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Clique Counting in MapReduce

Irene Finocchi, Marco Finocchi, Emanuele G. Fusco
2015 ACM Journal of Experimental Algorithmics  
We tackle the problem of counting the number of k-cliques in large-scale graphs, for any constant k > 3. Clique counting is essential in a variety of applications, among which social network analysis. Due to its computationally intensive nature, we settle for parallel solutions in the MapReduce framework, which has become in the last few years a de facto standard for batch processing of massive data sets. We give both theoretical and experimental contributions. On the theory side, we design the
more » ... first exact scalable algorithm for counting (and listing) k-cliques. Our algorithm uses O(m^3/2) total space and O(m^k/2) work, where m is the number of graph edges. This matches the best-known bounds for triangle listing when k=3 and is work-optimal in the worst case for any k, while keeping the communication cost independent of k. We also design a sampling-based estimator that can dramatically reduce the running time and space requirements of the exact approach, while providing very accurate solutions with high probability. We then assess the effectiveness of different clique counting approaches through an extensive experimental analysis over the Amazon EC2 platform, considering both our algorithms and their state-of-the-art competitors. The experimental results clearly highlight the algorithm of choice in different scenarios and prove our exact approach to be the most effective when the number of k-cliques is large, gracefully scaling to non-trivial values of k even on clusters of small/medium size. Our approximation algorithm achieves extremely accurate estimates and large speedups, especially on the toughest instances for the exact algorithms. As a side effect, our study also sheds light on the number of k-cliques of several real-world graphs, mainly social networks, and on its growth rate as a function of k.
doi:10.1145/2794080 fatcat:hjibwlgr5za75dbcz3hymkavsy

Quantum versus classical protons in pure and salty ice under pressure

Yael Bronstein, Philippe Depondt, Livia E. Bove, Richard Gaal, Antonino Marco Saitta, Fabio Finocchi
2016 Physical review B  
It is generally accepted that nuclear quantum effects (NQEs) trigger the transition to the nonmolecular form of ice under increasing pressure. This picture is challenged in salty ice, where Raman scattering measurements up to 130 GPa of molecular ice VII containing NaCl or LiCl impurities show that the transition pressure to the symmetric phase ice X is shifted up by about 30 GPa, even at small salt concentrations. We address the question of how the inclusion of salt induces the drastic
more » ... n of NQEs by selectively including NQEs in ab initio calculations of ice in the presence of distinct ionic impurities. We quantitatively show that this is mainly a consequence of the electric field generated by the ions. We propose a simple model that is able to capture the essence of this phenomenon, generalizing this picture to other charged defects and for any concentration. This result is potentially generalizable to most "dirty" ices in which the electric field due to the doping is much more significant than local lattice distortions. Ice under extreme conditions is present in many planets, both within our solar system [1] and beyond [2] . These ices are usually "dirty": Planetary real ices unavoidably contain impurities such as salt. In pure ice, nuclear quantum effects (NQEs) play a crucial role by drastically decreasing the VII-X phase transition pressure [3, 4] . However, recent experiments question the role of NQEs in LiCl-doped ice [5] . Whether this is specific to LiCl ice and the mechanism by which the quantum behavior of the protons can be hindered is still an issue. At high pressure, the two molecular phases of ice, proton disordered ice VII and proton ordered ice VIII [6,7], transform to ice X, the only known atomic phase of ice. Below the transition, the oxygens form a body-centered-cubic structure, and the hydrogen bonds are characterized by a prototypical double-well proton transfer potential. As the atoms get closer under the effect of increasing pressure, the intrinsic quantum nature of the protons produces more evident effects and favors the onset of quantum tunneling. Upon further reducing the distance between oxygens, the proton potential degenerates into a single-well potential [8] , giving rise to a symmetric hydrogen bond, where the hydrogen is located midway between two neighboring O atoms. By including NQEs, the transition pressure P t is drastically reduced from about 90 GPa as classically predicted [9] to approximately 60 GPa [10] [11] [12] [13] [14] [15] [16] , that is, the pressure for which the zero-point energy equals the barrier height [3, 4] . However, the effect of a perturbation on a prototype of structural quantum effects in crystals is not a priori trivial from a fundamental point of view. Recent studies [5] on LiCl-water solutions at different salt to water ratios pointed out that the properties of ice change drastically when LiCl salt is homogeneously included into ice VII and that the transition pressure to the phase X strongly depends on the presence of ionic impurities. Here, we report high resolution Raman scattering experiments on NaCl ice up to Mbar pressures. These challenging conditions have been achieved by the use of a diamond anvil cell equipped with extra low-fluorescence synthetic diamonds and by fast quenching of a 5 μm droplet of 2% NaCl water solution in order to produce ice VII-doped ice following the procedure described in the Supplemental Material [5, 17, 18] . The upper panel of Fig. 1 shows the 200-1000 cm −1 region of the Raman spectra recorded at different pressures up to 130 GPa. The oxygen-oxygen T 2g vibrational mode, which is indicative of the cupritelike structure of phase X, clearly appears at 87 ± 5 GPa, similarly to what is observed in LiCl ice [5] . Thus, the presence of small quantities of salt impurities (here, 1 NaCl for 53 H 2 O), which is likely in natural ices, shifts P t by about 30 GPa, roughly the same pressure shift as observed when quantum effects are neglected in pure ice [3, 4] . This observation confirms that the measured shift of P t in LiCl ice is actually a general effect of ionic impurities on the ice lattice. We address this issue by comparing simulations that do or do not include NQEs and quantify their impact on the transition. The first kinds of calculations are done via quantum thermal bath ab initio molecular dynamics (QTB-AIMD) [19, 20] ; this semiclassical approximation quantitatively describes the VII-X transition in pure ice [4] . The second kinds of calculations are standard ab initio molecular dynamics (AIMD). In both cases, the atomic forces are computed within the density functional theory (DFT), via the generalized gradient approximation [21] , as implemented in the QUANTUM ESPRESSO package [22] . Simulations including NaCl or LiCl impurities were run over a time length of about 25 ps with a 0.484 fs integration time step. Our simulation cell contains 53 water molecules and one LiCl or NaCl pair, corresponding to a concentration of 2% mol. The Li + ion is small enough to occupy an interstitial site within the oxygen lattice, while Cl − is substituted for a water molecule [17] . Two configurations are considered in our calculations for the larger Na + cation: an interstitial site (I), as for Li + , and a substitutional site (S), where Na + replaces a water molecule, as does Cl − (the method and initial configurations are described in the Supplemental Material). The incorporation of salt has non-negligible effects on the hydrogen bonds, as shown by the OH pair correlation function (PCF) (see the figure and related description in the Supplemental Material). In particular, the first peak of the 2469-9950/2016/93(2)/024104 (5) 024104-1
doi:10.1103/physrevb.93.024104 fatcat:x4dsg56gmnhabixrh3tvc5dhmm

Bronchogenic cyst of the ileal mesentery: a case report and a review of literature

Adolfo Petrina, Carlo Boselli, Roberto Cirocchi, Piero Covarelli, Emilio Eugeni, Marco Badolato, Luigi Finocchi, Stefano Trastulli, Giuseppe Noya
2010 Journal of Medical Case Reports  
Bronchogenic cyst is a rare clinical entity that occurs due to abnormal development of the foregut; the majority of bronchogenic cysts have been described in the mediastinum and they are rarely found in an extrathoracic location. Case presentation: We describe the case of an intra-abdominal bronchogenic cyst of the mesentery, incidentally discovered during an emergency laparotomy for a perforated gastric ulcer in a 33-year-old Caucasian man. Conclusions: Bronchogenic cyst should be considered
more » ... the differential diagnosis of subdiaphragmatic masses, even in an intraperitoneal location.
doi:10.1186/1752-1947-4-313 pmid:20863380 pmcid:PMC2955622 fatcat:4btdsy4tcbdyrmmeqebp6cazry

Colo-rectal cancer (CRC) in elderly patient: anagraphical age as not a determinant key for a radical surgery

Adolfo Petrina, Luigi Finocchi, Carla Cini, Marco Badolato, Carlo Boselli, Fabio Rondelli, Giuseppe Noya
2009 BMC Geriatrics  
Purpose To determine whether the biological age of the patient and ASA score are discriminatory for a radical surgical approach in colo-rectal cancer. Materials and methods Monocentric and mono-surgeon case record about 135 patients undergoing surgery for CRC between June 2004 and April 2008. Patients were divided into two groups (see Table 1 ): (A: <70 years, n = 44, 27 and ǩ = Ǩ = 17; B:>= 70 years, n = 91, ǩ and Ǩ = 49 = 42) comparing clinical, surgical and pathological data. We examined and
more » ... compared range of age and average age, ASA score, the average time of hospitalization, the postoperative complications (major and minor), mortality at 30 days and during the follow-up (in progress). Results The average age of group A is 59.6 years (range 41-69); for Group B it is 78.6 years (range 70-96). Oncological radicality was achieved in 41 (93%) and 76 (83%) patients respectively in groups A and B; ASA score was distributed in this way in Group A: I = 2, II = 40, III = 2 and IV = 1, so in Group B: I = 1, II = 23, III and IV = 54 = 13. The average time of hospitalization was of 11.7 days (range 4-24 days) in Group A and 10.16 days (range 1-29 days) in Group B.
doi:10.1186/1471-2318-9-s1-a64 pmcid:PMC4291004 fatcat:jcu4f7or25d5rfqti37gn5vr7a

Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001)

Sara Laporte, Fabio Finocchi, Lorenzo Paulatto, Marc Blanchard, Etienne Balan, François Guyot, Antonino Marco Saitta
2015 Physical Chemistry, Chemical Physics - PCCP  
We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field.
doi:10.1039/c5cp02097b pmid:26193818 fatcat:x7yvfgeod5a4ljnfmeryv6jjsm

Pancytopenia and severe sepsis in an adult case of congenital X-linked agammaglobulinemia (XLA)

Andrea Tendas, Pasquale Niscola, Teresa Dentamaro, Luca Cupelli, Gigliola Di Matteo, Andrea Finocchi, Agostina Siniscalchi, Stefano Fratoni, Teresa Scimò, Laura Scaramucci, Marco Giovannini, Micaela Ales (+2 others)
2010 Annals of Hematology  
et al.. Pancytopenia and severe sepsis in an adult case of congenital X-linked agammaglobulinemia (XLA).
doi:10.1007/s00277-009-0891-7 pmid:20077117 fatcat:3hvxsg7gcbhybearcuvmddg3mq

The Use of Botulinum Toxin A as an Adjunctive Therapy in the Management of Chronic Musculoskeletal Pain: A Systematic Review with Meta-Analysis

Simone Battista, Luca Buzzatti, Marialuisa Gandolfi, Cinzia Finocchi, Luca Falsiroli Maistrello, Antonello Viceconti, Benedetto Giardulli, Marco Testa
2021 Toxins  
Several studies have investigated the effect of botulinum toxin A (BoNT-A) for managing chronic musculoskeletal pain, bringing contrasting results to the forefront. Thus far, however, there has been no synthesis of evidence on the effect of BoNT-A as an adjunctive treatment within a multimodal approach. Hence, Medline via PubMed, EMBASE, and the Cochrane Library-CENTRAL were searched until November 2020 for randomised controlled trials (RCTs) that investigated the use of BoNT-A as an adjunctive
more » ... therapy for chronic musculoskeletal pain. The risk of bias (RoB) and the overall quality of the studies were assessed through RoB 2.0 and the GRADE approach, respectively. Meta-analysis was conducted to analyse the pooled results of the six included RCTs. Four were at a low RoB, while two were at a high RoB. The meta-analysis showed that BoNT-A as an adjunctive therapy did not significantly decrease pain compared to the sole use of traditional treatment (SDM −0.89; 95% CI −1.91; 0.12; p = 0.08). Caution should be used when interpreting such results, since the studies displayed very high heterogeneity (I = 94%, p < 0.001). The overall certainty of the evidence was very low. The data retrieved from this systematic review do not support the use of BoNT-A as an adjunctive therapy in treating chronic musculoskeletal pain.
doi:10.3390/toxins13090640 pmid:34564644 pmcid:PMC8473399 fatcat:fpmvx2thc5eqhf5d2m6yiee24y

The Interplay between CD27dull and CD27bright B Cells Ensures the Flexibility, Stability, and Resilience of Human B Cell Memory

Ola Grimsholm, Eva Piano Mortari, Alexey N. Davydov, Mikhail Shugay, Anna S. Obraztsova, Chiara Bocci, Emiliano Marasco, Valentina Marcellini, Alaitz Aranburu, Chiara Farroni, Domenico Alessandro Silvestris, Cristina Cristofoletti (+21 others)
2020 Cell Reports  
., Marco Scarsella, A.A., C.B., Cristina Cristofoletti, C.F., E.M., E.P.M., O.G., S.B., and Valentina Marcellini carried out experiments.  ... 
doi:10.1016/j.celrep.2020.02.022 pmid:32130900 fatcat:jieyitv6kfdc3nfrwzvcm5nyyy

Preclinical Safety and Efficacy of Human CD34+ Cells Transduced With Lentiviral Vector for the Treatment of Wiskott-Aldrich Syndrome

Samantha Scaramuzza, Luca Biasco, Anna Ripamonti, Maria C Castiello, Mariana Loperfido, Elena Draghici, Raisa J Hernandez, Fabrizio Benedicenti, Marina Radrizzani, Monica Salomoni, Marco Ranzani, Cynthia C Bartholomae (+12 others)
2013 Molecular Therapy  
Gene therapy with ex vivo-transduced hematopoietic stem/progenitor cells may represent a valid therapeutic option for monogenic immunohematological disorders such as Wiskott-Aldrich syndrome (WAS), a primary immunodeficiency associated with thrombocytopenia. We evaluated the preclinical safety and efficacy of human CD34(+) cells transduced with lentiviral vectors (LV) encoding WAS protein (WASp). We first set up and validated a transduction protocol for CD34(+) cells derived from bone marrow
more » ... ) or mobilized peripheral blood (MPB) using a clinical grade, highly purified LV. Robust transduction of progenitor cells was obtained in normal donors and WAS patients' cells, without evidence of toxicity. To study biodistribution of human cells and exclude vector release in vivo, LV-transduced CD34(+) cells were transplanted in immunodeficient mice, showing a normal engraftment and differentiation ability towards transduced lymphoid and myeloid cells in hematopoietic tissues. Vector mobilization to host cells and transmission to germline cells of the LV were excluded by different molecular assays. Analysis of vector integrations showed polyclonal integration patterns in vitro and in human engrafted cells in vivo. In summary, this work establishes the preclinical safety and efficacy of human CD34(+) cells gene therapy for the treatment of WAS.
doi:10.1038/mt.2012.23 pmid:22371846 pmcid:PMC3538318 fatcat:tlsxjafgf5aarmnhjdmc3ear3y

Shift from intravenous or 16% subcutaneous replacement therapy to 20% subcutaneous immunoglobulin in patients with primary antibody deficiencies

Clementina Canessa, Jessica Iacopelli, Antonio Pecoraro, Giuseppe Spadaro, Andrea Matucci, Cinzia Milito, Alessandra Vultaggio, Carlo Agostini, Francesco Cinetto, Maria Giovanna Danieli, Simona Gambini, Carolina Marasco (+13 others)
2016 International Journal of Immunopathology and Pharmacology  
In patients with primary antibody deficiencies, subcutaneous administration of IgG (SCIG) replacement is effective, safe, well-tolerated, and can be self-administered at home. A new SCIG replacement at 20% concentration (Hizentra ® ) has been developed and has replaced Vivaglobin ® (SCIG 16%). An observational prospective multi-centric open-label study, with retrospective comparison was conducted in 15 Italian centers, in order to investigate whether and to what extent switching to Hizentra ® would affect frequency of
doi:10.1177/0394632016681577 pmid:27927705 pmcid:PMC5806788 fatcat:4u5rxpstkzaklfl4fqbhddqqni

Galcanezumab for the prevention of high frequency episodic and chronic migraine in real life in Italy: a multicenter prospective cohort study (the GARLIT study)

Fabrizio Vernieri, Claudia Altamura, Nicoletta Brunelli, Carmelina Maria Costa, Cinzia Aurilia, Gabriella Egeo, Luisa Fofi, Valentina Favoni, Giulia Pierangeli, Carlo Lovati, Marco Aguggia, Florindo d'Onofrio (+10 others)
2021 The Journal of Headache and Pain  
The clinical benefit of galcanezumab, demonstrated in randomized clinical trials (RCTs), remains to be quantified in real life. This study aimed at evaluating the effectiveness, safety and tolerability of galcanezumab in the prevention of high-frequency episodic migraine (HFEM) and chronic migraine (CM) in a real-life setting. This multicenter prospective observational cohort study was conducted between November 2019 and January 2021 at 13 Italian headache centers. Consecutive adult HFEM and CM
more » ... patients clinically eligible were enrolled and treated with galcanezumab subcutaneous injection 120 mg monthly with the first loading dose of 240 mg. The primary endpoint was the change in monthly migraine days (MMDs) in HFEM and monthly headache days (MHDs) in CM patients after 6 months of therapy (V6). Secondary endpoints were the Numerical Rating Scale (NRS), monthly painkiller intake (MPI), HIT-6 and MIDAS scores changes, ≥50% responder rates (RR), the conversion rate from CM to episodic migraine (EM) and Medication Overuse (MO) discontinuation. One hundred sixty-three patients (80.5% female, 47.1 ± 11.7 years, 79.8% CM) were included. At V6, MMDs reduced by 8 days in HFEM and MHDs by 13 days in CM patients (both p < .001). NRS, MPI, HIT-6 and MIDAS scores significantly decreased (p < .001). Ten patients (6.1%) dropped out for inefficacy and classified as non-responders. Patients with ≥50%RRs, i.e. responders, were 76.5% in the HFEM and 63.5% in the CM group at V6. Among CM patients, the V6 responders presented a lower body mass index (p = .018) and had failed a lower number of preventive treatments (p = .013) than non-responders. At V6, 77.2% of CM patients converted to EM, and 82.0% ceased MO. Adverse events, none serious, were reported in up to 10.3% of patients during evaluation times. Galcanezumab in real life was safe, well tolerated and seemed more effective than in RCTs. Normal weight and a low number of failed preventives were positively associated with galcanezumab effectiveness in CM patients. NCT04803513 .
doi:10.1186/s10194-021-01247-1 pmid:33941080 fatcat:6ehprdyxenev3lrzarut5w2d4a

Corrigendum: Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies

Cristina Cifaldi, Immacolata Brigida, Federica Barzaghi, Matteo Zoccolillo, Valentina Ferradini, Davide Petricone, Maria Pia Cicalese, Dejan Lazarevic, Davide Cittaro, Maryam Omrani, Enrico Attardi, Francesca Conti (+28 others)
2019 Frontiers in Immunology  
Attardi, Conti, Scarselli, Chiriaco, Di Cesare, Licciardi, Davide, Ferrua, Canessa, Pignata, Giliani, Ferrari, Fousteri, Barera, Merli, Palma, Cesaro, Gattorno, Trizzino, Moschese, Chini, Villa, Azzari, Finocchi  ... 
doi:10.3389/fimmu.2019.01184 pmid:31214169 pmcid:PMC6554535 fatcat:vklizxv34naz7bijlig3mg2ziq

Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies

Cristina Cifaldi, Immacolata Brigida, Federica Barzaghi, Matteo Zoccolillo, Valentina Ferradini, Davide Petricone, Maria Pia Cicalese, Dejan Lazarevic, Davide Cittaro, Maryam Omrani, Enrico Attardi, Francesca Conti (+28 others)
2019 Frontiers in Immunology  
Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders. Objective: To evaluate the strength and
more » ... akness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes. Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology. Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage. Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
doi:10.3389/fimmu.2019.00316 pmid:31031743 pmcid:PMC6470723 fatcat:5igicvjjhbbcthzeznyqenhekm

Tavola rotonda Metaromanzo e romanzo editoriale

Marco Bazzocchi, Alberto Cadioli, Laura Di Nicola, Claudio Milanini, Elisabetta Mondello, Luisa Finocchi, Paolo Giovannetti, Marina Paino, Stefano Giovannuzzi, Clelia Martignoni, Bruno Falcetto
Marco Bazzocchi Università degli Studi di Bologna Rispondo molto velocemente a Bruno Falcetto.  ...  Volevo segnalare però due cose, tenendo sullo sfondo le riflessioni che faceva Marco Bazzocchi poco fa.  ... 
doi:10.13130/2037-2426/14875 fatcat:7wsvoy22jzc6lhaebn34omf4oa

A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function

Michael T. Lam, Simona Coppola, Oliver H.F. Krumbach, Giusi Prencipe, Antonella Insalaco, Cristina Cifaldi, Immacolata Brigida, Erika Zara, Serena Scala, Silvia Di Cesare, Simone Martinelli, Martina Di Rocco (+48 others)
2019 Journal of Experimental Medicine  
Hemophagocytic lymphohistiocytosis (HLH) is characterized by immune dysregulation due to inadequate restraint of overactivated immune cells and is associated with a variable clinical spectrum having overlap with more common pathophysiologies. HLH is difficult to diagnose and can be part of inflammatory syndromes. Here, we identify a novel hematological/autoinflammatory condition (NOCARH syndrome) in four unrelated patients with superimposable features, including neonatal-onset cytopenia with
more » ... hematopoiesis, autoinflammation, rash, and HLH. Patients shared the same de novo CDC42 mutation (Chr1:22417990C>T, p.R186C) and altered hematopoietic compartment, immune dysregulation, and inflammation. CDC42 mutations had been associated with syndromic neurodevelopmental disorders. In vitro and in vivo assays documented unique effects of p.R186C on CDC42 localization and function, correlating with the distinctiveness of the trait. Emapalumab was critical to the survival of one patient, who underwent successful bone marrow transplantation. Early recognition of the disorder and establishment of treatment followed by bone marrow transplant are important to survival.
doi:10.1084/jem.20190147 pmid:31601675 pmcid:PMC6888978 fatcat:ofruraaj3batdguliwpzisfbgi
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