Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome.

BACKGROUND: Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors. RESULTS: We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation "blacklist" in the BED region to reduce errors in downstream analyses. CONCLUSIONS: We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation.

Unveiling Liquid-Phase Exfoliation of Graphite and Boron Nitride Using Fluorescent Dyes Through Combined Experiments and Simulations.

Liquid-phase exfoliation (LPE) in aqueous solutions provides a simple, scalable, and green approach to produce 2D materials. By combining atomistic simulations with exfoliation experiments, the interaction between a surfactant and a 2D layer at the molecular scale can be better understood. In this work, two different dyes, corresponding to rhodamine B base (Rbb) and to a phenylboronic acid BODIPY (PBA-BODIPY) derivative, are employed as dispersants to exfoliate graphene and hexagonal boron nitride (hBN) through sonication-assisted LPE. The exfoliated 2D sheets, mostly as few-layers, exhibit good quality and high loading of dyes. Using molecular dynamics (MD) simulations, the binding free energies are calculated and the arrangement of both dyes on the layers are predicted. It has been found that the dyes show a higher affinity toward hBN than graphene, which is consistent with the higher yields of exfoliated hBN. Furthermore, it is demonstrated that the adsorption behavior of Rbb molecules on graphene and hBN is quite different compared to PBA-BODIPY.

Small extracellular vesicle-based delivery of interleukin-10 improves treatment of experimental autoimmune uveitis.

Non-infectious uveitis is an intraocular autoimmune disease mainly characterized by immune dysregulation of the eye, which may cause blindness if not well treated. Interleukin 10 (IL-10) is a potent cytokine with multiple immunoregulatory functions. However, it's in vivo activity is unstable owing to its inherent protein instability and short plasma half-life. Therefore, our previous research tried to establish IL-10-overexpressing MSC-sEVs (sEVs-IL10) using lentiviral transfection. While this approach indeed improved drug delivery, it also suffered from tedious procedures and limited loading efficiency. Accordingly, we constructed a novel MSC-sEVs-based delivery system for IL-10 (IL-10@sEVs) by sonication. The obtained formulation (IL-10@sEVs) had relatively higher loading efficiency and exerted a more profound immunomodulatory effect than sEVs-IL10 in vitro. Furthermore, IL-10@sEVs had significant therapeutic effects in a mouse model of experimental autoimmune uveitis (EAU) by decreasing the percentage of Th17 cells, increasing regulatory T cells in the eye, and draining lymph nodes. In summary, sonication outperforms conventional transfection methods for loading IL-10 into MSC-sEVs.

Results of a monocentric field study: value of histology compared to sonication method and conventional tissue culture in the diagnosis of periprosthetic joint infection (PJI).

BACKGROUND: To confirm the diagnosis of periprosthetic joint infection (PJI), the Infectious Diseases Society of America (IDSA) and the International Consensus Meeting (ICM) have defined criteria that include histology as a minor criterion and the sonication method only as an additional criterion. The aim of this monocentric, retrospective study was to investigate the value of histology and whether sonication leads to a more accurate diagnosis. MATERIALS AND METHODS: All revision surgeries for knee and hip arthroplasty between 2017 and 2020 were included. With regard to microbiological diagnostic, conventional culture of periprosthetic biopsies and sonication of explant material were performed. In addition, histology and non-specific inflammatory markers (CRP, leukocytes) were recorded. RESULTS: A total of 78 patients with PJI and 62 aseptic controls were included. From both microbiological methods (conventional culture / sonication), Staphyloccus (S.) epidermidis and S. aureus were detected most frequently. However, compared to the conventional microbiology, a higher sensitivity was calculated for sonication, albeit with a lower specificity in relation to a PJI. In two logistic regression models for the significance of all diagnostic parameters in PJI, the AUC was 0.92 and 0.96 with histology in particular making the decisive contribution in both models (p < 0. 001, both models). CONCLUSION: Since histology showed the highest accuracy in the current study, its importance in the PJI criteria should be reevaluated. Sonication shows a high sensitivity for germ detection with a lower specificity and should only be used in combination with the conventional culture for microbiolgical diagnostics.

Optimal ultrasonic treatment frequency and duration parameters were used to detect the pathogenic bacteria of orthopedic implant-associated infection by ultrasonic oscillation.

INTRUDUCTON: The most accurate method for detecting the pathogen of orthopedic implant-associated infections (OIAIs) is sonication fluid (SF). However, the frequency and duration of ultrasound significantly influence the number and activity of microorganisms. Currently, there is no consensus on the selection of these two parameters. Through this study, the choice of these two parameters is clarified. METHODS: We established five ultrasonic groups (40kHz/10min, 40kHz/5min, 40 kHz/1min, 20kHz/5min, and 10kHz/5min) based on previous literature. OIAIs models were then developed and applied to ultrasound group treatment. Subsequently, we evaluated the efficiency of bacteria removal by conducting SEM and crystal violet staining. The number of live bacteria in the SF was determined using plate colony count and live/dead bacteria staining. RESULTS: The results of crystal violet staining revealed that both the 40kHz/5min group and the 40kHz/10min group exhibited a significantly higher bacterial clearance rate compared to the other groups. However, there was no significant difference between the two groups. Additionally, the results of plate colony count and fluorescence staining of live and dead bacteria indicated that the number of live bacteria in the 40kHz/5min SF group was significantly higher than in the other groups. CONCLUSION: 40kHz/5min ultrasound is the most beneficial for the detection of pathogenic bacteria on the surface of orthopedic implants.

Magnetic Resonance-Guided Focused Ultrasound without Anesthesiologist Support.

INTRODUCTION: Magnetic resonance-guided focused ultrasound (MRgFUS) is an effective treatment option for essential tremor (ET) and tremor dominant Parkinson's disease (TDPD), which is often performed with sedation or in the presence of an anesthesiologist in an effort to minimize adverse events and maximize patient comfort. This study explores the safety, feasibility, and tolerability of performing MRgFUS without an anesthesiologist. METHODS: This is a single academic center, retrospective review of 180 ET and TDPD patients who underwent MRgFUS treatment without anesthesiologist support. Patient demographics, intra-procedural treatment parameters, peri-procedural adverse events, and 3-month Clinical Rating Scale for Tremor Part B (CRST-B) scores were compared to MRgFUS studies that utilized varying degrees of anesthesia. RESULTS: There were no anesthesia related adverse events or unsuccessful treatments. There were no early treatment terminations due to patient discomfort, regardless of skull density ratio. 94.6% of patients would repeat the procedure again. The most common side effects during treatment were facial/tongue paresthesia (26.3%), followed by nausea (22.3%), dysarthria (8.6%), and scalp pain (8.0%). No anxiolytic, pain, or antihypertensive medications were administered. The most common early adverse event after MRgFUS procedure was gait imbalance (58.3%). There was a significant reduction of 83.1% (83.4% ET and 80.5% TDPD) of the mean CRST-B scores of the treated hand when comparing 3-month and baseline scores (1.8 vs. 10.9, n = 109, p < 0.0001). CONCLUSION: MRgFUS without intra-procedural anesthesiologist support is a safe, feasible, and well-tolerated option, without an increase in peri-procedural adverse events.

Differences in Diagnostic Sensitivity of Cultures Between Sample Types in Periprosthetic Joint Infections: A Systematic Review and Meta-Analysis.

BACKGROUND: Differences between the bacterial culture results of the preoperative fluid, intraoperative tissue, and sonication fluid of implants in the diagnosis of periprosthetic joint infection (PJI) are important issues in clinical practice. This study aimed to identify the differences in pooled diagnostic accuracy between culture sample types for diagnosing PJI by performing a systematic review and meta-analysis. METHODS: This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis statement. A comprehensive literature search of PubMed, Cumulative Index to Nursing and Allied Health Literature, and Cochrane Library databases was performed. Data extraction and study assessment using the quality assessment of diagnostic accuracy studies were performed independently by two reviewers. The pooled sensitivity, specificity, summary receiver operating characteristic curve, and area under the summary receiver operating characteristic curve were estimated for each sample type. RESULTS: There were thirty-two studies that were included in the analysis after screening and eligibility assessment. The pooled sensitivities of preoperative fluid, intraoperative tissue, and sonication fluid for the diagnosis of PJI were 0.63 (95% confidence interval [CI] 0.56 to 0.70), 0.71 (95% CI 0.63 to 0.79), and 0.78 (95% CI 0.68 to 0.85), while the specificities were 0.96 (95% CI 0.93 to 0.98), 0.92 (95% CI 0.86 to 0.96), and 0.91 (95% CI 0.83 to 0.95), respectively. The area under the curves for preoperative fluid, intraoperative tissue, and sonication fluid were 0.86, 0.88, and 0.90, respectively. CONCLUSIONS: Sonication fluid culture demonstrated better sensitivity compared with the conventional culture method, and preoperative fluid culture provided lower sensitivity in diagnosing PJI.

Sonocatalytic Activity of Porous Carbonaceous Materials for the Selective Oxidation of 4-Hydroxy-3,5-dimethoxybenzyl Alcohol.

Selective oxidation, which is crucial in diverse chemical industries, transforms harmful chemicals into valuable compounds. Heterogeneous sonocatalysis, an emerging sustainable approach, urges in-depth exploration. In this work, we investigated N-doped or non-doped carbonaceous materials as alternatives to scarce, economically sensitive metal-based catalysts. Having synthesized diverse carbons using a hard-template technique, we subjected them to sonication at frequencies of 22, 100, 500, and 800 kHz with a 50% amplitude. Sonochemical reaction catalytic tests considerably increased the catalytic activity of C-meso (non-doped mesoporous carbon material). The scavenger test showed a radical formation when this catalyst was used. N-doped carbons did not show adequate and consistent sonoactivity for the selective oxidation of 4-Hydroxy-3,5 dimethoxybenzyl alcohol in comparison with control conditions without sonication, which might be associated with an acid-base interaction between the catalysts and the substrate and sonoactivity prohibition by piridinic nitrogen in N-doped catalysts.

Process Optimization of Tinospora cordifolia Extract-Loaded Water in Oil Nanoemulsion Developed by Ultrasound-Assisted Homogenization.

Nanoemulsions are gaining interest in a variety of products as a means of integrating easily degradable bioactive compounds, preserving them from oxidation, and increasing their bioavailability. However, preparing stable emulsion compositions with the desired characteristics is a difficult task. The aim of this study was to encapsulate the Tinospora cordifolia aqueous extract (TCAE) into a water in oil (W/O) nanoemulsion and identify its critical process and formulation variables, like oil (27-29.4 mL), the surfactant concentration (0.6-3 mL), and sonication amplitude (40% to 100%), using response surface methodology (RSM). The responses of this formulation were studied with an analysis of the particle size (PS), free fatty acids (FFAs), and encapsulation efficiency (EE). In between, we have studied a fishbone diagram that was used to measure risk and preliminary research. The optimized condition for the formation of a stable nanoemulsion using quality by design was surfactant (2.43 mL), oil concentration (27.61 mL), and sonication amplitude (88.6%), providing a PS of 171.62 nm, FFA content of 0.86 meq/kg oil and viscosity of 0.597 Pa.s for the blank sample compared to the enriched TCAE nanoemulsion with a PS of 243.60 nm, FFA content of 0.27 meq/kg oil and viscosity of 0.22 Pa.s. The EE increases with increasing concentrations of TCAE, from 56.88% to 85.45%. The RSM response demonstrated that both composition variables had a considerable impact on the properties of the W/O nanoemulsion. Furthermore, after the storage time, the enriched TCAE nanoemulsion showed better stability over the blank nanoemulsion, specially the FFAs, and the blank increased from 0.142 to 1.22 meq/kg oil, while TCAE showed 0.266 to 0.82 meq/kg.

Seed germination and seedling development assisted by ultrasound: gaps and future research directions.

Since the early 1930s, when the first corn hybrids were grown commercially, innovations in the agriculture industry have had an unprecedent impact worldwide, helping to meet the demands for food of an exponentially growing population. In particular, seed technology research has contributed substantially to the improvement of crop performance over the years. Ultrasonic treatment of seeds is a green technology that promises to have an impact on the food industry, enhancing germination and seedling development in different species through the stimulation of water and oxygen uptake and seed metabolism. The increase in starch degradation has been associated with the stimulation of the α-amylases of the endosperm, but relatively few reports focus on how ultrasound affects seed germination at the biochemical and molecular levels. For instance, the picture is still unclear regarding the impact of ultrasound on transcriptional reprogramming in seeds. The purpose of this review is to assess the literature on ultrasound seed treatment accurately and critically, ultimately aiming to encourage new scientific and technological breakthroughs with a real impact on worldwide agricultural production while promoting sustainable practices on biological systems. © 2023 Society of Chemical Industry.

Fabrication of composite hydrogels by sonication-assisted assembly of okara cellulose nanofibers and chitosan: structure and properties.

BACKGROUND: Okara cellulose is a highly abundant, green, sustainable, and biodegradable polymer with many potential industrial applications. In this study, we fabricated composite hydrogels with okara cellulose nanofibers (CNFs) and chitosan (CH) by hydrating, sonicating, and heating them at 100 °C for 30 min, and then induced their assembly by cooling. The effects of okara CNF (with and without 2,2,6,6-tetramethylpiperidinyloxy (TEMPO) oxidation) and CH concentration on the structure and properties of the hydrogels was examined, including their microstructure, surface properties, rheological properties, and thermal stability. RESULTS: Our results indicate that there was an electrostatic attraction between the anionic okara CNF and cationic CH, which facilitated hydrogel formation. The surface, textural, rheological, and thermal stability properties were better for the composite hydrogels than for the single CH ones, as well as for the CNF that had undergone TEMPO oxidation. For the TC-CH hydrogels, the contact angle was 39.5°, the interfacial tension was 69.1 mN m-1 , and the surface tension was 1.44 mN m-1 . CONCLUSION: In this study, the novel hydrogels developed may be useful as a soft material in a range of applications in foods, supplements, health care products, cosmetics, and drugs. © 2023 Society of Chemical Industry.

Cryptococcus neoformans capsule regrowth experiments reveal dynamics of enlargement and architecture.

The polysaccharide capsule of fungal pathogen Cryptococcus neoformans is a critical virulence factor that has historically evaded complete characterization. Cryptococcal polysaccharides are known to either remain attached to the cell as capsular polysaccharides (CPSs) or to be shed into the extracellular space as exopolysaccharides (EPSs). While many studies have examined the properties of EPS, far less is known about CPS. In this work, we detail the development of new physical and enzymatic methods for the isolation of CPS which can be used to explore the architecture of the capsule and isolated capsular material. We show that sonication or Glucanex enzyme cocktail digestion yields soluble CPS preparations, while use of a French pressure cell press or Glucanex digestion followed by cell disruption removed the capsule and produced cell wall-associated polysaccharide aggregates that we call "capsule ghosts", implying an inherent organization that allows the CPS to exist independent of the cell wall surface. Since sonication and Glucanex digestion were noncytotoxic, it was also possible to observe the cryptococcal cells rebuilding their capsule, revealing the presence of reducing end glycans throughout the capsule. Finally, analysis of dimethyl sulfoxide-extracted and sonicated CPS preparations revealed the conservation of previously identified glucuronoxylomannan motifs only in the sonicated CPS. Together, these observations provide new insights into capsule architecture and synthesis, consistent with a model in which the capsule is assembled from the cell wall outward using smaller polymers, which are then compiled into larger ones.

Latanoprost-Loaded Nanotransfersomes Designed for Scalp Administration Enhance Keratinocytes Proliferation.

Latanoprost (LAT) has been shown to have a hypertrichotic effect, which makes it a promising candidate for alopecia treatments. For the first time, LAT has been encapsulated in nanotransfersomes in order to increase its efficacy. Ex vivo skin biodistribution was studied by confocal laser microscopy both in human scalp and pig skin. Results showed that nanotransfersomes increase the penetration of two different fluorochromes, with similar patterns in both species, compared with fluorochrome solutions containing no nanotransfersomes. Nanotransfersomes were stable under accelerated conditions (40 °C/75% RH) and long-term conditions (25 °C/60% RH) for up to 1 year, with no differences in vesicle size and polydispersity when LAT was loaded. Nanotransfersomes increased the LAT cell proliferation effect in HaCaT cell via MAPK signaling pathway. Collectively, our results demonstrate LAT-nanotransfersomes formulation could be a promising therapy for hair growth disorders.

Probe sonication-assisted rapid synthesis of highly fluorescent sulfur quantum dots.

A new type of heavy-metal free single-element nanomaterial, called sulfur quantum dots (SQDs), has gained significant attention due to its advantages over traditional semiconductor QDs for several biomedical and optoelectronic applications. A straightforward and rapid synthesis approach for preparing highly fluorescent SQDs is needed to utilize this nanomaterial for technological applications. Until now, only a few synthesis approaches have been reported; however, these approaches are associated with long reaction times and low quantum yields (QY). Herein, we propose a novel optimized strategy to synthesize SQDs using a mix of probe sonication and heating, which reduces the reaction time usually needed from 125 h to a mere 15 min. The investigation employs cavitation and vibration effects of high energy acoustic waves to break down the bulk sulfur into nano-sized particles in the presence of highly alkaline medium and oleic acid. In contrast to previous reports, the obtained SQDs exhibited excellent aqueous solubility, desirable photostability, and a relatively high photoluminescence QY up to 10.4% without the need of any post-treatment. Additionally, the as-synthesized SQDs show excitation-dependent emission and excellent stability in different pH (2-12) and temperature (20 °C-80 °C) environments. Hence, this strategy opens a new pathway for rapid synthesis of SQDs and may facilitate the use of these materials for biomedical and optoelectronic applications.

Design, synthesis and molecular docking of novel substituted azepines as inhibitors of PI3K/Akt/TSC2/mTOR signaling pathway in colorectal carcinoma.

A series of novel substituted azepines (2-7) was synthesized using both traditional and ultrasonic techniques. The efficiency of the reaction rate and yield was improved by sonication technique. We identified the newly synthesized compounds based on their melting points, elemental analyses, and spectral data. Human cancers are regulated mainly by the phosphatidylinositol 3-kinase/protein kinases B (PI3K/Akt) pathway, and its abnormal activation is linked to carcinogenesis, and angiogenesis. Using in-silico studies, we evaluated the ability of all the novel substituted diazepines and oxazepines to prevent cancer growth and metastasis by targeting the PI3K/Akt signaling pathway. Based on our findings, compounds 4a and 7a were chosen for in-vitro testing as they ranked via molecular docking the highest binding energies of -10.9, -10.3, -10.6, and -10.4 kcal/mol respectively. Compounds 4a and 7a displayed significant cytotoxicity on Caco-2 colorectal cancer cells with IC50 values of 8.445 ± 2.26 and 33.04 ± 2.06 µM, respectively. Additionally, they considerably suppressed the PI3K/Akt proteins and generated reactive oxygen species (ROS), which increased p53 and Bax, decreased Bcl-2 levels, and arrested the cell cycle at sub-G0/G1 phase. We also observed a remarkable overexpression of the Tuberous Sclerosis Complex 2 (TSC2) gene, an inhibitor of the mammalian target of rapamycin (mTOR). These results showed that compounds 4a and 7a obeyed Lipinski's rule of five and might be potential cancer treatment scaffolds by preventing metastasis and proliferation via blocking the PI3K/Akt/TSC2/m-TOR signaling pathway. This supports our hypothesis that diazepine 4a and oxazepine 7a are promising drug candidates for colorectal cancer.

Multifarious extraction methodologies for ameliorating lipid recovery from algae.

Amongst the current alternatives, algae were proven to be a promising source of biofuel, which is renewable and capable of meeting world demand for transportation fuels. However, a suitable lipid extraction method that efficiently releases the lipids from different algal strains remains a bottleneck. The multifarious pretreatment methods are prevalent in this field of lipid extraction, and therefore, this article has critically reviewed the various lipid extraction methods for ameliorating the lipid yield from algae, irrespective of the strains/species. Physical, mechanical, and chemical are the different types of pretreatment methods. In this review, methodologies such as homogenization, sonication, Soxhlet extraction, microwave treatment, and bead-beating, have been studied in detail and are the most commonly used methods for lipid extraction. Specific advanced/emerging processes such as supercritical CO2 extraction, ionic liquid, and CO2 switchable solvent-based algal lipid extraction are yet to be demonstrated at pilot-scale, though promising. The extraction of lipids has to be financially conducive, environmentally sustainable, and industrially applicable for further conversion into biodiesel. Hence, this paper discusses variable pretreatment for lipid extraction and imparts a comparative analysis to elect an efficient, economically sound lipid extraction method for pilot-scale biodiesel production.

A prospective study to identify preoperative serum parameters for spinal implant infection detected by sonication fluid culture.

PURPOSE: Low-virulent microorganisms identified on pedicle screws by sonication fluid culture (SFC) are an important cause of implant loosening. While sonication of explanted material improves the detection rate, the risk of contamination exists and no standardized diagnostic criteria for chronic low-grade spinal implant-related infection (CLGSII) are stablished. Besides, the role of serum C-reactive protein (CRP) and procalcitonin (PCT) in CLGSII has not been adequately investigated. METHODS: Blood samples were collected prior to implant removal. To increase sensitivity, the explanted screws were sonicated and processed separately. Patients exhibiting at least one positive SFC were classified in the infection group (loose criteria). To increase specificity, the strict criteria only considered multiple positive SFC (≥ 3 implants and/or ≥ 50% of explanted devices) as meaningful for CLGSII. Factors which might promote implant infection were also recorded. RESULTS: Thirty-six patients and 200 screws were included. Among them, 18 (50%) patients had any positive SFCs (loose criteria), whereas 11 (31%) patients fulfilled the strict criteria for CLGSII. Higher serum protein level was the most accurate marker for the preoperative detection of CLGSSI, exhibiting an area under the curve of 0.702 (loose criteria) and 0.819 (strict criteria) for the diagnosis of CLGSII. CRP only exhibited a modest accuracy, whereas PCT was not a reliable biomarker. Patient history (spinal trauma, ICU hospitalization and/or previous wound-related complications) increased the likelihood of CLGSII. CONCLUSION: Markers of systemic inflammation (serum protein level) and patient history should be employed to stratify preoperative risk of CLGSII and decide the best treatment strategy.

The value of sonication on orthopaedic implants in an everyday clinical setting - an exploratory study.

BACKGROUND: Sonication of removed orthopaedic implants in suspected implant-associated infections (IAI) is widely applied internationally. However, evaluation of the utility of sonication on all implants removed in everyday standard practice is scarce. This exploratory study was performed to evaluate the application of sonication fluid (SF) culture on removed orthopaedic implants, irrespective of the reason for removal. METHODS: Out of 100 removed orthopaedic implants collected between August 2019 and September 2020, 77 implants with availability of concurrent tissue culture samples were included in the study. Removed implants were categorized into a confirmed or suspected IAI group and a presumed aseptic group based on pre-operative diagnosis by the responsible surgeon. Implants were sonicated and SF culture performed under both aerobic and anaerobic conditions. The significance of all bacterial isolates was evaluated based on the CFU/mL cut-offs of the EBJIS guidelines, except for C. acnes where additional investigations were performed. RESULTS: The results of SF culture in the two groups were compared with their corresponding tissue cultures. Out of the 12 cases in the confirmed/suspected IAI group, SF culture was positive in 11 cases and had increased diagnostic yield in two (17%) cases compared to tissue culture. Increased diagnostic yield of SF compared to tissue culture was seen in seven (11%) of the 65 implants in the presumed aseptic group. If growth of Cutibacterium species isolates were interpreted based on EBJIS cut-off for SF culture instead of the study-specific criteria, then two isolates considered to represent infection might have been missed while three other isolates considered contaminants would have fallen under the 'infection confirmed' category in the EBJIS guidelines. CONCLUSION: Sonication with SF culture has increased diagnostic yield compared to tissue cultures in all implants irrespective of reason for removal. However, positive SF cultures with Cutibacterium species should always be interpreted with extreme care.

Sonication as a pre-processing step to alter acid whey generation during Greek yoghurt manufacture.

We investigated sonication as a pre-processing step to reduce acid whey generation during Greek yoghurt manufacture. The generation of a large amount of acid whey during the production of Greek yoghurt is an ongoing problem in the dairy industry and many studies are currently focusing on reducing it. We focused on the use of ultrasonication as a novel approach to minimize the casein fraction in the acid whey stream and simultaneously improve the gel properties. Ultrasound applied before the fermentation modified the structural properties and bonding behaviours of milk proteins, and enhanced the retention of casein in the yoghurt gel after the fermentation and straining steps. Therefore, the use of low-frequency ultrasonication as a pre-processing step may have the potential to provide significant economic benefits to the Greek yoghurt manufacturing process. Moreover, it improved the nutritional and physicochemical properties compared to regular Greek yoghurts.

Optimizing the use of low-frequency ultrasound for bacterial detachment of in vivo biofilms in dental research-a methodological study.

OBJECTIVES: Low-frequency, low-intensity ultrasound is commonly utilized in various dental research fields to remove biofilms from surfaces, but no clear recommendation exists in dental studies so far. Therefore, this study aims to optimize the sonication procedure for the dental field to efficiently detach bacteria while preserving viability. MATERIALS AND METHODS: Initial biofilm was formed in vivo on bovine enamel slabs (n = 6) which were worn by four healthy participants for 4 h and 24 h. The enamel slabs covered with biofilm were then ultrasonicated ex vivo for various time periods (0, 1, 2, 4, 6 min). Colony-forming units were determined for quantification, and bacteria were identified using MALDI-TOF. Scanning electron microscopic images were taken to also examine the efficiency of ultrasonications for different time periods. RESULTS: Ultrasonication for 1 min resulted in the highest bacterial counts, with at least 4.5-fold number compared to the non-sonicated control (p < 0.05). Most bacteria were detached within the first 2 min of sonication, but there were still bacteria detached afterwards, although significantly fewer (p < 0.0001). The highest bacterial diversity was observed after 1 and 2 min of sonication (p < 0.03). Longer sonication periods negatively affected bacterial counts of anaerobes, Gram-negative bacteria, and bacilli. Scanning electron microscopic images demonstrated the ability of ultrasound to desorb microorganisms, as well as revealing cell damage and remaining bacteria. CONCLUSIONS: With the use of low-frequency, low-intensity ultrasound, significantly higher bacterial counts and diversity can be reached. A shorter sonication time of 1 min shows the best results overall. CLINICAL RELEVANCE: This standardization is recommended to study initial oral biofilms aged up to 24 h to maximize the outcome of experiments and lead to better comparability of studies.