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The aim of this study was to test a newly developed LED-based fluorescence device for approximal caries detection in vitro. We assembled 120 extracted molars without frank cavitations or fillings pairwise in order to create contact areas. The teeth were independently assessed by two examiners using visual caries detection (International Caries Detection and Assessment System, ICDAS), bitewing radiography (BW), laser fluorescence (LFpen), and LED fluorescence (Midwest Caries I.D., MW). The measurements were repeated at least 1 week later. The diagnostic performance was calculated with Bayesian analyses. Post-test probabilities were calculated in order to judge the diagnostic performance of combined methods. Reliability analyses were performed using kappa statistics for nominal data and intraclass correlation (ICC) for absolute data. Histology served as the gold standard. Sensitivities/specificities at the enamel threshold were 0.33/0.84 for ICDAS, 0.23/0.86 for BW, 0.47/0.78 for LFpen, and 0.32/0.87 for MW. Sensitivities/specificities at the dentine threshold were 0.04/0.89 for ICDAS, 0.27/0.94 for BW, 0.39/0.84 for LFpen, and 0.07/0.96 for MW. Reliability data were fair to moderate for MW and good for BW and LFpen. The combination of ICDAS and radiography yielded the best diagnostic performance (post-test probability of 0.73 at the dentine threshold). The newly developed LED device is not able to be recommended for approximal caries detection. There might be too much signal loss during signal transduction from the occlusal aspect to the proximal lesion site and the reverse. [ABSTRACT FROM AUTHOR]

The aim of the study was to compare fissure sealant quality after mechanical conditioning of erbium-doped yttrium aluminium garnet (Er:YAG) laser or air abrasion prior to chemical conditioning of phosphoric acid etching or of a self-etch adhesive. Twenty-five permanent molars were initially divided into three groups: control group ( n = 5), phosphoric acid etching; test group 1 ( n = 10), air abrasion; and test group 2, ( n = 10) Er:YAG laser. After mechanical conditioning, the test group teeth were sectioned buccolingually and the occlusal surface of one half tooth (equal to one sample) was acid etched, while a self-etch adhesive was applied on the other half. The fissure system of each sample was sealed, thermo-cycled and immersed in 5 % methylene dye for 24 h. Each sample was sectioned buccolingually, and one slice was analysed microscopically. Using specialized software microleakage, unfilled margin, sealant failure and unfilled area proportions were calculated. A nonparametric ANOVA model was applied to compare the Er:YAG treatment with that of air abrasion and the self-etch adhesive with phosphoric acid ( α = 0.05). Test groups were compared to the control group using Wilcoxon rank sum tests ( α = 0.05). The control group displayed significantly lower microleakage but higher unfilled area proportions than the Er:YAG laser + self-etch adhesive group and displayed significantly higher unfilled margin and unfilled area proportions than the air-abrasion + self-etch adhesive group. There was no statistically significant difference in the quality of sealants applied in fissures treated with either Er:YAG laser or air abrasion prior to phosphoric acid etching, nor in the quality of sealants applied in fissures treated with either self-etch adhesive or phosphoric acid following Er:YAG or air-abrasion treatment. [ABSTRACT FROM AUTHOR]

The German electronics component firm Isola Group is used to illustrate leadership methods involving and empowering employees. These were drawn from the Japanese management tool called the five S's: sort, store, shine, standardize, and sustain.

Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription. [ABSTRACT FROM AUTHOR]

Overlapping embedded genes, such as htgA / yaaW, are assumed to be rare in prokaryotes. In Escherichia coli O157: H7, gfp fusions of both promoter regions revealed activity and transcription start sites could be determined for both genes. Both htgA and yaaW were inactivated strand specifically by introducing a stop codon. Both mutants exhibited differential phenotypes in biofilm formation and metabolite levels in a nontargeted analysis, suggesting that both are functional despite Yaa W but not Htg A could be expressed. While yaaW is distributed all over the Gammaproteobacteria, an overlapping htgA-like sequence is restricted to the Escherichia- Klebsiella clade. Full-length htgA is only present in Escherichia and Shigella, and htgA showed evidence for purifying selection. Thus, htgA is an interesting case of a lineage-specific, nonessential and young orphan gene. [ABSTRACT FROM AUTHOR]

Aims The aim of this single-site, randomized, controlled, double-blind, 3-arm parallel study was to determine the effectiveness of a prophylaxis paste containing 15% calcium sodium phosphosilicate ( CSPS; NovaMin®) with and without fluoride in reducing dentine hypersensitivity immediately after a single application and 28 days following dental scaling and root planing. Materials & Methods Overall, 151 subjects were enrolled in this study. All subjects received a scaling and root planing procedure followed by a final prophylaxis step using one of three different prophylaxis pastes: Test-A (15% NovaMin® and NaF), Test-B (15% NovaMin®) and a control. Dentine hypersensitivity was assessed by tactile stimulus (Yeaple Probe®) and by air blast (Schiff scale) at baseline, immediately after and 28 days after a prophylaxis procedure. One hundred and forty-nine subjects completed the study. Results Subjects having received the test prophylaxis pastes showed statistically lower ( anova, p < 0.05) dentine hypersensitivity compared with the control group immediately after the prophylaxis procedure (Yeaple Probe®: Test-A = 20.9 ± 12.6, Test-B = 22.7 ± 12.9, Control=11.2 ± 3.1; Schiff score: Test-A = 1.1 ± 0.6, Test-B = 1.1 ± 0.6, Control = 2.0 ± 0.7) and after 28 days (Yeaple probe: Test-A = 21.5 ± 11.9, Test-B = 20.6 ± 11.3, Control = 11.8 ± 6.0; Schiff score: Test-A = 1.0 ± 0.6, Test-B = 1.0 ± 0.6, Control = 2.0 ± 0.7). Conclusions In conclusion, the single application of both fluoridated and non-fluoridated prophylaxis pastes containing 15% CSPS (NovaMin®) provided a significant reduction of dentine hypersensitivity up to at least 28 days. [ABSTRACT FROM AUTHOR]

Objectives: This study examined the near visual acuity of dentists in relation to age and magnification under simulated clinical conditions. Materials and methods: Miniaturized visual tests were performed in posterior teeth of a dental phantom head in a simulated clinical setting (dental chair, operating lamp, dental mirror). The visual acuity of 40 dentists was measured under the following conditions: (1) natural visual acuity, distance of 300 mm; (2) natural visual acuity, free choice of distance; (3) Galilean loupes, magnification of ×2.5; (4) Keplerian loupes, ×4.3; (5) operating microscope, ×4, integrated light; (6) operating microscope, ×6.4, integrated light. Results: The visual acuity varied widely between individuals and was significantly lower in the group ≥40 years of age ( p < 0.001). Significant differences were found between all tested conditions ( p < 0.01). Furthermore, a correlation between visual acuity and age was found for all conditions. The performance with the microscope was better than with loupes even with comparable magnification factors. Some dentists had a better visual acuity without optical aids than others with Galilean loupes. Conclusions: Near visual acuity under simulated clinical conditions varies widely between individuals and decreases throughout life. Visual deficiencies can be compensated for with optical aids. Clinical relevance: Newly developed miniaturized vision tests have allowed, in a clinically relevant way, to evaluate the influence of magnification and age on the near visual acuity of dentists. [ABSTRACT FROM AUTHOR]

The aim of this in vitro study was to assess the agreement among four techniques used as gold standard for the validation of methods for occlusal caries detection. Sixty-five human permanent molars were selected and one site in each occlusal surface was chosen as the test site. The teeth were cut and prepared according to each technique: stereomicroscopy without coloring (1), dye enhancement with rhodamine B (2) and fuchsine/acetic light green (3), and semi-quantitative microradiography (4). Digital photographs from each prepared tooth were assessed by three examiners for caries extension. Weighted kappa, as well as Friedman's test with multiple comparisons, was performed to compare all techniques and verify statistical significant differences. Results: kappa values varied from 0.62 to 0.78, the latter being found by both dye enhancement methods. Friedman's test showed statistical significant difference ( P < 0.001) and multiple comparison identified these differences among all techniques, except between both dye enhancement methods (rhodamine B and fuchsine/acetic light green). Cross-tabulation showed that the stereomicroscopy overscored the lesions. Both dye enhancement methods showed a good agreement, while stereomicroscopy overscored the lesions. Furthermore, the outcome of caries diagnostic tests may be influenced by the validation method applied. Dye enhancement methods seem to be reliable as gold standard methods. Microsc. Res. Tech., 2012. © 2011 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The aim of this in vitro study was to compare the performance of two laser fluorescence devices (LF, LFpen), conventional visual criteria (VE), ICDAS and radiographic examination on occlusal surfaces of primary teeth. Thirty-seven primary human molars were selected from a pool of extracted teeth, which were stored frozen at −20°C until use. Teeth were assessed twice by two experienced examiners using laser fluorescence devices (LF and LFpen), conventional visual criteria, ICDAS and bitewing radiographs, with a 2-week interval between measurements. After measurement, the teeth were histologically prepared and assessed for caries extension. The highest sensitivity was observed for ICDAS at D and D thresholds, with no statistically significant difference when compared to the LF devices, except at the D threshold. Bitewing radiographs presented the lowest values of sensitivity. Specificity at D was higher for LFpen (0.90) and for VE at D (0.94). When VE was combined with LFpen the post-test probabilities were the highest (94.0% and 89.2% at D and D thresholds, respectively). High values were observed for the combination of ICDAS and LFpen (92.0% and 80.0%, respectively). LF and LFpen showed the highest values of ICC for interexaminer reproducibility. However, regarding ICDAS, BW and VE, intraexaminer reproducibility was not the same for the two examiners. After primary visual inspection using ICDAS or not, the use of LFpen may aid in the detection of occlusal caries in primary teeth. Bitewing radiographs may be indicated only for approximal caries detection. [ABSTRACT FROM AUTHOR]

The article discusses the evidence on methods for prevention of adult dental caries, with focus on the reduction of dietary carbohydrates, limitation of cariogenic dental biofilm and the promotion of invasive technologies. It says that the caries increment is the outcome parameter of choice for the assessment of the efficacy of caries preventive strategies. It relates on several caries and lesion detection system including visual inspection, bite-wing radiography and laser fluorescence.

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The aim of this in vitro study was to assess the influence of varying examiner's clinical experience on the reproducibility and accuracy of radiographic examination for occlusal caries detection. Standardized bitewing radiographs were obtained from 166 permanent molars. Radiographic examination was performed by final-year dental students from two universities (A, n = 5; B, n = 5) and by dentists with 5 to 7 years of experience who work in two different countries (C, n = 5; D, n = 5). All examinations were repeated after 1-week interval. The teeth were histologically prepared and assessed for caries extension. For intraexaminer reproducibility, the unweighted kappa values were: A (0.11-0.40), B (0.12-0.33), C (0.47-0.58), and D (0.42-0.71). Interexaminer reproducibility statistics were computed based on means ± SD of unweighted kappa values: A (0.07 ± 0.05), B (0.12 ± 0.09), C (0.24 ± 0.08), and D (0.33 ± 0.10). Sensitivity, specificity, and accuracy were calculated at D and D thresholds and compared by performing McNemar test ( p = 0.05). D sensitivity ranged between 0.29 and 0.75 and specificity between 0.24 and 0.85. D specificity was moderate to high (between 0.62 and 0.95) for all groups, with statistically significant difference between the dentists groups (C and D). Sensitivity was low to moderate (between 0.21 and 0.57) with statistically significant difference for groups B and D. Accuracy was similar for all groups (0.55). Spearman's correlations were: A (0.12), B (0.24), C (0.30), and D (0.38). In conclusion, the reproducibility of radiographic examination was influenced by the examiner's clinical experience, training, and dental education as well as the accuracy in detecting occlusal caries. [ABSTRACT FROM AUTHOR]

When Listeria monocytogenes EGDe (serovar 1/2a) was cultivated in cell-free supernatants prepared from red smear cheese microbial ripening consortia grown for 8 h in liquid medium, 8 out of 49 supernatants exhibited a bactericidal activity, sometimes even reducing the inoculum of L. monocytogenes from 5 × 10 CFU/ml to zero after 24 h of incubation. Another five consortia displayed a bacteriostatic capacity. No inhibition in supernatants was observed when the complex consortia were incubated for a 10-min period only, indicating that the activity depends on actively growing consortia. Consortia displayed a very high biodiversity (Simpson's strain diversity index up to 0.97, species diversity up to 0.89). However, biodiversity did not correlate with anti-listerial activity. There was no obvious similarity between the anti-listerial consortia studied, and no general difference in comparison to non-inhibitory communities. The proportion of lactic acid bacteria (LAB) in the consortia ranged between 3 and 45%. Therefore, the presence of 23 different LAB bacteriocin genes was investigated using specific PCR primers, identifying one to five bacteriocin genes in several consortia. In situ transcription of lactococcin G mRNA on the cheese surface was demonstrated by RT-PCR in five samples, but this bacteriocin displayed no anti-listerial activity. Supernatants subjected to thermal and enzymatic treatment suggested the presence of heat-stable, non-proteinaceous molecules as well as heat-labile compounds which are sensitive to proteolytic digestion. Probably, substances other than LAB bacteriocins are responsible for the pronounced antilisterial action of some supernatants. [ABSTRACT FROM AUTHOR]

Lean Six Sigma is the bedrock of quality initiatives in manufacturing companies. Can this approach be used in service companies? It already is, and Peter Guarraia, Gib Carey, Alistair Corbett and Klaus Neuhaus show how techniques long used by Motorola and Toyota can be used in your company. [ABSTRACT FROM AUTHOR]

Abstract: This review provides an overview of recent progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism utilized by the bacteria when growing in diverse and varied environments. [Copyright &y& Elsevier]

We have used Salmonella enterica serovar Typhimurium ( S. typhimurium) which are able to colonize tumours besides spleen and liver. Bacteria were equipped with constructs encoding green fluorescent protein or luciferase as reporters under control of the promoter PBAD that is inducible withl-arabinose. Reporter genes could be induced in culture but also when the bacteria resided within the mouse macrophages J774A.1. More important, strong expression of reporters by the bacteria could be detected in mice after administration ofl-arabinose. This was especially pronounced in bacteria colonizing tumours. Histology demonstrated that the bacteria had accumulated in and close to necrotic areas of tumours. Bacterial gene induction was observed in both regions. PBAD is tightly controlled also in vivo because gene E of bacteriophage ΦX174 could be introduced as inducible suicide gene. The possibility to deliberately induce genes in bacterial carriers within the host should render them extremely powerful tools for tumour therapy. [ABSTRACT FROM AUTHOR]

Caries diagnostic studies differ with respect to their design, included patients/tooth samples, use of diagnostic and reference methods, calibration, blinding and data reporting. Such heterogeneity makes comparisons between studies difficult and could represent a substantial risk of bias (RoB) when it is not identified. Therefore, the present report aims to describe the development and background of a RoB assessment tool for caries diagnostic studies. The expert group developed and agreed to use a RoB assessment tool during three workshops. Here, existing instruments (e.g., QUADAS 2 and the Joanna Briggs Institute Reviewers' Manual) influenced the hierarchy and phrasing of the signalling questions that were adapted to the specific dental purpose. The tailored RoB assessment tool that was created consists of 16 signalling questions that are organized in four domains. This tool considers the selection/spectrum bias (1), the bias of the index (2) and reference tests (3), and the bias of the study flow and data analysis (4) and can be downloaded from the journal website. This paper explores possible sources of heterogeneity and bias in caries diagnostic studies and summarizes the relevant methodological aspects. [ABSTRACT FROM AUTHOR]

Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines. [ABSTRACT FROM AUTHOR]

Simple Summary: Feed for laboratory mice is available in different physical forms. However, there is insufficient standardization in nutrient composition and physical forms. Results pertaining to energy and nutrient digestibility show that differentially processed feed (pelleted vs. extruded) and even batches from the same provider (pelleted vs. pelleted) differ in starch gelatinization. Here we show that feed processing impacts the mice's gastrointestinal microbiome. Reproducibility and comparability between experiments with differently processed feeds in laboratory mice should not be taken for granted. Therefore, details on dietary ingredients and feed processing should be specified in studies that include animal experiments. The composition of the microbiome is subject to the host's diet. In commercial laboratory mouse diets, different physical forms of the same diets are available, containing—according to their labels—identical ingredients and nutrient compositions. However, variations in nutrient composition and starch gelatinization due to production processes and their impact on digestibility have been described. In this study, a total of 48 C57BL/J6 mice were assigned to two equal groups and were fed diets (produced with different processes—extruded vs. pelleted) for eight weeks in two biological replicates. At the end of the experiment, samples were collected from five different gastrointestinal regions, including the stomach, small intestine, cecum, large intestine, and an extracorporeal region (feces), and the microbiome was analyzed with 16S rRNA gene amplicon sequencing. The replicates in both experiments differed significantly in their relative abundances of Muribaculaceae species. Furthermore, the gastrointestinal content of pellet-fed mice contained larger numbers of Lactobacillus species. These results indicate that starch gelatinization and ingredient composition significantly influence microbial makeup. In conclusion, different feed processing methods may affect fundamental digestive and metabolic processes, impacting animal experiments and biasing microbiome data. [ABSTRACT FROM AUTHOR]

Genomic studies revealed the glycoside hydrolases of family 48 (GH48) as a powerful marker for the identification of truly cellulolytic bacteria. Here we report an improved method for detecting cellulolytic bacteria in lab-scale biogas fermenters by using GH48 genes as a molecular marker in DNA and RNA samples. We developed a mixture of primers for the specific amplification of a GH48 gene region in a broad range of bacteria. Additionally, we built a manually curated reference database containing GH48 gene sequences directly linked to the corresponding taxonomic information. Phylogenetic correlation analysis of GH48 to 16S rRNA gene sequences revealed that GH48 gene sequences with 94% identity belong with high confidence to the same genus. Applying this analysis, GH48 amplicon reads revealed that at mesophilic fermenter conditions, 50–99% of the OTUs appear to belong to novel taxa. In contrast, at thermophilic conditions, GH48 gene sequences from the genus Hungateiclostridium dominated with 60–91% relative abundance. The novel primer combinations enabled detection and relative quantification of a wide spectrum of GH48 genes in cellulolytic microbial communities. Deep phylogenetic correlation analysis and a simplified taxonomic identification with the novel database facilitate identification of cellulolytic organisms, including the detection of novel taxa in biogas fermenters. [ABSTRACT FROM AUTHOR]

Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases. • Human gut microbiome exhibits diurnal rhythmicity across populations and individuals • Obese and T2D individuals show disrupted circadian rhythms in the gut microbiome • Arrhytmic bacterial signatures contribute to risk classification and prediction of T2D • These risk signatures show regional differences in applicability across three cohorts Reitmeier et al. show that specific gut microbes exhibit rhythmic oscillations in relative abundance and identified taxa with disrupted rhythmicity in individuals with type 2 diabetes (T2D). This arrhythmic signature contributed to the classification and prediction of T2D, suggesting functional links between circadian rhythmicity and the microbiome in metabolic diseases. [ABSTRACT FROM AUTHOR]

The analysis of the gut microbiome with respect to health care prevention and diagnostic purposes is increasingly the focus of current research. We analyzed around 2000 stool samples from the KORA (Cooperative Health Research in the Region of Augsburg) cohort using high-throughput 16S rRNA gene amplicon sequencing representing a total microbial diversity of 2089 operational taxonomic units (OTUs). We evaluated the combination of three different components to assess the reflection of obesity related to microbiota profiles: (i) four prediction methods (i.e., partial least squares (PLS), support vector machine regression (SVMReg), random forest (RF), and M5Rules); (ii) five OTU data transformation approaches (i.e., no transformation, relative abundance without and with log-transformation, as well as centered and isometric log-ratio transformations); and (iii) predictions from nine measurements of obesity (i.e., body mass index, three measures of body shape, and five measures of body composition). Our results showed a substantial impact of all three components. The applications of SVMReg and PLS in combination with logarithmic data transformations resulted in considerably predictive models for waist circumference-related endpoints. These combinations were at best able to explain almost 40% of the variance in obesity measurements based on stool microbiota data (i.e., OTUs) only. A reduced loss in predictive performance was seen after sex-stratification in waist–height ratio compared to other waist-related measurements. Moreover, our analysis showed that the contribution of OTUs less prevalent and abundant is minor concerning the predictive power of our models. [ABSTRACT FROM AUTHOR]

Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency. [ABSTRACT FROM AUTHOR]

Objectives: The aim of the present consensus paper was to provide recommendations for clinical practice on the individual etiological and modifying factors to be assessed in the individual diagnosis of caries, and the methods for their assessment, supporting personalized treatment decisions. Material and Methods: The executive councils of the European Organisation for Caries Research (ORCA) and the European Federation of Conservative Dentistry (EFCD) nominated ten experts each to join the expert panel. The steering committee formed three work groups which were asked to provide recommendations on (1) caries detection and diagnostic methods, (2) caries activity assessment, and (3) forming individualized caries diagnoses. The experts responsible for "individualised caries diagnosis" searched and evaluated the relevant literature, drafted this manuscript and made provisional consensus recommendations. These recommendations were discussed and refined during the structured process in the whole work group. Finally, the agreement for each recommendation was determined using an anonymous eDelphi survey. The threshold for approval of recommendations was determined at 70% agreement. Results: Ten recommendations were approved and agreed by the whole expert panel, covering medical history, caries experience, plaque, diet, fluoride, and saliva. While the level of evidence was low, the level of agreement was typically very high, except for one recommendation on salivary flow measurement, where 70% agreed. Conclusion: It is recommended that all aspects of caries lesion progression and activity, recent caries experience, medical conditions and medications, plaque, diet, fluoride and saliva should be synthesized to arrive at an individual diagnosis. Clinical Relevance: The expert panel merged evidence from existing guidelines and scientific literature with practical considerations and provided recommendations for their use in daily dental practice. [ABSTRACT FROM AUTHOR]

Background: One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. Results: Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. Conclusion: Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared. [ABSTRACT FROM AUTHOR]

The article offers study on the establishment and persistence of Salmonella enterica in agricultural systems. It discusses the increasingly food-borne diseases associated with contaminated fruits and vegetables. It mentions the need to consider the plant production environment as a whole system, including the soil type, the fertilization management practice.