Combination of MALDI-TOf mass spectrometry and machine learning for rapid antimicrobial resistance screening: the CASE of Campylobacter spp

While MALDI-TOF mass spectrometry (MS) is widely considered as the reference method for the rapid and inexpensive identification of microorganisms in routine laboratories, less attention has been addressed to its ability for detection of antimicrobial resistance (AMR). Recently, some studies assessed its potential application together with machine learning for the detection of AMR in clinical pathogens. The scope of this study was to investigate MALDI-TOF MS protein mass spectra combined with a prediction approach as an AMR screening tool for relevant foodborne pathogens, such as Campylobacter coli and Campylobacter jejuni. A One-Health panel of 224 C. jejuni and 116 C. coli strains was phenotypically tested for seven antimicrobial resistances, i.e., ciprofloxacin, erythromycin, tetracycline, gentamycin, kanamycin, streptomycin, and ampicillin, independently, and were submitted, after an on- and off-plate protein extraction, to MALDI Biotyper analysis, which yielded one average spectra per isolate and type of extraction. Overall, high performance was observed for classifiers detecting susceptible as well as ciprofloxacin- and tetracycline-resistant isolates. A maximum sensitivity and a precision of 92.3 and 81.2%, respectively, were reached. No significant prediction performance differences were observed between on- and off-plate types of protein extractions. Finally, three putative AMR biomarkers for fluoroquinolones, tetracyclines, and aminoglycosides were identified during the current study. Combination of MALDI-TOF MS and machine learning could be an efficient and inexpensive tool to swiftly screen certain AMR in foodborne pathogens, which may enable a rapid initiation of a precise, targeted antibiotic treatment

Seroprevalence of Immunoglobulin G antibodies against pertussis toxin among asymptomatic medical students in the west of Iran: a cross sectional study

<p>Abstract</p> <p>Background</p> <p>Pertussis is a highly communicable, vaccine-preventable respiratory infection. Immune response against this disease can be induced by infection or vaccination. Protection after childhood vaccination is minimal after ten years. Our aim was to assess pertussis immunity state in a population of healthy young medical students.</p> <p>Methods</p> <p>In this seroepidemiological survey, blood samples were obtained from 163 first-year medical students in Hamedan University, Iran. Serum level of IgG against pertussis toxin (IgG-PT) was measured by Enzyme-Linked Immunosorbent Assay (ELISA) method. For qualitative assessment, IgG-PT levels more than 24 unit (U)/ml were considered positive. Data was analysed qualitatively and quantitatively considering gender and age groups.</p> <p>Results</p> <p>There were 83 males and 80 females, with a mean age of 19.48 years, Prevalence of IgG-PT was 47.6% with mean level of 71.7 u/ml (95% confidence interval: 68.1–75.3). No statistically significant difference was observed with respect to sero-positivity of IgG-PT between males and females (45 cases (54%) vs. 34 cases (42%); P = 0.06). Mean IgG-PT levels in males and females were 84 U/ml and 58.8 U/ml, respectively (P = 0.91).</p> <p>Conclusion</p> <p>A considerable proportion of our study population with a positive history of childhood vaccination for pertussis was not serologically immune to pertussis. A booster dose of acellular pertussis vaccine may be indicated in Iranian, medical students regarding their serologic conditions and outstanding role in health care systems.</p

Development of 3D PUFEM with linear tetrahedral elements for the simulation of acoustic waves in enclosed cavities

International audienceThis work is concerned with the numerical simulation of sound pressure field in three-dimensional cavities in which absorbing materials are present. Standard techniques such as the Finite Element Method are known to be extremely demanding computationally when the frequency increases and thus limited to low frequency applications. To alleviate these difficulties, an alternative formulation based on the Partition of Unity Finite Element Method is proposed. The method involves enriching the approximation finite element space by expanding the acoustic pressure in a set of plane waves propagating in various directions over the unit sphere. Particular attention is devoted to the fast and accurate computation of highly oscillatory integrals which is required by the method. Convergence studies show that these wave finite elements allow to capture accurately the wave field with a number of degrees of freedom that only grows quadratically with the frequency yielding drastic data reduction compared to classical FEM. Results of practical interest are shown for the case of a sound source placed in a reverberation room with absorbing materials

Recherche d'ADN de leptospires pathogènes dans le sang et l'urine de 30 chiens apparemment sains

International audienceAsymptomatic carriage of leptospires in dogs has not been extensively studied. A prospective study was conducted on thirty apparently healthy male dogs to screen for Leptospiral DNA in their blood and urine. All dogs were up to date with a bivalent vaccine against Leptospirosis. Microscopic agglutination test (MAT) and real-time PCR analysis in blood and urine were performed for each dog. Six of 30 (20%) dogs had positive PCR results: two from blood samples (all MAT titres ≤ 160) and four from urine samples (one with maximal MAT titres of 2560 and three with all MAT titres ≤ 160). Ten months later, PCR analyses of blood and urine were repeated for these six dogs. Four had negative PCR results from blood and urine. The other two, with positive urine results at the first sampling, had negative PCR results from urine and positive PCR results from blood. In this study, the urinary shedding of leptospires appeared to be transient. As shown previously, serological status was not correlated with PCR results. Low but detectable amounts of Leptospiral DNA in the blood of some apparently healthy dogs raises questions regarding the pathophysiology of Leptospirosis and the diagnostic consequences of high-sensitivity PCR assays.Le portage asymptomatique des leptospires chez le chien est encore mal connu. Une étude prospective sur 30 chiens mâles apparemment sains a recherché la présence d'ADN de leptospires pathogènes dans leur sang et leur urine. Chaque chien était à jour de ses vaccins contre la leptospirose (vaccins inactivés bivalents sur tous les chiens). Une sérologie par technique de microagglutination (MAT) et une PCR en temps réel sur l'urine et le sang ont été réalisées pour chaque chien. Six chiens sur 30 (20 %) avaient des résultats PCR positifs : deux chiens sur sang (titres MAT ≤ 160 pour ces deux chiens), quatre chiens sur urine (titre MAT maximal de 2560 pour un chien, titres MAT ≤ 160 pour les trois autres). Dix mois plus tard, les analyses PCR ont été répétées pour les six chiens avec un résultat positif. Quatre chiens avaient des résultats négatifs sur sang et urines. Deux chiens, qui avaient initialement une PCR positive sur urines, avaient une PCR positive sur sang et négative sur urines. Dans cette étude, l'excrétion urinaire des leptospires apparaissait discontinue. Comme dans d'autres études, les profils sérologiques n'étaient pas corrélés aux résultats PCR. Trouver dans le sang de chiens apparemment sains des quantités faibles mais détectables d'ADN de leptospires interroge sur la physiopathologie de la leptospirose et les conséquences diagnostiques de tests PCR très sensibles

On the efficiency of parallel baffle-type silencers in rectangular ducts: prediction and measurement

International audienceTo estimate the efficiency of parallel baffle-type silencers in rectangular ducts, a two-dimensional multi-layer model is presented for predicting their transmission loss. The approach takes into account an arbitrary number of bulk reacting baffles of finite length bounded at both ends by a metallic fairing. Each layer is described by a mean pressure, which allows computing a piecewise constant modal basis for the mean pressure over the cross section. The continuity between the incoming and outgoing waves is performed by axial mode matching at the inlet and outlet cross-sections of the baffle silencer. It is shown that the model is easy to implement and suitable for optimization purposes based on design parameters such as the height of each baffle, their relative positions in the duct, and material properties. Relatively complex configurations can be simulated with relatively modest computational effort. An experimental campaign was carried out on a reduced scale test bench for standard configurations. The numerical results are in good agreement with the measurements. Noise reduction performances are analyzed in terms of reflected and dissipated sound powers. Finally, more complex geometric configurations are simulated in order to examine the influence of the relative transverse and axial positions of each baffle as well as the effect of a resistive screen between the baffles and the airways

Adjustable cerebrospinal fluid shunt valves in 3.0-Tesla MRI: a phantom study using explanted devices

Considering the rapidly increasing number of clinical high-field MR imagers and the lack of data regarding interference with magnetically adjustable cerebrospinal fluid (CSF) shunt valves, valve safety was assessed with regard to magnetic field interactions: imaging artifacts, heating, magnetic forces, and functional changes in a phantom study at 3.0 Tesla using explanted devices as a realistic model for in vivo conditions

DTI of commissural fibers in patients with Chiari II-malformation

Chiari II-malformation is a complex congenital deformity of the brain which is frequently associated with hydrocephalus. Abnormalities of the corpus callosum are known to occur in the majority of patients. The objective of the present study was to study the microstructure of the corpus callosum (CC) and the anterior commissure (AC) to differentiate between different mechanisms of damage to these structures. We investigated 6 patients with Chiari II-malformation and 6 well-matched healthy volunteers employing T1-weighted 3D imaging and diffusion tensor imaging (DTI) to determine the fractional anisotropy (FA) and cross-sectional area of the CC and AC, as well as with neuropsychological testing. Four patients showed hydrocephalus, two patients had callosal dysplasia and four had a hypoplastic CC. The callosal FA in the patients was significantly reduced which was less pronounced for the genu alone. The area of CC was also reduced in Chiari II-patients. There was a strong correlation between the size and FA of the CC in the patients. In contrast, the thickness of the AC was significantly increased and was associated with higher FA in the patients. In psychological tests all patients showed reduced verbal memory; all but one patient showed reduced IQ as well as impaired visuo-spatial performance, indicating deficits in tasks requiring parieto-occipital integration. The existence of callosal dysplasia in two patients, the diminished FA reduction in the genu and the correlation of the cross-sectional area and FA in the patients point to a developmental white matter damage beside that exerted by hydrocephalus alone

Exploring social and cognitive engagement in small groups through a community of learners (CoL) lens

A variety of research studies reveal the advantages of actively engaging students in the learning process through collaborative work in the classroom. However, the complex nature of the learning environment in large college general chemistry courses makes it challenging to identify the different factors that affect students’ cognitive and social engagement while working on in-class tasks. To provide insights into this area, we took a closer look at students’ conversations during in-class activities to characterize typical discourse patterns and expressed chemical thinking in representative student groups in samples collected in five different learning environments across four universities. For this purpose, we adapted and applied a ‘Community of Learners’ (CoL) theoretical perspective to characterize group activity through the analysis of student discourse. Within a CoL perspective, the extent to which a group functions as a community of learners is analyzed along five dimensions including Community of Discourse (CoD), Legitimization of Differences (LoD), Building on Ideas (BoI), Reflective Learning (RL), and Community of Practice (CoP). Our findings make explicit the complexity of analyzing student engagement in large active learning environments where a multitude of variables can affect group work. These include, among others, group size and composition, the cognitive level of the tasks, the types of cognitive processes used to complete tasks, and the motivation and willingness of students to substantively engage in disciplinary reasoning. Our results point to important considerations in the design and implementation of active learning environments that engage more students with chemical ideas at higher levels of reasoning. © 2023 The Royal Society of Chemistry.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]