From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.

Benchmarking multi-platform sequencing technologies for human genome assembly.

Genome assembly is a computational technique that involves piecing together deoxyribonucleic acid (DNA) fragments generated by sequencing technologies to create a comprehensive and precise representation of the entire genome. Generating a high-quality human reference genome is a crucial prerequisite for comprehending human biology, and it is also vital for downstream genomic variation analysis. Many efforts have been made over the past few decades to create a complete and gapless reference genome for humans by using a diverse range of advanced sequencing technologies. Several available tools are aimed at enhancing the quality of haploid and diploid human genome assemblies, which include contig assembly, polishing of contig errors, scaffolding and variant phasing. Selecting the appropriate tools and technologies remains a daunting task despite several studies have investigated the pros and cons of different assembly strategies. The goal of this paper was to benchmark various strategies for human genome assembly by combining sequencing technologies and tools on two publicly available samples (NA12878 and NA24385) from Genome in a Bottle. We then compared their performances in terms of continuity, accuracy, completeness, variant calling and phasing. We observed that PacBio HiFi long-reads are the optimal choice for generating an assembly with low base errors. On the other hand, we were able to produce the most continuous contigs with Oxford Nanopore long-reads, but they may require further polishing to improve on quality. We recommend using short-reads rather than long-reads themselves to improve the base accuracy of contigs from Oxford Nanopore long-reads. Hi-C is the best choice for chromosome-level scaffolding because it can capture the longest-range DNA connectedness compared to 10× linked-reads and Bionano optical maps. However, a combination of multiple technologies can be used to further improve the quality and completeness of genome assembly. For diploid assembly, hifiasm is the best tool for human diploid genome assembly using PacBio HiFi and Hi-C data. Looking to the future, we expect that further advancements in human diploid assemblers will leverage the power of PacBio HiFi reads and other technologies with long-range DNA connectedness to enable the generation of high-quality, chromosome-level and haplotype-resolved human genome assemblies.

Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.

BACKGROUND: Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed to correct these errors, but it is uncertain if they obtain the accuracy needed for the high-resolution source tracking of foodborne illness outbreaks. RESULTS: We tested 132 combinations of assembly and short- and long-read polishing tools to assess their accuracy for reconstructing the genome sequences of 15 highly similar Salmonella enterica serovar Newport isolates from a 2020 onion outbreak. While long-read polishing alone improved accuracy, near perfect accuracy (99.9999% accuracy or ~ 5 nucleotide errors across the 4.8 Mbp genome, excluding low confidence regions) was only obtained by pipelines that combined both long- and short-read polishing tools. Notably, medaka was a more accurate and efficient long-read polisher than Racon. Among short-read polishers, NextPolish showed the highest accuracy, but Pilon, Polypolish, and POLCA performed similarly. Among the 5 best performing pipelines, polishing with medaka followed by NextPolish was the most common combination. Importantly, the order of polishing tools mattered i.e., using less accurate tools after more accurate ones introduced errors. Indels in homopolymers and repetitive regions, where the short reads could not be uniquely mapped, remained the most challenging errors to correct. CONCLUSIONS: Short reads are still needed to correct errors in nanopore sequenced assemblies to obtain the accuracy required for source tracking investigations. Our granular assessment of the performance of the polishing pipelines allowed us to suggest best practices for tool users and areas for improvement for tool developers.

Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2.

As the accuracy and throughput of nanopore sequencing improve, it is increasingly common to perform long-read first de novo genome assemblies followed by polishing with accurate short reads. We briefly introduce FMLRC2, the successor to the original FM-index Long Read Corrector (FMLRC), and illustrate its performance as a fast and accurate de novo assembly polisher for both bacterial and eukaryotic genomes.

Piezocatalysis for Chemical-Mechanical Polishing of SiC: Dual Roles of t-BaTiO3 as a Piezocatalyst and an Abrasive.

Chemical mechanical polishing (CMP) offers a promising pathway to smooth third-generation semiconductors. However, it is still a challenge to reduce the use of additional oxidants or/and energy in current CMP processes. Here, a new and green atomically smoothing method: Piezocatalytic-CMP (Piezo-CMP) is reported. Investigation shows that the Piezo-CMP based on tetragonal BaTiO3 (t-BT) can polish the rough surface of a reaction sintering SiC (RS-SiC) to the ultra-smooth surface with an average surface roughness (Ra) of 0.45 nm and the rough surface of a single-crystal 4H-SiC to the atomic planarization Si and C surfaces with Ra of 0.120 and 0.157 nm, respectively. In these processes, t-BT plays a dual role of piezocatalyst and abrasive. That is, it piezo-catalytically generates in-situ active oxygen species to selectively oxidize protruding sites of SiC surface, yielding soft SiO2, and subsequently, it acts as a usual abrasive to mechanically remove these SiO2. This mechanism is further confirmed by density functional theory (DFT) calculation and molecular simulation. In this process, piezocatalytic oxidation is driven only by the original pressure and friction force of a conventional polishing process, thus, the piezo-CMP process do not require any additional oxidant and energy, being a green and effective polishing method.

Triple Synergism Effect of Ammonium Nitrilotriacetate on the Chemical Mechanical Polishing Performance of Ruthenium Barrier Layers.

As the feature size of integrated circuits continues to decrease, ruthenium (Ru) has been suggested as the successor to traditional Ta/TaN bilayers for barrier layer materials due to its unique properties. This research delves into the effects of ammonium nitrilotriacetate (NTA(NH4)3) on the chemical mechanical polishing (CMP) performance of Ru in H2O2-based slurry. The removal rate (RR) of Ru surged from 47 to 890 Å min-1, marking an increase of about 17 times. The essence of this mechanism lies in the triple synergistic effects of NTA(NH4)3 in promoting ruthenium (Ru) removal: 1) The interaction between NH 4 + ${\mathrm{NH}}_{\mathrm{4}}^{\mathrm{+}}$ from NTA(NH4)3 and SiO2 abrasives; 2) The chelating action of [(NH4)N(CH2COO)3]2- from NTA(NH4)3 on Ru and its oxides; 3) The ammoniation and chelation of Ru and its oxides by NH 4 + ${\mathrm{NH}}_{\mathrm{4}}^{\mathrm{+}}$ from NTA(NH4)3, which enhance the dissolution and corrosion of oxidized Ru, making its removal during the barrier layer CMP process more efficient through mechanical means. This research introduces a synergistic approach for the effective removal of Ru, shedding light on potential applications of CMP in the field of the integrated circuits.

Strongly-Confined CsPbBr3 Perovskite Quantum Dots with Ultralow Trap Density and Narrow Size Distribution for Efficient Pure-Blue Light-Emitting Diodes.

The development of pure-blue perovskite light-emitting diodes (PeLEDs) faces challenges of spectral stability and low external quantum efficiency (EQE) due to phase separation in mixed halide compositions. Perovskite quantum dots (QDs) with strong confinement effects are promising alternatives to achieve high-quality pure-blue PeLEDs, yet their performance is often hindered by the poor size distribution and high trap density. A strategy combining thermodynamic control with a polishing-driven ligand exchange process to produce high-quality QDs is developed. The strongly-confined pure-blue (≈470 nm) CsPbBr3 QDs exhibit narrow size distribution (12% dispersion) and are achieved in Br-rich ion environment based on growth thermodynamic control. Subsequent polishing-driven ligand exchange process removes imperfect surface sites and replaces initial long-chain organic ligands with short-chain benzene ligands. The resulting QDs exhibit high photoluminescence quantum yield (PLQY) to near-unity. The resulting PeLEDs exhibit a pure-blue electroluminescence (EL) emission at 472 nm with narrow full-width at half-maximum (FWHM) of 25 nm, achieving a maximum EQE of 10.7% and a bright maximum luminance of 7697 cd m-2. The pure-blue PeLEDs show ultrahigh spectral stability under high voltage, a low roll-off of EQE, and an operational half-lifetime (T50) of 127 min at an initial luminance of 103 cd m-2 under continuous operation.

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).

Finishing technique effect on strength of zirconia-reinforced lithium silicate ceramic.

The aim of this study was to evaluate the effect of two finishing techniques, glazing or polishing, in comparison with the as-cut condition, on the biaxial-flexural-strength (BFS) of a zirconia-reinforced lithium silicate ceramic (ZLS). Cylinders were milled from CAD/CAM blocks and sliced to obtain disc-shaped specimens (ISO6872:2015). Polished and glazed specimens were processed following the manufacturer's instructions. Thirty-three specimens were obtained for each condition and microstructural and BFS/fractographic characterizations were performed. BFS and roughness data were analyzed using Weibull statistics and ANOVA one-way with Tukey post-hoc test, respectively. While a rougher surface was observed for as-cut specimens, smoother surfaces were observed for polished and glazed ZLS at microscopical evaluation and confirmed through surface-roughness evaluation. X-ray spectra depicted a glass phase for all groups and characteristic metasilicate, lithium disilicate, and lithium phosphate peaks for the as-cut and polished specimens. Glazed specimens showed higher characteristic strength than polished and as-cut specimens, which did not differ significantly. While higher Weibull-modulus was observed for the polished than for the as-cut specimens, no statistically significant differences were noted between glazed and polished, and between glazed and as-cut specimens. ZLS presents higher strength when glazed, and polishing increases the structural reliability of the material relative to the as-cut condition. Both finishing techniques reduced surface roughness similarly.

Active Compliance Smart Control Strategy of Hybrid Mechanism for Bonnet Polishing.

Compliance control strategies have been utilised for the ultraprecision polishing process for many years. Most researchers execute active compliance control strategies by employing impedance control law on a robot development platform. However, these methods are limited by the load capacity, positioning accuracy, and repeatability of polishing mechanisms. Moreover, a sophisticated actuator mounted at the end of the end-effector of robots is difficult to maintain in the polishing scenario. In contrast, a hybrid mechanism for polishing that possesses the advantages of serial and parallel mechanisms can mitigate the above problems, especially when an active compliance control strategy is employed. In this research, a high-frequency-impedance robust force control strategy is proposed. It outputs a position adjustment value directly according to a contact pressure adjustment value. An open architecture control system with customised software is developed to respond to external interrupts during the polishing procedure, implementing the active compliance control strategy on a hybrid mechanism. Through this method, the hybrid mechanism can adapt to the external environment with a given contact pressure automatically instead of relying on estimating the environment stiffness. Experimental results show that the proposed strategy adapts the unknown freeform surface without overshooting and improves the surface quality. The average surface roughness value decreases from 0.057 um to 0.027 um.

In vitro comparison of one-step, two-step, and three-step polishing systems on the surface roughness and gloss of different resin composites.

OBJECTIVES: This laboratory study evaluated the effect of three polishing systems on the surface roughness and gloss of resin composites. MATERIALS AND METHODS: Thirty specimens (6 mm Ø × 8 mm) were fabricated from each of three resin composites: Z 350 XT (nanofill), Harmonize (nanohybrid), and Estelite Omega (supranonofill). All specimens were photopolymerized using a multi-peak LED curing unit (VALO-Standard mode), having a exitance irradiance of approximately 1000 mW/cm2 against a polyester strip (PS). 2 mm was then removed from the irradiated end (finished) using #320 abrasive paper (F). Specimens were then randomly polished (P) using a one-step (1S) (OneGloss), two-step (2S) (EVE Diacomp Twist Basic CA), or 3-step (3S) (Astropol P) system (n = 10). For PS, F, and P groups, surface roughness (Ra) was measured using a surface roughness tester, and surface gloss was measured with a glossmeter. For each specimen, the percent recovery to the PS value (%R) of surface roughness and surface gloss were calculated. Data were analyzed using two-way ANOVA, followed by Tukey's test. Surface roughness and gloss values were submitted to Pearson's correlation test (α = 0.05). All statistical testing was performed using a pre-set alpha of 0.05. RESULTS: The interaction term [resin composite × polishing system] was significant for both surface roughness (p = 0.001) and gloss (p = 0.0001). For all resin composites, the 2S and 3S systems provided a higher %R of surface roughness and gloss compared to those of the 1S system. There was a negative correlation between surface roughness and gloss, but only a few combinations showed strong correlations. CONCLUSIONS: The 2S and 3S polishing systems provided surfaces having greater smoothness and gloss compared to the 1S system. The ability to recover surface roughness and gloss was dependent on type of resin composite filler classification. CLINICAL SIGNIFICANCE: The 3S and 2S polishing systems were more effective in achieving PS values than was the 1S system for all tested resin composites. However, individual polishing systems performed differently depending on type of resin composite.

Effect of polishing and bleaching on color, whiteness, and translucency of CAD/CAM monolithic materials.

OBJECTIVE: To evaluate the effect of polishing and bleaching on the recovery of lightness, color, whiteness, and relative translucency parameter (RTP) in CAD/CAM materials and changes in these properties when another staining in coffee was conducted after the treatments. MATERIALS AND METHODS: Disks of Lava Ultimate (LU), Vita Enamic (VE), IPS Empress CAD (EMP), IPS e.max CAD (EMAX), and Vita Suprinity (VS) were (1) not treated (control), (2) polished with Proxyt or (3) Ceramisté, (4) bleached with Opalescence PF or (5) Whiteness HP Blue, and (6) air polished with Clinpro Prophy Powder. CIE L*a*b* color coordinates were registered at baseline (R0), after staining with coffee for 30 min daily for 36.5 days and treatment (R1), and after another staining (R2). Differences (R1-R0 and R2-R0) in lightness (ΔL00), color (ΔE00), RTP (ΔRTP00), and whiteness (ΔWID) were evaluated by mixed repeated measures ANOVA and 95% confidence intervals (α = 0.05) and interpreted in function of their respective 50:50% PT and AT thresholds. Topography was evaluated by scanning electron microscopy (SEM). RESULTS: In LU, Opalescence PF and Proxyt decreased Δ L 00 R 1 - R 0 $$ {\Delta L}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , Δ E 00 R 1 - R 0 $$ {\Delta E}_{00\left({R}_1\hbox{--} {\mathrm{R}}_0\right)} $$ , and ΔWI D R 1 - R 0 $$ {\Delta \mathrm{WI}}_{\mathrm{D}\left({R}_1\hbox{--} {R}_0\right)} $$ and showed lower Δ L 00 R 2 - R 0 $$ {\Delta L}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ , Δ E 00 R 2 - R 0 $$ {\Delta E}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ , and ΔWI D R 2 - R 0 $$ {\Delta \mathrm{WI}}_{\mathrm{D}\left({R}_2\hbox{--} {R}_0\right)} $$ . In VE, all treatments decreased Δ L 00 R 1 - R 0 $$ {\Delta L}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , Δ E 00 R 1 - R 0 $$ {\Delta E}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , and ΔWI D R 1 - R 0 $$ {\Delta \mathrm{WI}}_{\mathrm{D}\left({R}_1\hbox{--} {R}_0\right)} $$ , whereas Δ L 00 R 2 - R 0 $$ {\Delta L}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ , Δ E 00 R 2 - R 0 $$ {\Delta E}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ , and ΔWI D R 2 - R 0 $$ {\Delta \mathrm{WI}}_{\mathrm{D}\left({R}_2\hbox{--} {R}_0\right)} $$ were lower in Opalescence PF than in the control group. In both moments, ΔE00 and ΔWID in EMP (also ΔL00) and EMAX were higher in Opalescence PF than in the control group, from which the other treatments did not differ in R1-R0. In EMP, Δ E 00 R 2 - R 0 $$ {\Delta E}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ in Whiteness HP Blue (also Δ L 00 R 2 - R 0 $$ {\Delta L}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ ) and Proxyt were also higher in comparison to the control group and in VS, Ceramisté decreased Δ L 00 R 1 - R 0 $$ {\Delta L}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , Δ E 00 R 1 - R 0 $$ {\Delta E}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , and Δ R T P 00 R 1 - R 0 $$ \varDelta RT{P}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ , whereas Opalescence PF increased ΔRTP 00 R 1 - R 0 $$ {\Delta \mathrm{RTP}}_{00\left({R}_1\hbox{--} {R}_0\right)} $$ . Δ E 00 R 2 - R 0 $$ {\Delta E}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ of Ceramisté and ΔWI D R 2 - R 0 $$ {\Delta \mathrm{WI}}_{\mathrm{D}\left({R}_2\hbox{--} {R}_0\right)} $$ and Δ R T P 00 R 2 - R 0 $$ \varDelta RT{P}_{00\left({R}_2\hbox{--} {R}_0\right)} $$ of Proxyt were lower than those of the control group. CONCLUSIONS: The most suitable treatment to recover the lightness, color, whiteness, and RTP without changing these properties after another coffee exposure is material-dependent. CLINICAL SIGNIFICANCE: Although the effectiveness of the treatment was material-dependent, Proxyt was the only treatment that promoted clinically acceptable changes for both LU and VE, while for purely ceramic materials, this condition was observed with Ceramisté and Clinpro Prophy Powder.

Efficient Self-cleaning and antibacterial ceramics with active sites fully exposed obtained from rare earth waste.

The utilization of rare earth polishing powder waste (RPW) to prepare antibacterial ceramics can effectively avoid problems of pollution in the recycling process and waste of rare earth resources. Herein, a novel RPW-based antibacterial ceramics was developed, which possesses the core-shell structure with ceramics as the cores and the CeO2/BiOCl as the superficial coating. The antibacterial ceramics display notable antibacterial activity, and the inactivation rates of 3.3 log under visible light irradiation in 30 min and 2.4 log under darkness in 1 h were achieved, and the zone of inhibition values was found to be 16.6 mm for E.coil. The hardness of antibacterial ceramics was measured to be 897 (±38) HV, higher than commercial porcelain's hardness (600 HV). The antibacterial mechanism was verified by the Ce ion release, reactive species, and fluorescence-based live/dead cells. This study presents a novel antibacterial ceramic structure and green economic reuse method of rare earth waste.

Naturalization of treated wastewater by a constructed wetland in a water-scarce Mediterranean region.

The effluents from conventional wastewater treatment plants (WWTP), even if accomplishing quality regulations, substantially differ in their characteristics with those of waters in natural environments. Constructed wetlands (CWs) serve as transitional ecosystems within WWTPs, mitigating these differences and restoring natural features before water is poured into the natural environment. Our study focused on an experimental surface-flow CW naturalizing the WWTP effluent in a semiarid area in Eastern Spain. Despite relatively low pollutant concentrations entering the CW, it effectively further reduced settled organic matter and nitrogen. Dissolved organic matter (DOM) reaching the CW was mainly protein-like, yet optical property changes in the DOM indicated increased humification, aromaticity, and stabilization as it flowed through the CW. Flow cytometry analysis revealed that the CW released less abundant but more active bacterial populations than those received. MiSeq Illumina sequencing highlighted changes in the prokaryotic community composition, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria dominating the CW outflow. Functional prediction tools (FaproTax and PICRUSt2) demonstrated a shift towards microbial guilds aligned with those of the natural aquatic environments, increased aerobic chemoheterotrophs, photoautotrophs, and metabolic reactions at higher redox potentials. Enhanced capabilities for degrading plant material correlated well with changes in the DOM pool. Our findings emphasize the role of CWs in releasing biochemically stable DOM and functionally suited microbial populations for natural receiving environments. Consequently, we propose CWs as a naturalization nature-based solution (NBS) in water-scarce regions like the Mediterranean, where reclaimed discharged water can significantly contribute to ecosystem's water resources compared to natural flows.

Enamel surface roughness following debonding resin clean up using high speed air-turbine and electric handpieces. In vitro study.

BACKGROUND: High speed electric handpieces have recently been growing in popularity among dental professionals. Advantages include smoother surface preparation and increased cutting efficiency. AIM: The primary objective was to compare enamel surface roughness following resin cleanup after bracket debonding using highspeed air turbine versus electric handpiece. The secondary objective was to record the time needed for resin-clean up. METHOD: Forty deidentified freshly extracted human premolars were cleaned and sectioned at the cement-enamel junction. The crowns were embedded in acrylic blocks. Enamel surface roughness parameters (Ra, Rz, Rp and Rv) were measured using a stylus profilometer. Brackets were bonded using a light-cure orthodontic adhesive and stored in distilled water for 24 h. Following bracket debonding, the specimens were randomly divided into 2 groups: First group: resin clean-up was carried out using a 12-fluted carbide bur mounted on a high-speed air turbine; and second group: where an electric handpiece was used. Surface roughness parameters were measured following resin clean up and after polishing using pumice and a rubber cup. Time needed for resin clean-up was recorded. Differences in enamel surface roughness and time between groups were compared using repeated measures ANOVA and independent samples t-test, respectively at P ≤ 0.05. RESULTS: The electric handpiece groups showed significantly higher values for Ra, Rz and Rp both following resin cleanup and polishing. Time taken for resin cleanup was significantly longer for the electric handpiece group. CONCLUSION: Considering both surface roughness and time, electric handpiece do not seem to add greater effectiveness or efficiency to resin cleanup following orthodontic bracket debonding.

In vitro study on the impact of various polishing systems and coffee staining on the color stability of bleach-shaded resin composite.

OBJECTIVE: To evaluate the effects of different polishing techniques and coffee staining on the color stability of four commercially available bleach-shade composite resins, namely microhybrid, nanohybrid, nanofilled, and injectable nanohybrids. MATERIAL AND METHODS: A total of 224 discs (8 mm diameter and 2 mm thickness) were fabricated from four different bleach-shade composite resins, namely microhybrid (Gradia Direct Anterior), nanohybrid (Palfique LX5), nanofilled (Filtek Universal), and injectable nanohybrid (flowable G-aenial universal injectable). The composite resin groups were polished via four techniques: no polishing, 4-step polishing using aluminum oxide discs, 3-step polishing using silicon rubber diamond discs, and one-step polishing. Half of each group was immersed in water, while the other half was immersed in coffee for 12 days (n = 7). Colors were measured using a clinical spectrophotometer, and color differences were calculated (ΔE). The results were analyzed statistically. RESULTS: The alterations in color were significantly influenced by the techniques employed for finishing and polishing techniques, composite resin type, and degree of coffee staining. Regardless of the polishing technique and storage medium, different material types showed a significant color change (ΔE) at P < 0.001. Filtek exhibited the most significant color change, followed by Gradia and Palfique, with no significant differences between them. In addition, Different polishing techniques resulted in significant color changes (P < 0.001). The highest degree of color change was seen in the no-polishing group, followed by the 4-step and 1-step polishing groups, with negligible differences between each other. Also, Storage media had a significant effect on ΔE values. CONCLUSION: Appropriate finishing and polishing procedures can improve the color stability of bleach-shaded composite resins. Coffee has a deleterious effect on color; however, injectable flowable nanohybrid composites are more resistant to staining.

Polishing methods for composites restoration: the influence on human gingival fibroblasts behaviour.

BACKGROUND: Carious/Non-carious cervical lesions with gingival recessions may require both dental and periodontal reconstructive therapy, where flaps/grafts may be placed in contact with a dental filling material. Human Gingival Fibroblasts (HGF-1) response during the early phase of healing could vary according to the procedures employed to cure the dental composite. Moreover, oxygen diffusion into dental composite inhibits the polymerization reaction, creating an oxygen-inhibited layer (OIL) that presents residual unreacted monomers. The aim of this study was to assess the effect of different polishing techniques and OIL on HGF-1. METHODS: Composite discs polished with different techniques (diamond rubber, abrasive discs and tungsten carbide burr) were used. An additional not polished smooth group obtained with and without OIL was used as control. Samples were physically characterized through the analysis of their hydrophilicity and surface topography through contact angle measurement and SEM, respectively; afterwards the biologic response of HGF-1 when cultured on the different substrates was analyzed in terms of cytotoxicity and gene expression. RESULTS: The finishing systems caused alterations to the wettability, even if without a proportional relation towards the results of the proliferation essay, from which emerges a greater proliferation on surfaces polished with one-step diamond rubber and with abrasive discs as well as a direct effect of the glycerin layer, confirming that surface roughness can heavily influence the biological response of HGF-1. CONCLUSIONS: Surfaces wettability as well as cellular behavior seem to be affected by the selection of the finishing system used to lastly shape the restoration. Especially, the presence of OIL act as a negative factor in the regards of human gingival fibroblasts. The present study may provide the first clinical instruction regarding the best polishing system of composite material when the restoration is placed directly in contact with soft tissue cells. Understanding HGF-1 behavior can help identifying the polishing treatment for direct restoration of carious/non-carious cervical lesions associated with gingival recessions.

In-vitro biofilm removal from TiUnite® implant surface with an air polishing and two different plasma devices.

BACKGROUND: We investigated the efficacy of two different cold atmospheric pressure jet plasma devices (CAP09 and CAPmed) and an air polishing device with glycine powder (AP) either applied as monotherapies or combined therapies (AP + CAP09; AP + CAPmed), in microbial biofilm removal from discs with anodised titanium surface. METHODS: Discs covered with 7-day-old microbial biofilm were treated either with CAP09, CAPmed, AP, AP + CAP09 or AP + CAPmed and compared with negative and positive controls. Biofilm removal was assessed with flourescence and electron microscopy immediately after treatment and after 5 days of reincubation of the treated discs. RESULTS: Treatment with CAP09 or CAPmed did not lead to an effective biofilm removal, whereas treatment with AP detached the complete biofilm, which however regrew to baseline magnitude after 5 days of reincubation. Both combination therapies (AP + CAP09 and AP + CAPmed) achieved a complete biofilm removal immediately after cleaning. However, biofilm regrew after 5 days on 50% of the discs treated with the combination therapy. CONCLUSION: AP treatment alone can remove gross biofilm immediately from anodised titanium surfaces. However, it did not impede regrowth after 5 days, because microorganisms were probably hidden in holes and troughs, from which they could regrow, and which were inaccessible to AP. The combination of AP and plasma treatment probably removed or inactivated microorganisms also from these hard to access spots. These results were independent of the choice of plasma device.

Long-term effect of simulated five years professional mechanical biofilm removal on the luting gap of ceramic restorations.

BACKGROUND: Achieving sufficient professional mechanical biofilm removal (PMPR) can be challenging in supportive periodontal therapy (SPT), particularly in patients with prosthetic restorations. This experimental study aimed to simulate five years of SPT with periodic PMPR near the luting gap of ceramic restorations using a rubber cup with polishing paste (RCP), air polishing with two different low-abrasive powders (LAPA-1: glycine powder, LAPA-2: erythritol powder), and non-professional mechanical cleaning (control group) to measure the extent of volume loss in the luting gap after baseline (∆V = Vbaseline-V1-5; in µm3). METHODS: Two operators randomly performed PMPR ten times for thirty seconds on one of four sides of 30 crown replicas fixed with glass-ionomer cement (CGIZ: n = 15) or adhesive bonding (CAB: n = 15). The replicas were separated in a template during PMPR, and afterward, cleaned for five seconds per side with a sonic brush under flowing water. The artificial aging process between two PMPRs simulated a 5-year SPT with two PMPRs per year. Profilometric measurements were performed at baseline and after each second PMPR to obtain the mean change of ∆V. The statistical evaluation of the data was carried out using nonparametric tests with Bonferroni correction applied for multiple tests. RESULTS: Ninety-six out of 120 sides could be included in the analysis. PMPR methods showed a loss of substance in the luting gap with a ∆V (mean(standard deviation)) of -4.35 × 106(4.8 × 106)µm3 versus 8.79 × 104(1.05 × 106)µm3 for control at V5 (p ≤ 0.001). No significant differences of ∆V1-5 values could be identified in the control (p > 0.05), whereat all PMPRs showed a significant increasing loss of substance per simulated year (p ≤ 0.001). Intergroup comparison identified LAPA-1 as having the highest significant loss of substance determined on CAB (∆V: -1.05 × 107 (7,2 × 106) µm3), followed by LAPA-2 on CAB (∆V: -6.29 × 106 (4,24 × 106) µm3), LAPA-1 on CGIZ (∆V: -4.15 × 106 (3,25 × 106) µm3), LAPA-2 on CGIZ (∆V: -3.0 × 106 (2,23 × 106) µm3), RCP on CAB (∆V: -1.86 × 106 (2,23 × 106) µm3) and CGIZ (∆V: -1.2 × 106 (1,31 × 106) µm3; p ≤ 0.001)). CONCLUSIONS: Within study limitations, all PMPRs caused a significantly higher loss of substance in the luting gap versus control without professional intervention, with the highest values in the CAB group for LAPA-1, LAPA-2 and RCP. Similar findings were observed for CGIZ, although the loss values were lower.

Effect of toothbrushing on surface roughness, gloss, and topography of polished and glazed ultra-translucent zirconia.

PURPOSE: This study evaluated the effect of toothbrushing cycles on surface roughness (Ra), gloss (GU), and morphology of two zirconia finishing and polishing protocols. MATERIALS AND METHODS: An ultra-translucent zirconia disc was sectioned into rectangular plates (12 mm × 7 mm × 3 mm) and divided into two groups according to the polishing and finishing system used (diamond rubber abrasive/DRA or glazing/GLA). Bovine enamel (BEN) plates with the same dimensions were used as a Control. Specimens of zirconia and enamel were analyzed for Ra and GU (n = 11) and surface morphology by scanning electron microscopy (n = 3) before toothbrushing (baseline) and after 15,000 and 30,000 toothbrushing cycles. Ra and GU data were analyzed by ANOVA two-way and post-hoc Tukey's test (α = 0.05), while the surface morphology was analyzed qualitatively. RESULTS: The Ra decreased significantly after 30,000 toothbrushing cycles for DRA and GLA zirconia ceramics. DRA showed a higher GU at the baseline, after 15,000 and 30,000 toothbrushing cycles than GLA and BEN. Toothbrushing polished the zirconia, creating a smooth surface, while no changes were observed for BEN. CONCLUSIONS: The increase in toothbrushing cycles (30,000) changed the surface roughness of DRA and GLA zirconia ceramics. DRA zirconia presented the highest GU, which did not change with toothbrushing.