Automated classification of humpback whale (Megaptera novaeangliae) songs using hidden Markov models

Humpback whales songs have been widely investigated in the past few decades. This study proposes a new approach for the classification of the calls detected in the songs with the use of Hidden Markov Models (HMMs). HMMs have been used once before for such task but in an unsupervised algorithm with promising results. Here HMMs were trained and two models were employed to classify the calls into their component units and subunits. The results show that classification of humpback whale songs from one year to another is possible even with limited training. The classification is fully automated apart from the labelling of the training set and the input of the initial HMM prototype models. Two different models for the song structure are considered: one based on song units and one based on subunits. The latter model is shown to achieve better recognition results with a reduced need for updating when applied to a variety of recordings from different years and different geographic locations

Essays in Labour Economics

PhD ThesisThis thesis studies two important aspects of labour market earnings dynamics: the post-displacement earning losses experienced by high-tenure workers, and the evolution of the gender wage gap within rms linked to export activity. The rst two essays aim at understanding and quantifying the forces behind the post-displacement earning losses observed in the data. I rst introduce the main empirical and theoretical works in the literature. Then, I propose a structural model of the labour market with on the job search, in which rms are heterogeneous in productivity and workers accumulate both general and speci c skills while employed. Jobs are destroyed at an endogenous rate due to idiosyncratic productivity shocks and workers' skills depreciate during unemployment. The model is estimated via simulated method of moments using matched employer-employee data on Germany. By matching moments related to workers' mobility and wage dynamics, the model reproduces the size and persistence of the earning losses observed in the data. The key driver of the post-displacement earning losses is the interaction between the loss in speci c (mostly) and general human capital and endogenous separation. Finally, the third essay studies the e ect of rms' export activity on the gender wage gap among its workers. Using matched employer-employee data from Germany for the period between 1993 and 2007, we show that an increase in a rm's export widens the wage gap between male and female blue collar workers, while it reduces it between male and female white collars. In particular, the former e ect is stronger for workers in routine manual tasks, while the latter is driven by employees performing interactive tasks. This evidence is consistent with the hypothesis that serving foreign markets relies more on interpersonal skills, which reinforces female comparative advantage and reduces (widens) the gender wage gap in white (blue) collar occupations

Positive effect of the fluorine moiety on the oxygen storage capacity of UiO-66 metal–organic frameworks

The capacity to store oxygen and nitrogen within UiO-66 fluorine-containing MOFs has been tested through high pressure adsorption isotherms

Usefulness and Clinical Impact of Whole-Body MRI in Detecting Autoimmune Neuromuscular Disorders

: Autoimmune neuromuscular diseases are a group of heterogenous pathologies secondary to the activation of the immune system that damage the structures of the peripheric nerve, the neuromuscular junction, or the skeleton muscle. The diagnosis of autoimmune neuromuscular disorders comprises a combination of data from clinical, laboratory, electromyography, imaging exam, and biopsy. Particularly, the whole-body MRI examination in the last two decades has been of great use in the assessment of neuromuscular disorders. MRI provides information about the structures involved and the status of activity of the disease. It can also be used as a biomarker, detect the pattern of specific muscle involvement, and is a useful tool for targeting the optimal muscle site for biopsy. In this work, we summarized the most used technical protocol of whole-body MRI and the role of this imaging technique in autoimmune neuromuscular disorders

Investigating the inhibition of FTSJ1 a tryptophan tRNA-specific 2’-O-methyltransferase by NV TRIDs, as a mechanism of readthrough in nonsense mutated CFTR

Abstract: Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations, which generate a Premature Termination Codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ri-bosome’s capacity to skip a PTC, thus generating a full-length protein. “TRIDs” are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We in-vestigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their readthrough activity by in silico analysis and in vitro studies. Our results suggest a likely inhibition of FTSJ1, a tryptophan tRNA-specific 2’-O-methyltransferase

Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants

The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96-100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2-3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants

Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression

Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman–Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named “translational readthrough” and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins’ (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs

Changing in the post-surgery infective complications following the shortening of the antibiotic prophylaxis in the patients undergoing skin dermal substitutes reconstruction

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue, both in massive deep burns, extensive full-thickness wounds, and reconstruction after cancer resection. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material & Methods: Infective complications at the site of SDS were compared in two groups of patients: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a >24h-antibiotic prophylaxis, and subjects undergoing surgical reconstruction between May 2016 and June 2017 (PERIOD B) who received a ≤24h-antibiotic prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Univariate linear regression analysis was performed to evaluate the risk factors for infection (sex, age, ASA code, perioperative antibiotic prophylaxis, site of SDS intervention, type of SDS, dimensions of surgical area, chronic renal impairment, and diabetes mellitus). Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The 66.4% (n=77) of the study population was male, and the mean age was 73 years (22-92 years). Seventy-eight patients (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were former or current smokers, and 45 (38.8%) had an ASA code ≥3. In the 94.8% of the patients (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the arm or the hand in 9 (7.8%), the leg in 12 (10.3%) and the foot in 12 (10.3%). Among 116 patients undergoing SDS surgical reconstruction, 62 (53.4%) received a >24h-prophylaxis and 54 (46.6%) received a ≤24h-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limb/foot had higher infection rate in comparison with those undergoing SDS reconstruction in chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received >24h or ≤24h-antibiotic prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. No significant differences in pathogen prevalence were found (p=0.692). Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed to reduce of 6 days-per-patient the antibiotic exposure

Egress-related osmiophilic bodies

© 2014 John Wiley & Sons Ltd. Summary: Gametogenesis is the earliest event after uptake of malaria parasites by the mosquito vector, with a decisive impact on colonization of the mosquito midgut. This process is triggered by a drop in temperature and contact with mosquito molecules. In a few minutes, male and female gametocytes escape from the host erythrocyte by rupturing the parasitophorous vacuole and the erythrocyte membranes. Electron-dense, oval-shaped organelles, the osmiophilic bodies (OB), have been implicated in the egress of female gametocytes. By comparative electron microscopy and electron tomography analyses combined with immunolocalization experiments, we here define the morphological features distinctive of male secretory organelles, hereafter named MOB (male osmiophilic bodies). These organelles appear as club-shaped, electron-dense vesicles, smaller than female OB. We found that a drop in temperature triggers MOB clustering, independently of exposure to other stimuli. MDV1/PEG3, a protein associated with OB in Plasmodium berghei females, localizes to both non-clustered and clustered MOB, suggesting that clustering precedes vesicle discharge. A P.berghei mutant lacking the OB-resident female-specific protein Pbg377 displays a dramatic reduction in size of the OB, accompanied by a delay in female gamete egress efficiency, while female gamete fertility is not affected. Immunolocalization experiments indicated that MDV1/PEG3 is still recruited to OB-remnant structures

Infective complications in patients undergoing surgical reconstruction with dermal matrix: the Modena experience

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue1,2,3. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material & Methods: Infective complications at the site of SDS were compared in 2 groups: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a >24H-antibiotic-prophylaxis, and between May 2016 and June 2017 (PERIOD B) who received a ≤24H-antibiotic-prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The mean age was 73-years, 77 were male (66.4%), 78 (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were smokers, and 45 (38.8%) had an ASA score ≥3. In the 94.8% (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the limbs in 33 (28.5%). Among 116 patients, 62 (53.4%) received >24H-antibiotic and 54 (46.6%) ≤24H-antibiotic-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limbs had higher infection rate in comparison with chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received >24H or ≤24H-antibiotic-prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. Discussion: As far as we know, this is the first study that compared two perioperative antibiotic prophylaxis regimes in patients undergoing SDS reconstruction. Comparing the two patient groups (≤24-hour and >24-hour prophylaxis), no differences in the rate of infection were found. The result is very important: it shows that prolongation of prophylaxis in this type of surgical patients does not reduce the rate of infection. Shortening of antibiotic prophylaxis allowed to reduce of 6 days-per-patient the antibiotic exposure. It was surprising that only the reconstruction of the limbs, in comparison with other sites, was associated with a higher risk of infection (33.3 and 15.7 respectively). Nor the most critical patients (with an ASA score ≥3), nor patients undergoing major surgical reconstructions (surgical area >60 cm2) resulted associated with a higher risk. Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed a reduction of 6 days-per-patient the antibiotic exposure. Randomized and controlled trials, with greater population, could give a more accurate response on the duration of antibiotic prophylaxis in patients undergoing surgical SDS reconstruction