	Book ; Online
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Article: A Rare Case of Coexisting Breast Cancer and Refractory Acute Myeloid Leukemia.

Ballotta, L / Trisolini, S M / Iori, A P / La Rocca, U / Micozzi, A / Gentile, G / De Giacomo, T / Guarini, A / Foà, R / Capria, S

Case reports in hematology

2020 Volume 2020, Page(s) 8893185

Abstract: The occurrence of acute myeloid leukemia (AML) within six months from a diagnosis of breast cancer (BC) is rarely reported in the literature, and it is associated with a poor prognosis. We report herein the case of a 40-year-old woman referred to our ... ...

Abstract	The occurrence of acute myeloid leukemia (AML) within six months from a diagnosis of breast cancer (BC) is rarely reported in the literature, and it is associated with a poor prognosis. We report herein the case of a 40-year-old woman referred to our centre affected by BC and simultaneous AML. The patient proved refractory to first line therapy and achieved complete remission (CR) with a clofarabine-based regimen followed by allogeneic stem cell transplantation (ASCT). Both during salvage chemotherapy and after ASCT, the patient presented severe infectious complications ( acute cholecistytis and
Language	English
Publishing date	2020-08-25
Publishing country	United States
Document type	Case Reports
ZDB-ID	2627639-2
ISSN	2090-6579 ; 2090-6560
ISSN (online)	2090-6579
ISSN	2090-6560
DOI	10.1155/2020/8893185
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