Search

PIK3CA variants are known to cause vascular malformations. We were interested in studying the phenotypic spectrum, the location within the PIK3CA gene, and the variant allele frequency (VAF) of somatic PI3KCA variants in vascular malformations. Clinical data of consecutive patients with extracranial/extraspinal vascular malformations were collected in the context of the VASCOM cohort (2008-2022, n = 558). Starting October 2020, biopsy samples were tested with the TSO500 gene panel (Illumina). All consenting patients with PIK3CA variants were included in this study. Eighty-nine patients had available genetic results by June 2022. PIK3CA variants (n = 25) were found in 16 simple/combined (nonsyndromic) vascular malformations and in nine vascular malformations associated with other anomalies (syndromic). Four hotspot variants in exons 9 and 20 (c.1624G>A, c.1633G>A, c.3140A>G, c.3140A>T) were identified in 16/25 patients (VAF 0.9%-9.7%). Six non-hotspot variants (c.328_330del, c.323_337del, c.353G>A, c.1258T>C, c.3132T>A, c.3195_3203delinsT) were detected in nine patients (VAF 3.6%-31.7%). Non-hotspot variants were more frequent in syndromic than nonsyndromic vascular malformations (p = 0.0034) and exhibited a higher VAF than hotspot variants (p = 0.0253). Our study contributes to the growing body of knowledge of the genetic background in vascular malformations. Further studies will enrich the ever-growing list of pathogenic PIK3CA variants associated with vascular malformations., (© 2024 The Author(s). American Journal of Medical Genetics Part A published by Wiley Periodicals LLC.)

Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present-day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here, we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP (Ancestral Reconstruction under PIP) on simulated data sets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction. [Ancestral sequences; dynamic programming; evolutionary stochastic process; indel; joint ancestral sequence reconstruction; maximum likelihood; Poisson Indel Process; phylogeny; SARS-CoV.]., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

This study presents a mathematical model describing the adsorption-desorption process of water dissolved elements onto reactive porous materials during filtering operations performed under dynamic flow conditions. The developed model is based on a reversible second order adsorption kinetic featuring the progressive reduction of the purifying capacity of the filtering material due to the gradual exhaustion of the active sites available for solute retention. It enables the simulation of the performances of water filtering systems through the use of parameters having a clear chemical-physical significance or it can be used for the estimation of these parameters to characterize the adsorption properties of the reactive material. Starting from the same adsorptive conceptual model used for the filtering system marked by ongoing flowing conditions, an adaptation for static systems was performed on the mathematical framework in order to process the same chemical physical parameters in both schemes. Adsorption laboratory tests were carried out to validate the developed model. Results show that the kinetic constants and adsorption capacities (a maximum of about 45 mg g -1 was obtained for the tested material) are highly comparable, both within the same experimental system, and between different experimental setup. This confirms the validity of the developed model which is able to perfectly fit the observed concentration data in all tested configurations., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests. Michele De Biase reports financial support was provided by European Commission., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The latest progress in information and communication technology (ICT) and the Internet of Things (IoT) have opened up new opportunities for real-time monitoring and controlling of cities' structures, infrastructures, and services. In this context, smart water management technology provides the data and tools to help users more effectively manage water usage. Data collected with smart water devices are being integrated with building management systems to show how much water is used by occupants as well as to identify the consumption areas to use water more efficiently. By this approach, smart buildings represent an innovative solution that enhances a city's sustainability and contributes to overcoming environmental challenges due to increasing population and climate change. One of the main challenges is resource-saving and recovery. Water is an all-important need of all living beings, and the concerns of its scarcity impose a transition to innovative and sustainable management starting from the building scale. Thus, this manuscript aims to provide an updated and valuable overview for researchers, consumers, and stakeholders regarding implementing smart and sustainable technologies for water resource management, primarily for building-scale uses.

Background: In 2020, the Italian Medicines Agency recommended to bring forward the flu vaccination campaign, whose importance was also emphasized for patients with Multiple Sclerosis (MS). We aimed to assess the safety profile of flu vaccines in terms of occurrence of short-term and long-term Adverse Events Following Immunization (AEFIs)., Methods: This is an observational study that enrolled MS patients who were eligible for any of the flu vaccines recommended by the Italian medicines Agency., Results: 194 patients were enrolled. Out of 133 patients who accepted to be vaccinated, 45 experienced not serious short-term AEFIs (pain at the injection site, headache, flu-like symptoms, fatigue). Long-term AEs were detected in 12 vaccinated patients (flu-like symptoms, COVID-19 and MS relapse). No statistically significant differences in terms of infections or MS relapse were found between vaccinated and unvaccinated groups. Using Kaplan-Meier analysis we observed no differences in the cumulative survival rate in both groups., Conclusion: Flu vaccines were well tolerated in MS patients, who mainly experienced not serious short term AEFIs. Considering that COVID-19 vaccines campaign is still ongoing among MS patients, our results might bring new knowledge concerning the safety profile of vaccines in this frail population.

Background: Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences., Results: We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model-the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license., Conclusions: The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns., (© 2021. The Author(s).)

Interaction between thyroid hormones and the immune system is reported in the literature. Thyroid hormones, thyroxine, T 4 , but also T 3 , act non-genomically through mechanisms that involve a plasma membrane receptor αvβ3 integrin, a co-receptor for insulin-like growth factor-1 (IGF-1). Previous data from our laboratory show a crosstalk between thyroid hormones and IGF-1 because thyroid hormones inhibit the IGF-1-stimulated glucose uptake and cell proliferation in L-6 myoblasts, and the effects are mediated by integrin αvβ3. IGF-1 also behaves as a chemokine, being an important factor for tissue regeneration after damage. In the present study, using THP-1 human leukemic monocytes, expressing αvβ3 integrin in their cell membrane, we focused on the crosstalk between thyroid hormones and either IGF-1 or monocyte chemoattractant protein-1 (MCP-1), studying cell migration and proliferation stimulated by the two chemokines, and the role of αvβ3 integrin, using inhibitors of αvβ3 integrin and downstream pathways. Our results show that IGF-1 is a potent chemoattractant in THP-1 monocytes, stimulating cell migration, and thyroid hormone inhibits the effect through αvβ3 integrin. Thyroid hormone also inhibits IGF-1-stimulated cell proliferation through αvβ3 integrin, an example of a crosstalk between genomic and non-genomic effects. We also studied the effects of thyroid hormone on cell migration and proliferation induced by MCP-1, together with the pathways involved, by a pharmacological approach and docking simulation. Our findings show a different downstream signaling for IGF-1 and MCP-1 in THP-1 monocytes mediated by the plasma membrane receptor of thyroid hormones, integrin αvβ3., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The handling editor declared a past co-authorship with one of the authors RDL., (Copyright © 2021 Candelotti, De Luca, Megna, Maiolo, De Vito, Gionfra, Percario, Borgatti, Gambari, Davis, Lin, Polticelli, Persichini, Colasanti, Affabris, Pedersen and Incerpi.)

Recently we presented a frequentist dynamic programming (DP) approach for multiple sequence alignment based on the explicit model of indel evolution Poisson Indel Process (PIP). This phylogeny-aware approach produces evolutionary meaningful gap patterns and is robust to the 'over-alignment' bias. Despite linear time complexity for the computation of marginal likelihoods, the overall method's complexity is cubic in sequence length. Inspired by the popular aligner MAFFT, we propose a new technique to accelerate the evolutionary indel based alignment. Amino acid sequences are converted to sequences representing their physicochemical properties, and homologous blocks are identified by multi-scale short-time Fourier transform. Three three-dimensional DP matrices are then created under PIP, with homologous blocks defining sparse structures where most cells are excluded from the calculations. The homologous blocks are connected through intermediate 'linking blocks'. The homologous and linking blocks are aligned under PIP as independent DP sub-matrices and their tracebacks merged to yield the final alignment. The new algorithm can largely profit from parallel computing, yielding a theoretical speed-up estimated to be proportional to the cubic power of the number of sub-blocks in the DP matrices. We compare the new method to the original PIP approach and demonstrate it on real data., (© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

Background: Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modelled by a Markov substitution model. In contrast, the dynamics of indels are not modelled explicitly, because the computation of the marginal likelihood under such models has exponential time complexity in the number of taxa. But the failure to model indel evolution may lead to artificially short alignments due to biased indel placement, inconsistent with phylogenetic relationship., Results: Recently, the classical indel model TKF91 was modified to describe indel evolution on a phylogeny via a Poisson process, termed PIP. PIP allows to compute the joint marginal probability of an MSA and a tree in linear time. We present a new dynamic programming algorithm to align two MSAs -represented by the underlying homology paths- by full maximum likelihood under PIP in polynomial time, and apply it progressively along a guide tree. We have corroborated the correctness of our method by simulation, and compared it with competitive methods on an illustrative real dataset., Conclusions: Our MSA method is the first polynomial time progressive aligner with a rigorous mathematical formulation of indel evolution. The new method infers phylogenetically meaningful gap patterns alternative to the popular PRANK, while producing alignments of similar length. Moreover, the inferred gap patterns agree with what was predicted qualitatively by previous studies. The algorithm is implemented in a standalone C++ program: https://github.com/acg-team/ProPIP . Supplementary data are available at BMC Bioinformatics online.

Anionic carbosilane dendrimers of generations 1-3 have been synthesized containing carboxylate G(n)X(C(2)H(4)CO(2)Na)(m) and sulfonate G(n)X(C(2)H(4)SO(3)Na)(m) peripheral groups and derived from two different cores, 1,3,5-(HO)(3)C(6)H(3) (X = O(3)) and Si(C(3)H(5))(4) (X = Si). The peripheral anionic groups make these dendrimers water soluble, despite their highly hydrophobic framework. These dendrimers present a net negative charge in water, which was influenced by the pH of the medium. This characteristic was studied by pH titration. Also molecular modeling calculations have been performed to study differences in an aqueous medium between carboxylate and sulfonate dendrimers of different cores. The results obtained were also compared with those obtained from DOSY NMR experiments and zeta-potential measurements.

Background: To test two different antiemetic regimens for preventing nausea and vomiting in patient with non-Hodgkin's lymphoma (NHL) undergoing systemic chemotherapy (CT) with ProMECE-CytaBOM (P-C)., Patients and Methods: Twenty consecutive untreated adult outpatients with histologically confirmed NHL and scheduled to receive P-C chemotherapy were registered in a randomized, double-blind, cross-over study to compare the antiemetic efficacy of a levosulpiride (LS)-based and metoclopramide (MTC)-based regimen., Results: Complete protection from vomiting was recorded in 93% (62/67) of courses with the LS-regimen and in 89% (62/70) with the MTC-regimen (p = 0.428). No nausea was observed in 84% (56/67) of courses with the LS-regimen and in 74% (52/70) with the MTC-regimen (p = 0.183). No differences in prevention of emesis were recorded when patients crossed to the other regimen. Both regimens were well tolerated; however, on day 8 of chemotherapy, when both antiemetic regimens were administered at a higher dose, the LS-based combination showed significantly lower toxicity (p = 0.035)., Conclusions: ProMECE-CytaBOM-induced emesis can be prevented in most cases with appropriate, specifically designed antiemetic therapy. Both the LS- and MTC-based combinations resulted in a high percentage of complete protection from emesis, but the higher incidence of side effects observed with MTC makes the LS-based regimen preferable for patients receiving P-C chemotherapy.