Benchmarking a wide spectrum of metaheuristic techniques for the radio network design problem

The radio network design (RND) is an NP-hard optimization problem which consists of the maximization of the coverage of a given area while minimizing the base station deployment. Solving RND problems efficiently is relevant to many fields of application and has a direct impact in the engineering, telecommunication, scientific, and industrial areas. Numerous works can be found in the literature dealing with the RND problem, although they all suffer from the same shortfall: a noncomparable efficiency. Therefore, the aim of this paper is twofold: first, to offer a reliable RND comparison base reference in order to cover a wide algorithmic spectrum, and, second, to offer a comprehensible insight into accurate comparisons of efficiency, reliability, and swiftness of the different techniques applied to solve the RND problem. In order to achieve the first aim we propose a canonical RND problem formulation driven by two main directives: technology independence and a normalized comparison criterion. Following this, we have included an exhaustive behavior comparison between 14 different techniques. Finally, this paper indicates algorithmic trends and different patterns that can be observed through this analysis.Publicad

Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules

A. baumannii is an important nosocomial and drug-resistant pathogen. The capsule is a major virulence factor that helps bacteria to avoid host immunity and viral predation. Acinetobacter phages can bind and degrade host capsules through capsular depolymerases with proven anti-virulence activity (1-3). Understanding the full reservoir of phage depolymerases against A. baumannii capsules, as well as relevant capsular types in clinical isolates, is crucial for developing depolymerase-based treatments. In this work, we 1) characterized 94 carbapenem-resistant A. baumannii Portuguese isolates; 2) isolated phages for relevant capsular types and characterized their depolymerases and 3) developed bioinformatic tools to collect the diversity of phage depolymerases. We show clonal shifts of A. baumannii KL2, KL7, KL9 and KL120 serotypes over time, with different virulence assessed in G. mellonella. Acinetobacter phages specific for particular k-types were isolated and several depolymerases (for KL1, KL2/KL19, KL9, KL30/KL45, KL32, KL38, KL44, KL67 types) characterized. We also demonstrate that most Acinetobacter phages encode capsular depolymerases (from 134 deposited in 2021, 73 contain capsular depolymerases), exclusively located in small viruses (<90 kb). To disclose the full genetic diversity, we developed PhageDPO (available in Galaxy uminho.pt server), a machine learning tool that identifies depolymerases in phages and bacteria genomes (prophages). We also present PhageKDB, a database that compiles available information of capsular depolymerases, retrieved through both manually and text-mining approaches, serving as an open portal to phage community. Overall, we present novel insights into A. baumannii isolates and phage depolymerase diversity and a collaborative tool to advance research in the field.info:eu-repo/semantics/publishedVersio

Design of a MAC protocol for e-emergency WSNs

The wide adoption of WSNs in healthcare is still conditioned by quality of service (QoS) issues, namely at the MAC level. Medium access protocols currently available for WSNs are incapable of providing the required QoS to healthcare applications in scenarios of emergency or intensive medical care. To fill this lacuna, this paper introduces a MAC protocol presenting novel concepts to assure the QoS of e-emergency WSNs. Preliminary validation tests showed that the proposed protocol presents a good performance regarding data transmission robustness without sacrificing the power consumption efficiency.This work is funded by FEDER through the Competitiveness Factors Operational Programme – COMPETE and Portuguese National Funds through FCT - Foundation for Science and Technology under the Project: FCOMP-01-FEDER-0124022674info:eu-repo/semantics/publishedVersio

CkP1 is a novel S16-like broad-host-range myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibres

Citrobacter spp. is an emerging Gram-negative bacterial pathogen. The genus is currently divided in several species, being Citrobacter koseri (formerly named Citrobacter diversus) one of the most common isolated species in human clinical specimens. C. koseri can cause localized (urinary track, wounds infection, pneumonia, meningitis) and systemic life-threatening diseases (bacteremia, septicemia), being neonates, immunocompromised and elderly people, groups with increased risk of infection. The prevalence rate of Citrobacter infections in humans, range between 36 % among all Enterobacteriaceae, but mortality rate in cases of bacteremia reaches 56 %. We have isolated a novel S16-like C. koseri myovirus vB_CkM_CkP1 (CKP1). CkP1 genome has a length of 168,463 bp and contains 261 coding sequences, encoding more than 100 proteins with unknown function. About 60% of the encoded proteins are shared with the Salmonella phage S16. CkP1 displays an extremely broad host range, infecting C. koseri, but not other species. The long tail fiber (gp267) was fused to a green florescence protein (GFP) and co-expressed with and without the gp268 chaperone as a bicistronic transcript. Functional analysis demonstrated that the tail fiber binds to, and is able to decorate, C. koseri cells, being equally broad and specific towards this species as observed with the phage. Surface plasmon resonance showed that the binding affinity of the tail fiber is in the nanomolar range, presenting similar values with and without the chaperone. Both phage and the tail fiber specifically bind to bacterial cells by the lipopolysaccharide polymer. This was demonstrated by creating deletion mutants, whole genome sequencing of resistant variants and complementation of insensitive CkP1 bacterial strains. We further demonstrate that CkP1 is highly stable towards different environmental conditions and able to control C. koseri cells in urine samples. In summary, CkP1 has high potential in the control and detection of C. koseri.info:eu-repo/semantics/publishedVersio

Transient receptor potential ankyrin 1 channel expression on peripheral blood leukocytes from rheumatoid arthritic patients and correlation with pain and disability

Patients with rheumatoid arthritis (RA) suffer from pain and joint disability. The transient receptor potential ankyrin 1 (TRPA1) channel expressed on sensory neurones and non-neuronal cells mediates pain transduction and inflammation and it has been implicated in RA. However, there is little information on the contribution of TRPA1 for human disease. Here, we investigated the expression of TRPA1 on peripheral blood leukocytes and the circulating levels of its endogenous activators 4-hydroxynonenal (4-HNE) and hydrogen peroxide (H(2)O(2)) in RA patients treated or not with the anti-rheumatic leflunomide (LFN) or the anti-TNFα adalimumab (ADA). We also assessed whether TRPA1 expression correlates with joint pain and disability, in addition to the immune changes in RA. TRPA1 expression on peripheral blood leukocytes correlated with pain severity and disability. TRPA1 levels on these cells were associated with the numbers of polymorphonuclear and the activation of CD14(+) cells. No correlations were found between the lymphocyte population and TRPA1 expression, pain or disability. Patients recently diagnosed with RA expressed increased levels of TRPA1 on their leukocytes whilst treatment with either LFN or ADA down-regulated this receptor probably by reducing the numbers of polymorphonuclears and the activation of CD14(+) cells. We suggest that the activation levels of CD14(+) cells, the numbers of PMNs in the peripheral blood and the expression of TRPA1 on peripheral blood leukocytes correlate with RA progression, affecting joint pain sensitivity and loss of function

Serological follow-up of patients with paracoccidioidomycosis treated with itraconazole using Dot-blot, ELISA and Western-blot

Twenty-seven mycologically proven cases of paracoccidioidomycosis (PCM) were treated with itraconazole (100-200 mg/day in month 1 and 100 mg/day until month 6-8) and evaluated clinically and serologically, up to 3.5 years post-therapy, using Dot-blot and ELISA for measuring the titers of IgG, IgA and IgM anti-P. brasiliensis antibodies and Western-blot for determining IgG, IgA and IgM antibodies against the antigen components of the fungus. Before treatment, 81.5% (Dot-blot) and 84% (ELISA) of the patients presented elevated IgG anti-P. brasiliensis antibody titers which dropped slightly with treatment. On the other hand, the percentages of pre-treatment high-titered sera for IgA and IgM anti-P.brasiliensis were lower (5l.9% and 5l.8%: Dot-blot; 16.5 and 36%: ELISA, respectively) but the titers tended to become negative more frequently with treatment. Prior to treatment, the percentages of positivity for IgG, IgA and IgM anti-P.brasiliensis antibodies in Western-blot were 96%, 20.8% and 41.6%, respectively. Antigens with molecular weights varying from 16-78 kDa, from 21-76 kDa and from 27-78 kDa were reactive for IgG, IgA and IgM antibodies, respectively. The most frequently reactive antigenic components had molecular weights of 27, 33 and 43 kDa for IgG, and 70 for IgA and IgM antibodies. During the period of study, the patients responded well to treatment. The present data confirm the diversity and complexity of the humoral response in PCM, and the importance of utilizing different serological tests to detect IgG, IgA and IgM anti-P. brasiliensis antibodies<br>Vinte e sete pacientes portadores de paracoccidioidomicose (PCM) foram tratados com itraconazole (100-200 mg/dia no primeiro mês e 100 mg/dia até 6-8 meses) e avaliados sob o ponto de vista clínico e sorológico, até 3 e meio anos após o início do tratamento, utilizando-se os testes de Dot-blot e ELISA para medir os títulos de anticorpos IgG, IgA e IgM anti-P. brasiliensis, e Western-blot para determinar os anticorpos IgG, IgA e IgM contra os componentes antigênicos do fungo. Antes do tratamento, 81,5% (Dot-blot) e 84% (ELISA) dos pacientes apresentaram títulos elevados de anticorpos IgG anti-P. brasiliensis, que decresceram levemente com o tratamento. Por outro lado, as porcentagens de soros pré-tratamento com títulos elevados para anticorpos IgA e IgM foram menores (51,9% e 51,8%: Dot-blot; 16% e 36 %: ELISA, respectivamente); com o tratamento, entretanto, estes títulos tenderam mais frequentemente a se negativar. Antes do tratamento, as porcentagens de positividade para anticorpos IgG, IgA e IgM, avaliados por Western-blot, foram 96%, 20,8% e 41,6%, respectivamente. Componentes antigênicos de massas moleculares variando entre 16-78 kDa, 21-76 kDa e 27-78 kDa reagiram com anticorpos das classes IgG, IgA e IgM, respectivamente, As frações antigênicas com massas moleculares de 27, 33 e 43 kDa foram as mais frequentemente reativas com anticorpos da classe IgG, e a de 70 kDa para anticorpos IgA e IgM. Todos os pacientes apresentaram remissão da sintomatologia com o tratamento, durante o período de estudo. Os dados do presente trabalho confirmam a diversidade e a complexidade da resposta humoral dos pacientes com PCM e reforçam a importância de se utilizar diferentes testes sorológicos para se detectar anticorpos IgG, IgA e IgM anti- P. brasiliensis