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Recent advances in next-generation sequencing have opened up new possibilities for utilizing the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not yet been fully integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in court for forensically relevant and challenging samples. We propose using Operational Taxonomic Units (OTUs) for read data processing and creating heterogeneous training datasets for training a random forest classifier. Our classifier incorporates six forensically relevant classes: saliva, semen, hand skin, penile skin, urine, and vaginal/menstrual fluid. Across these classes, our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mixed-source samples and underwear revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier shows promising results for the inference of sexual activity. In our study, we recommend the use of a novel random forest classifier trained on a heterogenous dataset for obtaining predictions from samples mimicking forensic evidence. We also highlight the potential of the sexome for assessing the nature of sexual activities in forensic investigations, while delineating areas that warrant further research. Furthermore, we underscore key considerations when presenting machine learning results for classifying mixed-source samples.

Inflammatory Bowel Disease (IBD) is characterized by chronic intestinal inflammation with no cure and limited treatment options that often have systemic side effects. In this study, we developed a target-specific system to potentially treat IBD by engineering the probiotic bacterium Escherichia coli Nissle 1917 (EcN). Our modular system comprises three components: a transcription factor-based sensor (NorR) capable of detecting the inflammation biomarker nitric oxide, a type 1 hemolysin secretion system, and a therapeutic cargo consisting of a library of humanized anti-TNFα nanobodies. Despite a reduction in sensitivity, our system demonstrated a concentration-dependent response to nitric oxide, successfully secreting functional nanobodies with binding affinities comparable to the commonly used drug Adalimumab, as confirmed by ELISA and in vitro assays. This newly validated nanobody library expands EcN therapeutic capabilities. The adopted secretion system, also characterized for the first time in EcN, can be further adapted as a platform for screening and purifying proteins of interest. Additionally, we provided a mathematical framework to assess critical parameters in engineering probiotic systems, including the production and diffusion of relevant molecules, bacterial colonization rates, and particle interactions. This integrated approach expands the synthetic biology toolbox for EcN-based therapies, providing novel parts, circuits, and a model for tunable responses at inflammatory hotspots. Graphical Table of Contents. The engineered probiotic system: Inflamed intestinal cells release the inflammatory regulator TNFα (depicted as red squares), which promotes inflammation through a positive feedback loop. Concurrently, these cells produce large amounts of nitric oxide (NO, represented by yellow circles) during inflammation. Our custom-engineered EcN biosensor can detect NO using a NorR-based sensor (in purple) and subsequently trigger the production of nanobodies (in turquoise). These nanobodies are then released into the extracellular environment via a specially engineered secretion system in the bacterial host (shown in dark blue). Once outside the cell, the nanobodies attach to TNFα, effectively sequestering them and reducing inflammation. The graph at the bottom of this panel illustrates the general behavior of our system: nanobody production starts upon reaching a certain NO concentration threshold and continues in an NO-dependent fashion. As nanobodies are produced, they capture TNFα, leading to a reduction in inflammation and a decrease in NO production. This decrease in NO then halts the nanobody production. Probiotics can be engineered to detect and act upon extracellular disease indicators, optimizing therapeutic outcomes. Particularly, self-regulating sense-and-respond genetic circuits have the potential to enhance the accuracy, efficacy, and adaptability of treatment interventions. In this study, we developed and characterized a new integrated and modular toolkit that detects a gut inflammation biomarker, specifically nitric oxide, and responds to it in an inducible manner by secreting humanized nanobodies targeting the pro-inflammatory molecule TNFα. We also develop a coarse-grained mathematical framework for modelling engineered probiotic activity in the gut. This novel system contributes to current efforts to develop new engineered probiotic systems and holds promise for inspiring new treatments for gut inflammation associated with various autoimmune diseases.

Background In the initial phase of the SARS-CoV-2 pandemic, masking has been widely accepted in healthcare institutions to mitigate the risk of healthcare-associated infection. Evidence, however, is still scant and the role of masks in preventing healthcare-associated SARS-CoV-2 acquisition remains unclear.We investigated the association of variation in institutional mask policies with healthcare-associated SARS-CoV-2 infections in acute care hospitals in Switzerland during the BA.4/5 2022 wave. Methods SARS-CoV-2 infections in hospitalized patients between June 1 and September 5, 2022, were obtained from the “Hospital-based surveillance of COVID-19 in Switzerland”-database and classified as healthcare- or community-associated based on time of disease onset. Institutions provided information regarding institutional masking policies for healthcare workers and other prevention policies. The percentage of healthcare-associated SARS-CoV-2 infections was calculated per institution and per type of mask policy. The association of healthcare-associated SARS-CoV-2 infections with mask policies was tested using a negative binominal mixed-effect model. Results We included 2’980 SARS-CoV-2 infections from 13 institutions, 444 (15%) were classified as healthcare-associated. Between June 20 and June 30, 2022, six (46%) institutions switched to a more stringent mask policy. The percentage of healthcare-associated infections subsequently declined in institutions with policy switch but not in the others. In particular, the switch from situative masking (standard precautions) to general masking of HCW in contact with patients was followed by a strong reduction of healthcare-associated infections (rate ratio 0.39, 95% CI 0.30–0.49). In contrast, when compared across hospitals, the percentage of health-care associated infections was not related to mask policies. Conclusions Our findings suggest switching to a more stringent mask policy may be beneficial during increases of healthcare-associated SARS-CoV-2 infections at an institutional level.

The aim of our study is to evaluate the performance of surface sealants and conventional polishing after ageing procedures. Eighty circular composite restorations were performed on extracted human molars. After standardised roughening, the restorations were either sealed with one of three surface sealants (Lasting Touch (LT), BisCover LV (BC), G-Coat Plus (GP) or a dentin adhesive Heliobond (HB)) or were manually polished with silicon polishers (MP) ( n  = 16). The average roughness (Ra) and colourimetric parameters (CP) (L*a*b*) were evaluated. The specimens underwent an artificial ageing process by thermocycling, staining (coffee) and abrasive (toothbrushing) procedures. After each ageing step, Ra and CP measurements were repeated. A qualitative surface analysis was performed with SEM. The differences between the test groups regarding Ra and CP values were analysed with nonparametric ANOVA analysis ( α  = 0.05). The lowest Ra values were achieved with HB. BC and GP resulted in Ra values below 0.2 μm (clinically relevant threshold), whereas LT and MP sometimes led to higher Ra values. LT showed a significantly higher discolouration after the first coffee staining, but this was normalised to the other groups after toothbrushing. The differences between the measurements and test groups for Ra and CP were statistically significant. However, the final colour difference showed no statistical difference among the five groups. SEM evaluation showed clear alterations after ageing in all coating groups. Surface sealants and dentin adhesives have the potential to reduce surface roughness but tend to debond over time. Surface sealants can only be recommended for polishing provisional restorations.

Objectives To evaluate the effect of a tin-containing fluoride (Sn/F) mouth rinse on microtensile bond strength (μTBS) between resin composite and erosively demineralised dentin. Materials and methods Dentin of 120 human molars was erosively demineralised using a 10-day cyclic de- and remineralisation model. For 40 molars, the model comprised erosive demineralisation only; for another 40, the model included treatment with a NaF solution; and for yet another 40, the model included treatment with a Sn/F mouth rinse. In half of these molars ( n  = 20), the demineralised organic matrix was continuously removed by collagenase. Silicon carbide paper-ground, non-erosively demineralised molars served as control ( n  = 20). Subsequently, μTBS of Clearfil SE/Filtek Z250 to the dentin was measured, and failure mode was determined. Additionally, surfaces were evaluated using SEM and EDX. Results Compared to the non-erosively demineralised control, erosive demineralisation resulted in significantly lower μTBS regardless of the removal of demineralised organic matrix. Treatment with NaF increased μTBS, but the level of μTBS obtained by the non-erosively demineralised control was only reached when the demineralised organic matrix had been removed. The Sn/F mouth rinse together with removal of demineralised organic matrix led to significantly higher µTBS than did the non-erosively demineralised control. The Sn/F mouth rinse yielded higher μTBS than did the NaF solution. Conclusions Treatment of erosively demineralised dentin with a NaF solution or a Sn/F mouth rinse increased the bond strength of resin composite. Clinical relevance Bond strength of resin composite to eroded dentin was not negatively influenced by treatment with a tin-containing fluoride mouth rinse.

This study evaluated (1) the micromorphology by scanning electron microscopy (SEM) and (2) the adhesive performance by microtensile bond strength (μTBS) of diamond bur-treated dentin compared to Er:YAG laser-treated dentin of human primary teeth. (1) For qualitative SEM evaluation, dentin of 18 second primary molars ( n  = 3/method) was treated with either diamond bur as a control (group 1a: 40 μm diamond bur only (clinical situation); group 1b: grinding + 40 μm diamond bur) or with Er:YAG laser (group 2a (clinical situation, manufacturer’s settings): 200 mJ/25 Hz (5 W) + 100 mJ/35 Hz (3.5 W) laser only; group 2b (experimental setting \"high\"): grinding + 400 mJ/20 Hz (8 W); group 2c (manufacturer’s setting \"finishing\"): grinding + 100 mJ/35 Hz (3.5 W); group 2d (experimental setting \"low\"): grinding + 50 mJ/35 Hz (1.75 W)). (2) For evaluation of adhesive performance, 64 second primary molars were divided into four groups and treated as described for group 1b and groups 2b/c/d ( n  = 16/method), and μTBS of Clearfil SE/Clearfil Majesty Esthetic to dentin was measured. The SEM micrographs were qualitatively analyzed. The μTBS values were compared with a Kruskal–Wallis test. The significance level was set at α = 0.05. SEM micrographs showed the typical micromorphologies with a smear layer for the diamond bur groups and open dentin tubules for all laser-treated groups. However, in group 2d, the laser beam had insufficiently irradiated the dentin area, rendering the underlying ground surface partly visible. There were no statistically significant differences between μTBS values of the four groups ( p  = 0.394). This suggests that Er:YAG laser treatment of dentin of primary molars provides bond strengths similar to those obtained following diamond bur treatment.

We present a new method for highly physical solar radiation pressure (SRP) modeling in Earth’s penumbra. The fundamental geometry and approach mirrors past work, where the solar radiation field is modeled using a number of light rays, rather than treating the Sun as a single point source. However, we aim to clarify this approach, simplify its implementation, and model previously overlooked factors. The complex geometries involved in modeling penumbra solar radiation fields are described in a more intuitive and complete way to simplify implementation. Atmospheric effects are tabulated to significantly reduce computational cost. We present new, more efficient and accurate approaches to modeling atmospheric effects which allow us to consider the high spatial and temporal variability in lower atmospheric conditions. Modeled penumbra SRP accelerations for the Gravity Recovery and Climate Experiment (GRACE) satellites are compared to the sub-nm / s 2 precision GRACE accelerometer data. Comparisons to accelerometer data and a traditional penumbra SRP model illustrate the improved accuracy which our methods provide. Sensitivity analyses illustrate the significance of various atmospheric parameters and modeled effects on penumbra SRP. While this model is more complex than a traditional penumbra SRP model, we demonstrate its utility and propose that a highly physical model which considers atmospheric effects should be the basis for any simplified approach to penumbra SRP modeling.

Objectives To determine the effect on resin composite-to-dentin bond strength of incorporation of an acidic tin–chloride pretreatment in two adhesive systems. Materials and methods Human molars were ground to expose mid-coronal dentin. For microtensile bond strength (μTBS) testing, dentin was treated with Optibond FL or Clearfil SE according to one of six protocols ( n  = 22/group). Group 1: Phosphoric acid etching, Optibond FL Prime, Optibond FL Adhesive (manufacturer’s instructions; control); Group 2: Tin–chloride pretreatment, Optibond FL Prime, Optibond FL Adhesive; Group 3: Phosphoric acid etching, tin–chloride pretreatment, Optibond FL Prime, Optibond FL Adhesive; Group 4: Clearfil SE Primer, Clearfil SE Bond (manufacturer’s instructions; control); Group 5: Phosphoric acid etching, Clearfil SE Primer, Clearfil SE Bond; and Group 6: Tin–chloride pretreatment, Clearfil SE Primer, Clearfil SE Bond. The molars were then built up with resin composite (Clearfil Majesty Esthetic). After storage (1 week, 100  % humidity, 37 °C) the μTBS was measured and failure mode was determined. Additionally, pretreated dentin surfaces were evaluated using SEM and EDX. The μTBS results were analyzed statistically by a Welch Two Sample t-test and a Kruskal–Wallis test followed by exact Wilcoxon rank sum tests with Bonferroni–Holm adjustment for multiple testing (α = 0.05). Results When Optibond FL was used, partial or total replacement of phosphoric acid with tin–chloride decreased μTBS significantly. In contrast, when Clearfil SE was used, inclusion of a tin–chloride pretreatment in the adhesive procedure increased μTBS significantly. Conclusions Tin–chloride pretreatment had a beneficial influence on the bond promoting capacity of the MDP-containing adhesive system Clearfil SE.