On the Atomic Polarization of the Ground Level of Na I

In a recent letter (Trujillo Bueno et al. 2002), we showed the remarkable result that the atomic alignment of the levels P$_{1/2}$ and S$_{1/2}$ of the D$_1$ line of Na I is practically destroyed in the presence of magnetic fields sensibly larger than 10 G, irrespectively of the field direction. In this paper, we demonstrate analytically that this property is a consequence of the decoupling of the electronic and nuclear angular momenta, J and I, in the excited state P$_{3/2}$, which is achieved when the Zeeman splitting from the local magnetic field becomes much larger than the typical hyperfine separation for that level.Comment: The Astrophysical Journal; 2002; in pres

The Physical Origin of the Scattering Polarization of the Na I D-Lines in the Presence of Weak Magnetic Fields

We demonstrate that the atomic alignment of the hyperfine-structure components of the ground level S$_{1/2}$ of Na {\sc i} and of the upper level P$_{1/2}$ of the D$_1$ line are practically negligible for magnetic strengths $B>10 \rm G$, and virtually zero for B\ga 100 \rm G. This occurs independently of the magnetic-field inclination on the stellar surface (also, in particular, for vertical fields). Consequently, the characteristic antisymmetric linear-polarization signature of the scattered light in the D$_1$ line is practically suppressed in the presence of magnetic fields larger than 10 G, regardless of their inclination. Remarkably, we find that the scattering polarization amplitude of the D$_2$ line increases steadily with the magnetic strength, for vertical fields above 10 G, while the contribution of alignment to the polarization of the D$_1$ line rapidly decreases. Therefore, we suggest that spectropolarimetric observations of the ``quiet'' solar chromosphere showing significant linear polarization peaks in both D$_1$ and D$_2$ cannot be interpreted in terms of one-component magnetic field models, implying that the magnetic structuring of the solar chromosphere could be substantially more complex than previously thought.Comment: 11 pages and 2 figures. The Astrophysical Journal Letter (in press

Host genetics and COVID-19 severity: increasing the accuracy of latest severity scores by Boolean quantum features

The impact of common and rare variants in COVID-19 host genetics has been widely studied. In particular, in Fallerini et al. (Human genetics, 2022, 141, 147–173), common and rare variants were used to define an interpretable machine learning model for predicting COVID-19 severity. First, variants were converted into sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. After that, the Boolean features, selected by these logistic models, were combined into an Integrated PolyGenic Score (IPGS), which offers a very simple description of the contribution of host genetics in COVID-19 severity.. IPGS leads to an accuracy of 55%–60% on different cohorts, and, after a logistic regression with both IPGS and age as inputs, it leads to an accuracy of 75%. The goal of this paper is to improve the previous results, using not only the most informative Boolean features with respect to the genetic bases of severity but also the information on host organs involved in the disease. In this study, we generalize the IPGS adding a statistical weight for each organ, through the transformation of Boolean features into “Boolean quantum features,” inspired by quantum mechanics. The organ coefficients were set via the application of the genetic algorithm PyGAD, and, after that, we defined two new integrated polygenic scores (IPGSph1 and IPGSph2). By applying a logistic regression with both IPGS, (IPGSph2 (or indifferently IPGSph1) and age as inputs, we reached an accuracy of 84%–86%, thus improving the results previously shown in Fallerini et al. (Human genetics, 2022, 141, 147–173) by a factor of 10%

Use of Maldi-Tof Mass spectrometry in direct microorganism identification in clinical laboratories

Mass Spectrometry is an old technique that has recently been introduced in the clinical microbiology laboratory as Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). MALDI is a soft ionization technique used in mass spectrometry that allows the analysis of biomolecules and large organic molecules which tend to be fragile and fragment when ionized.To obtain ions biological specimens are mixed with a matrix which specifically absorbs the ionization source (a laser beam). The high energy impact is followed by the formation of ions which are extract through an elastic field, focussed and detected as mass/charge (m/z) spectrum.The differences between ions are seen with TOF, a revelation system that relates the time of flight of a ion to the charge/mass value: ion with a higher m/z have are slower (a bigger time of flight) than ions with lower m/z. MALDI-TOF MS, in clinical microbiology laboratory, is used to identify bacteria and fungi directly from samples. The identification of microorganisms can be performed directly from body fluids (e.g. urine, blood culture, after centrifugation and recovery of microorganisms) or from colonies (after cultivation). The rapidity of identification is of great importance in blood cultures. Positive cultures with one microorganism are processed in a different way than those with more than one microorganism. In positive monomicrobial cultures, after separation of microbs from blood cells,we can perform an immediate identification with MALDI-TOF MS that we can communicate to the clinician, and that gives indication to perform the correct antibiogram. Major problems are present when more than one microorganism are in the culture: in this case we have to use the method of subcultivation and then the identification with mass-spectrometry can be performed. MALDI-TOF MS is a rapid, reliable and low cost technique, that can identify a growing number of microorganisms. This technique can significantly reduce the time to give an identification, that is of great importance, particularly in blood culture, where the success of therapy is strictly linked to its early beginning

Typization of Klebsiella pneumoniae strains collected from a immature pediatric ward by Mass Spectrometry using MALDI-TOF

Introduction. Klebsiella pneumoniae is often associated with nosocomial infections, especially in immature pediatric wards and intensive care, where the prolonged hospitalization and invasive procedures increase the risk.In this study we investigated the possibility of using MALDI-TOF mass spectrometry for the rapid identification of bacteria and to be able to be used for epidemiological circulation of a particular strain of Klebsiella pneumoniae in a pediatric ward immature at Mercy hospital of Prato and Dolce. Materials and Methods. Twenty Klebsiella pneumoniae strains were isolated and analyzed The isolates were collected from clinical specimens (7 urine, 12 stool samples, 1 skin swab) from 15 patients (9 females and 6 males) of the Department of Pediatrics, Hospital Misericordia and Dolce during the period from May to November 2010. Samples were collected using eSwab containers for urine and swab the skin FecalSwab, for fecal samples, and processed on suitable culture media with theWasp system (Copan Italy Spa distributed by ada Ltd.). Of all isolates were performed identification and susceptibility testing with the automatic Vitek2 (bioMérieux) at the time of isolation, then frozen at -20 °C in Trypticase Soy Broth with 20% Glycerol (Becton Dickinson). Subsequently, the bacterial strains were thawed, subcultured on Columbia Blood Agar with 5% sheep (BioMerieux), typed by means of MALDI-TOF (Shimadzu Axima - Biomerieux) and performed an antibiogram by Kirby-Bauer method (Table 3) on Agar Mueller-Hinton (Liofilchem S.r.l.) and diskettes Bio-Rad. The spectra obtained by MALDI-TOF were analyzed and compared with software-AgnosTec SARAMIS, used in our laboratory, both for the identification of the strains for the construction of a dendrogram. Results.Twenty strains of Klebsiella pneumoniae were studied.They were isolated from clinical specimens (7 urine, 12 stool samples, 1 skin swab) from 15 patients (9 females and 6 males) of the Department of Pediatrics. Of all isolates was performed to identify and sensitivity with automaticVitek2 (bioMérieux) samples from Italian patients and divided stranieri così: 570 endocervical swabs (71.2%), 98 urethral swabs (12.2%), 78 seminal fluids (9.8%), and 54 urine (6.8%).The number of female subjects was higher than those of males [629 (78.5%) vs 172 (21.5%)], the average age of females was 38.4 ± 12.2 years while that of males was 47.7 ± 13.3 years. The prevalence of urogenital pathogens was: 13 T.vaginalis positive (1.6%), 52 for M.hominis (6.5%), 64 for M.genitalium (8.8%), 18 for C.trachomatis (2.2%), 2 for N.gonorrheae (0.2%) and 79 for U.urealyticum (9.9%): of all the 18 positive subjects were positive for more than one pathogen, namely: 1 totaled 4 pathogens, pathogens 5 for 3 and 9 for 2 pathogens. Conclusions.This study provides data on the prevalence of sexually transmitted diseases in the hospital in Prato

MALDI-TOF mass spectrometry for the rapid identification of aetiological agents of sepsis

Introduction: The MALDI-TOF has recently become part of the methods of microbiological investigation in many laboratories of bacteriology with advantages both practical and economical.The use of this technique for the rapid identification of the causative agents of sepsis is of strategic importance to the ability to provide the clinician with useful information for a prompt and rapid establishment of an empirical antimicrobial “targeted” therapy. Methods: It was tested a total of 343 positive blood culture bottles from 211 patients. The samples after collection were incubated in the BACTEC FX (Becton Dickinson, USA). From these bottles were taken a few milliliters of broth culture and transferred into a vacutainer tube containing gel. This was centrifuged, the supernatant was decanted, and finally recovered the bacterial suspension on the gel. With micro-organisms recovered in this way, after several washes with distilled water, was prepared a slide for microscopic examination with Gram stain, and a plate for mass spectrometry (MS-Vitek, bioMérieux, France).Then, the same samples were inoculated on solid agar media according to the protocol in use in our laboratory.The next day was checked the possible bacterial growth on solid media; we then proceeded to the identification of the colonies by Vitek MS and / or with the system Vitek2 (bioMérieux, France). Results: 258 (75.2%) positive vials show concordant results between direct identification and identification after growth on agar. For 83 (24.2%) positive bottles there has been full compliance with the microscopic examination but not with culture. In particular, two bottles (0.6%) have given complete discordance between the direct identification and that after growth. Conclusions: The protocol we use for the direct identification of organisms responsible for sepsis, directly on positive bottles, seems to be a quick and inexpensive procedure, which in less than 60 minutes can give valuable feedback to the clinician

Usefulness of MALDI-TOF mass spectrometry in epidemiological control of etiologic agents of infection

Introduction: The use of the MALDI-TOF mass spectrometry in the routine of microbiological diagnostics has revolutionized procedures and response times of bacteriology.The use of this technique aims to epidemiological investigations in a hospital environment and represents a further significant opportunity, quickly feasible and extremely economical. Methods: By means of the MALDI-TOF-MS Vitek2 (MS Vitek2) mass spectrometer, accompanied by the AgnosTec-SARAMIS (bioMérieux, France) software, were analyzed the spectra of 149 bacterial isolates (139 Staphylococcus aureus and 10 Staphylococcus epidermidis) obtained from cultures of 148 patients (141 inpatients and 7 outpatients). Clinical isolates were stored at a temperature of -20°C.The isolates were then thawed and immediately cultured on agar blood medium. The colonies were subjected to analysis by MS Vitek on the day after sowing. The spectra obtained were analyzed and compared using the software AgnosTec-SARAMIS, which allowed the construction of a dendrogram. Results and conclusions: The evaluation of the data collected suggests that mass spectrometry could be an useful tool in epidemiological surveys. Speed of analysis and low costs make the MS Vitek2 an usable tool by many microbiology laboratories

Prevalence of Clostridium difficile infections in Prato hospital in the years 2010-2011

Clostridium difficile, a Gram positive, spore-forming, anaerobic bacillus, is an important nosocomial enteric pathogen causing diarrhoea and pseudomembranous colitis. Aim of this study was to evaluate the prevalence of Clostridium difficile in Prato Hospital. Stool samples were collected from 1197 patients hospitalized from January 2010 to December 2011. In all the samples the common antigen GDH was investigated and only in samples positive for the antigen the presence of the A and B toxins was investigated. Our results showed that 170/1197 samples (14%) were positive for the antigen, and of these 170 patients, 84 (49%) were found positive also for the toxins. In addition the percentage of samples positive for toxins was higher in 2010 (8.6%) than in 2011 (5.9%)

Detection of T. vaginalis,M. hominis,M. genitalium, C. trachomatis, N. gonorrhoeae and U. urealyticum using Multiplex PCR

Intoduction. The sexually transmitted diseases include a large group of infections affecting both the sexes. In this study we evaluated the prevalence of Trichomonas vaginalis, Mycoplasma hominis, Mycoplasma genitalium, Chlamydia trachomatis, Neisseria gonorrhoeae and Ureaplasma urealyticum in the Prato area during the period September 2010 – July 2011. Methods.We analysed different kind of samples (urine, endocervical swabs, urethral swabs, seminal fluids) from hospitalized patients or referred to the Prato clinic subjects.The DNA was obtained using EZ1-DNA extraction kit and EZ1 instrument.The DNA was then amplified using the Seeplex STD6 kit (Seegene, Korea), identifying multiple pathogens simultaneously (T. vaginalis, M. hominis, M. genitalium, C. trachomatis, N. gonorrhoeae e U. urealyticum). The revelation was performed by electrophoresis on microchip (instrument Multina, Shimadzu, Japan). Results. 1136 samples from Italian and foreign patients were examined: 876 were endocervical swabs (77%), 103 urethral swabs (9%), 103 seminal fluids (9%), and 54 urines (5%). The number of females was higher than males [894 (78.7%) vs 242 (21.3%)]; the mean age of females was 37.0±11.6 years, whereas that of males was 41.5 ±12.63 years.The prevalence of urogenital pathogens was: 15 positive samples for T. vaginalis (1.3%), 56 for M. hominis (4.9%), 13 for M. genitalium (1.1%), 28 for C. trachomatis (2.5%), 8 for N. gonorrhoeae (0.7%) and 87 for U. urealyticum (7.7%).Among all positive, 25 subjects were positive for more than one pathogen and in particular: one was positive for the presence of 4 pathogens, five presented 3 pathogens simultaneously and the remaining nineteen for 2 pathogens. Conclusions. This study provides data on the prevalence of sexually transmitted diseases in the hospital of Prato