Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Low-cycle fatigue of nickel-titanium rotary root-canal instruments

published_or_final_versionDentistryDoctoralDoctor of Philosoph

PROMs Following Root Canal Treatment and Surgical Endodontic Treatment

The FDI is currently working on developing a tool to encompass patient-reported outcome measures (PROMs) within the overall assessment of outcomes of endodontic treatment. The outcome of endodontic treatment has traditionally been determined by various clinical and radiographic criteria. However, these parameters do not address the impact of treatment on a patient's oral health–related quality of life (OHRQoL). OHRQoL, a crucial PROM, can be used to understand treatment outcome from a patient-centred perspective, thus improving clinician–patient communication whilst guiding decision-making. This focussed review aims to recount the OHRQoL of patients following nonsurgical root canal treatment and surgical endodontic treatment, with a specific focus on the minimal important difference (MID; the minimum score changes of an outcome instrument for a patient to register a clinically significant change in their OHRQoL and/or oral condition) and the methods used to determine it. The current evidence indicates that the OHRQoL of patients requiring root canal treatment is poorer than those without such need. Accordingly, the literature suggests that OHRQoL improves following nonsurgical or surgical endodontic treatment. However, study methodologies vary widely, and conclusions cannot be drawn with high confidence, nor can MID recommendations be provided. Well-designed clinical studies with baseline measurements and appropriate follow-up time frames are therefore needed. Despite that the literature is rife with outcome studies, research on PROMs is an area that deserves greater attention, particularly in relation to the MID. Determining the MID will facilitate the understanding of changes in outcome scores from the patients’ perspective, thus allowing for more informed decision-making in clinical practice

Effects of recombinant overexpression of Bcl2 on the proliferation, apoptosis, and osteogenic/odontogenic differentiation potential of dental pulp stem cells

© 2016 American Association of Endodontists.Introduction The therapeutic usefulness of dental pulp stem cells (DPSCs) is severely limited by low survivability upon transplantation in situ because of the presence of various proapoptotic factors within damaged/diseased tissues (ie, hypoxia and inflammation). One strategy to enhance the survivability of grafted DPSCs could be recombinant overexpression of antiapoptotic genes, such as the B-cell lymphoma 2 gene (Bcl2). Methods DPSCs were transfected with the Bcl2 and/or GFP gene. Cell density and mitotic activity of transfected DPSCs within in vitro culture were evaluated with the water soluble tetrazolium salt-8 (WST-8) and bromodeoxyuridine assay, respectively, whereas apoptosis was evaluated through the detection of cytoplasmic histone-associated DNA fragments. The osteogenic/odontogenic differentiation potential of these cells was evaluated with quantitative real-time polymerase chain reaction, alkaline phosphatase, and alizarin red staining. Results Bcl2-transfected DPSCs exhibited consistently higher cell densities than the GFP-transfected control within in vitro culture, and this was not because of the higher mitotic rate but was instead attributed to enhanced cell survivability because of the inhibition of apoptosis by Bcl2. Recombinant overexpression of Bcl2 inhibited the osteogenic/odontogenic potential of DPSCs, as indicated by lower levels of alkaline phosphatase activity and mineralized calcium deposition, together with the down-regulated expression of several key osteogenic/odontogenic gene markers including collagen I, osteocalcin, dentin matrix protein-1, bone sialoprotein, and alkaline phosphatase. Conclusions The results place a "caveat" or limitation on the use of recombinant Bcl2 overexpression as a therapeutic strategy for improving the survivability of grafted DPSCs in that the osteogenic/odontogenic potential of these cells may be compromised despite enhanced survival within the host.Link_to_subscribed_fulltex

Enterococcus faecalis Shields Porphyromonas gingivalis in Dual-Species Biofilm in Oxic Condition

Aim: To develop a reproducible biofilm model consisting of Enterococcus faecalis (E. faecalis) and Porphyromonas gingivalis (P. gingivalis) and to evaluate the interaction between the two bacterial species. Methodology: E. faecalis and P. gingivalis were grown in mono-culture, sequential, and co-culture models for 96 h in a 96-well polystyrene microtiter plate under both aerobic and anaerobic conditions separately. The viability of the two bacterial species in the biofilms was quantified by polymerase chain reaction (qPCR). Biofilm thickness and protein contents were measured using confocal laser scanning microscopy (CLSM). Two-way analysis of variance (ANOVA) was performed to analyze cell viability and biofilm thickness among different culture models cultivated under either aerobic or anaerobic conditions. The level of significance was set at p < 0.05. Results: Different culture models tested did not show any significant difference between the viable cell counts of both E. faecalis and P. gingivalis cultivated under aerobic and anaerobic conditions (p > 0.05). Biofilm was significantly thicker (p < 0.05) in the co-culture models compared to the mono-culture and sequential models. Protein contents in the biofilms were more pronounced when both bacterial species were co-cultured under aerobic conditions. Conclusions: E. faecalis appeared to shield P. gingivalis and support its continued growth in oxic (aerobic) conditions. The co-culture model of E. faecalis and P. gingivalis produced a significantly thicker biofilm irrespective of the presence or absence of oxygen, while increased protein contents were only observed in the presence of oxygen

Cyclic Fatigue and Torsional Resistance of Two New Nickel-Titanium Instruments Used in Reciprocation Motion: Reciproc Versus WaveOne

Introduction: The use of reciprocating movement was claimed to increase the resistance of nickel-titanium (NiTi) file to fatigue in comparison with continuous rotation. Recently 2 new brands of NiTi files have been marketed for use in a RM mode. The purpose of this study was to compare the cyclic fatigue resistance and torsional resistance of these 2 files, Reciproc and Wave- One. Methods: Cyclic fatigue test with a simultaneous pecking motion was performed with the instrument (n = 10 each) operating in the recommended reciprocation motion until fracture for the Reciproc R25 and WaveOne Primary files. ProTaper F2 was tested in continuous rotation to serve as a control for comparison. The number of cycles to fracture (NCF) was determined by measuring the time to fracture. The length of the fragment was measured and the fracture surface was examined by using scanning electron microscopy. Torsional strength was measured by using a torsiometer after fixing the apical 5 mm of the instrument rigidly. Statistical analysis was performed by using one-way analysis of variance. Results: The results showed that Reciproc had a higher NCF and WaveOne had a higher torsional resistance than the others. Both reciprocating files demonstrated significantly higher cyclic fatigue and torsional resistances than ProTaper (P < .05). The fractographic analysis showed typical features of cyclic fatigue and torsional failure for all instruments. Conclusions: The 2 brands of NiTi file for use with a reciprocation motion seem to have superior mechanical properties.OAIID:oai:osos.snu.ac.kr:snu2012-01/102/0000027976/4SEQ:4PERF_CD:SNU2012-01EVAL_ITEM_CD:102USER_ID:0000027976ADJUST_YN:NEMP_ID:A076085DEPT_CD:861CITE_RATE:2.88FILENAME:JOE- 04 김현철.pdfDEPT_NM:치의학과EMAIL:[email protected]_YN:YCONFIRM:YCONFIRM:

Effect of instrumentation systems on endotoxin reduction from root canal systems: a systematic review of clinical studies and meta-analysis

This systematic review assessed the effect of different root canal instrumentation systems on endotoxin reduction from the root canal system. The literature search was conducted in two electronic databases (PubMed and Scopus) using specific key words. The search strategy followed the PRISMA guidelines. Qualitative synthesis and quantitative synthesis of the data were performed and data interpretation was done based on the guidelines in the Cochrane Handbook. The risk of bias was assessed using Cochrane criteria. The initial search yielded 600 citations, of which three papers met the criteria for inclusion in this review. Studies showed a significant reduction in endotoxin following rotary and reciprocating instrumentation, with no significant differences between them. The meta-analysis showed no statistical significant difference between reciprocation and rotary files (P > 0.05). In conclusion, the instrumentation techniques compared in this review decrease endotoxin content from root canals, with no significant difference between them45340741