Sequence Labeling for Disambiguating Medical Abbreviations.

Abbreviations are unavoidable yet critical parts of the medical text. Using abbreviations, especially in clinical patient notes, can save time and space, protect sensitive information, and help avoid repetitions. However, most abbreviations might have multiple senses, and the lack of a standardized mapping system makes disambiguating abbreviations a difficult and time-consuming task. The main objective of this study is to examine the feasibility of sequence labeling methods for medical abbreviation disambiguation. Specifically, we explore the capability of sequence labeling methods to deal with multiple unique abbreviations in a single text. We use two public datasets to compare and contrast the performance of several transformer models pre-trained on different scientific and medical corpora. Our proposed sequence labeling approach outperforms the more commonly used text classification models for the abbreviation disambiguation task. In particular, the SciBERT model shows a strong performance for both sequence labeling and text classification tasks over the two considered datasets. Furthermore, we find that abbreviation disambiguation performance for the text classification models becomes comparable to that of sequence labeling only when postprocessing is applied to their predictions, which involves filtering possible labels for an abbreviation based on the training data.

Molecular and hematological investigation of Trypanosoma evansi infection in Iranian one-humped camels (Camelus dromedarius).

Trypanosoma species cause animal trypanosomiasis that infects many animals. Trypanosoma evansi is an organism that infects camels. There are many economic problems associated with this disease, including lower milk and meat yields and abortions. The purpose of the current survey was molecular study of the presence of Trypanosoma in dromedary camel blood in the south of Iran, and its effects on the hematologic, and some acute-phase protein changes. Blood samples were aseptically collected from the jugular vein of dromedary camels (n = 100; aged from 1 to 6 years) originating from Fars Province in EDTA-coated vacutainers. Genomic DNA from 100 µL of the whole blood was extracted and amplified using a PCR assay based on ITS1, 5.8S, and ITS2 ribosomal regions. Also, the PCR products obtained were sequenced. Moreover, the changes in hematological parameters and serum acute-phase proteins (serum amyloid A, alpha-1 acid glycoprotein, and haptoglobin) were measured. Among 100 tested blood, nine samples (9%, 95% CI: 4.2-16.4%) were found positive by the PCR assay. The phylogenetic tree and blast analysis showed four different genotypes closely related to the strains (accession numbers: JN896754 and JN896755) previously reported from dromedary camels in Yazd Province, center Iran. Based on hematological analysis, normocytic and normochromic anemia and lymphocytosis were detected in the PCR-positive cases compared with the negative group. Furthermore, alpha-1 acid glycoprotein was significantly increased in the positive cases. There was a substantial and positive relation between the number of lymphocytes, and the levels of alpha-1 acid glycoprotein and serum amyloid A in the blood (p = 0.045, r = 0.223 and p = 0.036, r = 0.234, respectively). A noticeable frequency of T. evansi infection was reported in dromedary camels in south Iran. This is the first report on the genetic diversity of T. evansi in this region. There was a significant association among Trypanosoma infection, lymphocytosis, and alpha-1 acid glycoprotein. Trypanosoma-positive camels had a significant decrease in hematocrit (HCT), hemoglobin (Hb), and red blood cell (RBC) values compared to the non-infected group. Further experimental studies are needed to elucidate the hematological and acute-phase protein alteration during a different phase of Trypanosoma spp. infection.

Quantitative analysis of optical coherence tomography angiography metrics in diabetic retinopathy.

PURPOSE: To evaluate the correlation of the visual acuity and diabetic retinopathy stage using optical coherence tomography and optical coherence tomography angiography metrics. METHODS: In this prospective study, optical coherence tomography and optical coherence tomography angiography images of patients with different stages of diabetic retinopathy were obtained. In optical coherence tomography angiography images, the size of foveal avascular zone, central macular thickness, and vessel density at superficial and deep capillary layers of the macula were measured. In optical coherence tomography images, the presence of intraretinal cyst, disorganization of retinal inner layer, and ellipsoid zone and external limiting membrane disruption were evaluated. The associations between the variables with visual acuity and diabetic retinopathy stage were analyzed. RESULTS: In total, 68 eyes of 38 patients with a mean age of 58.96 ± 10.59 years were included. In total, 34 eyes were categorized as non-proliferative diabetic retinopathy, 14 as active, and 20 as regressed proliferative diabetic retinopathy. Univariate analysis showed deep parafoveal vessel density, central macular thickness, ellipsoid zone disruption, disorganization of retinal inner layer, and external limiting membrane disruption had a significant relationship with visual acuity. However, in multivariate analysis, only central macular thickness and ellipsoid zone disruption had significant association with visual acuity (p = 0.02 and p = 0.01, respectively). There was a significant difference in deep parafoveal vessel density (p = 0.04), but not in foveal avascular zone area, between different stages of diabetic retinopathy. CONCLUSION: In this study, the foveal avascular zone area did not correlate with visual acuity and different stages of diabetic retinopathy. Structural abnormalities on optical coherence tomography images with especial focus on outer retinal disruption provided more reliable predictors for visual acuity outcomes in patients with diabetic retinopathy.

Thieno[2,3-b]pyridine amines: Synthesis and evaluation of tacrine analogs against biological activities related to Alzheimer's disease.

In search of safer tacrine analogs, various thieno[2,3-b]pyridine amine derivatives were synthesized and evaluated for their inhibitory activity against cholinesterases (ChEs). Among the synthesized compounds, compounds 5e and 5d showed the highest activity towards acetylcholinesterase and butyrylcholinesterase, with IC50 values of 1.55 and 0.23 µM, respectively. The most active ChE inhibitors (5e and 5d) were also candidates for further complementary assays, such as kinetic and molecular docking studies as well as studies on inhibitory activity towards amyloid-beta (ßA) aggregation and ß-secretase 1, neuroprotectivity, and cytotoxicity against HepG2 cells. Our results indicated efficient anti-Alzheimer's activity of the synthesized compounds.

The Effect of Submucosal Injection of Corticosteroids on Pain Perception and Quality of Life after Root Canal Treatment of Teeth with Irreversible Pulpitis: A Randomized Clinical Trial.

INTRODUCTION: The aim of the present investigation was to study the effect of local infiltration of corticosteroids on postoperative pain and quality of life (QOL) in teeth with irreversible pulpitis after 1-visit endodontic treatment. METHODS: In this double-blind randomized clinical trial, 242 healthy patients with irreversible pulpitis undergoing 1-visit endodontic treatment were included. Forty-five patients were lost during the follow-up, and the remaining 197 patients were followed for 7 days (67 patients in the placebo group, 66 in the long-acting betamethasone group, and 64 in the dexamethasone group). The patients marked their level of pain and QOL before treatment and at 6-, 12-, 24-, 48-, and 72-hour and 7-day postoperative intervals using a questionnaire. Freidman and Kruskal-Wallis tests were used for statistical analysis. P ≤ .05 was considered significant. RESULTS: The pain was more severe in the placebo group compared with the other groups at all time intervals. A significant increase was observed in pain severity after 12 hours in all 3 groups. In general, the pain was less severe in the dexamethasone group compared with the betamethasone group at 6-, 12-, and 24-hour intervals. The pain severity was similar in both groups at 48 hours, and it was less severe in the long-acting betamethasone group compared with the dexamethasone group after 72 hours and 7 days. There were no significant differences in the betamethasone and dexamethasone groups in pain intensity between males and females. Moreover, overall pain perception was higher in the mandible than in the maxilla. There was an inverse and significant relationship between pain severity and QOL. CONCLUSIONS: Infiltration of long-acting betamethasone and dexamethasone resulted in decreased postoperative pain experience. Dexamethasone was more effective in alleviating pain within the first 24-hour period after treatment. Infiltration of long-acting betamethasone and dexamethasone exhibited the same efficacy in 48 hours. The efficacy of long-acting betamethasone in pain relief lasted for 7 days. The QOL in the 2 groups receiving corticosteroids was higher than that in the placebo group.

Genotoxicity, Bioactivity and Clinical Properties of Calcium Silicate Based Sealers: A Literature Review.

An ideal endodontic sealer should have many properties such as excellent seal after setting, dimensional stability, slow setting time to ensure sufficient working time, insolubility to tissue fluids, adequate adhesion with canal walls and biocompatibility. Genotoxicity is one of the important factors that influence biocompatibility of an endodontic sealer. This literature review was conducted to survey the genotoxicity, bioactivity and clinical perspectives of calcium silicate based sealers. We searched PubMed using appropriate MeSH keywords. Also a hand search was conducted in the related journals. Sixty eight articles were assessed finally. Genotoxicity and acute inflammation were high in calcium silicate based sealers. Both resin-based and calcium silicate based sealers caused perceptible tooth discoloration. There were controversies regarding the fracture resistance, apical patency and retreatability of different sealers. Clinical properties of calcium silicate-based sealers are also outlined.

Composition and physicochemical properties of calcium silicate based sealers: A review article.

BACKGROUND: Recently a new generation of endodontic sealers has been developed based on calcium silicate as MTA Fillapex, Endoseal MTA, Total Fill BC Sealer, EndoSequence BC Sealer, iRoot SP, Endo CPM sealer, MTA-Angelus and ProRoot Endo Sealer. A review of literature was conducted to discuss the composition, physicochemical properties, and clinical perspectives of calcium silicate based sealers. MATERIAL AND METHODS: A literature search was conducted in PubMed and web of knowledge databases with appropriate MeSh terms and keywords. A total of 71 studies were reviewed for data extraction. RESULTS AND CONCLUSIONS: Calcium silicate based sealers showed suitable physical properties to be used as an endodontic sealer. However, its high solubility remains an important issue. They show good performance regarding calcium ion release, film thickness, and fowability. More researches are required about features of calcium silicate based sealers before recommending them for clinical applications. Key words:Calcium silicate, root canal filling materials, composition, physical properties.

Endodontic microleakage studies: correlation among different methods, clinical relevance, and potential laboratory errors.

INTRODUCTION: Creation of a tight seal in endodontically treated root canals is of utmost importance. Clinical and laboratory studies have a great role in the assessment of the sealing ability of endodontic materials. The present review was undertaken to evaluate correlation between different techniques used in microleakage studies in endodontics and the potential laboratory errors. EVIDENCE ACQUISITION: A systematic search was run using Medline, Biosis, Cochrane Database, Embase, Google Scholar, and Web of Science databases. Furthermore, the reference lists of the articles published on the subject were thoroughly searched. There was no language restriction in the search. Two reviewers separately evaluated the titles and abstracts. EVIDENCE SYNTHESIS: All the methods used might have proved useful if the study could have been carried out with a larger sample size, with carefully designed control groups. Furthermore, extra evaluations are recommended on the reliability of the method used. Examinations like glucose reactivity test, assessment of antimicrobial activity of the tested materials and in situ FISH examination for the reliability of bacterial leakage model have been recommended. It has been recommended that two or more methods be considered for each material in the same study. On the other hand, long-term animal studies can be useful with histological and radiographic evaluations for meticulous assessment of leakage. Furthermore, long-term clinical trials on humans might be helpful on the condition that confounding factors are controlled. CONCLUSIONS: Studies on microleakage should be focused on animal studies, clinical trials or laboratory tests. On the basis of available evidence, it appears that despite potential errors on microleakage studies they are very valuable.

Importance and methodologies of endodontic microleakage studies: A systematic review.

INTRODUCTION: It is very important to obtain a tight seal in obturated root canal, making it necessary to conduct clinical or laboratory studies on the sealability of endodontic materials. Different methodologies have been historically used to assess microleakage of different endodontic materials. The aim of the present study was to comprehensively review different material testing methods used in microleakage studies, their interpretation and importance in endodontic literature. MATERIAL AND METHODS: A systematic search was conducted in Medline, Cochrane, and Web of Science databases. In addition, the reference lists of review articles on the topic were searched. No language restriction was applied. Two independent reviewers screened the article. RESULTS: Microleakage is considered the single most important risk factor responsible for apical periodontitis. Dye penetration, dye diffusion, bacterial and endototoxin infiltration, fluid filtration, glucose, caffeine and protein infiltration, radioisotope penetration, animal studies, and electrochemical or 3D evaluation are different methodologies used to assess dental leakage. 91 out of 177 articles in the primary search were included in the study. These methods are very divergent in their viewpoints; that is why their results cannot be easily compared. It is necessary to standardize microleakage detection methods in order to more correctly evaluate the phenomena that are found between the root canal wall and the root canal filling materials. CONCLUSIONS: All the methods are useful if studies are performed strictly with large sample sizes and proper control groups and if the technique can be standardized. Furthermore, more evaluations of the reliability of the methods are strongly recommended. Key words:Dental leakage, review, root canal, material testing methods, data interpretation.

In vitro Cytotoxicity Comparison of MTA Fillapex, AH-26 and Apatite Root Canal Sealer at Different Setting Times.

INTRODUCTION: This study aimed to compare the cytotoxicity of MTA Fillapex, AH-26 and Apatite root canal sealers at different times after mixing. METHODS AND MATERIALS: In this in vitro study, MTA Fillapex, AH-26 and Apatite root canal sealer were spilled uniformly by 40 µm mesh in a 96-well plate. Then, human fetal foreskin fibroblast cell line (HFFF2) were added to each sealer cell culture medium. Cytotoxicity was measured using MTT assay after 24, 48 and 72 h and seven days. Multiple comparisons were done using analysis of variances (ANOVA) and Scheffe's post hoc test. RESULTS: All studied sealers exhibited severe cytotoxicity (more than 70%) except for Apatite sealer (95%) at 48 h after mixing. Cytotoxicity of MTA Fillapex and AH-26 were similar (P>0.05) at 24, 48 and 72 h and 7 days after mixing of sealers. Cytotoxicity of MTA Fillapex and Apatite root canal sealer, at 24 and 48 h, were significantly different (P=0.003 and P=0.000, respectively); MTA Fillapex was more cytotoxic. However in 72 h and 7 days after mixing, the difference was not significant (P>0.05). At 24 and 48 h after mixing, AH-26 was more cytotoxic (P=0.002 and P=0.000, respectively). Same as above at 72 h and 7 days after mixing, their cytotoxicity were similar (P>0.05). CONCLUSION: Overall cytotoxicity of all studied materials were severe. However, it was observed that the cytotoxicity of MTA Fillapex, AH-26 and Apatite root canal sealer decreased over time. Apatite root canal sealer exhibited the least cytotoxicity. Cytotoxicity of MTA Fillapex and AH-26 were similar at different time intervals.

Antifungal Activity of Two Root Canal Sealers against Different Strains of Candida.

INTRODUCTION: Microorganisms and microbial products are the main etiologic factors in pulp and periapical diseases. The present study aimed to compare the antifungal activity of two different sealers, AH-26 and MTA Fillapex against three strains of Candida, 24, 48, 72 h and 7 days after mixing. METHODS AND MATERIALS: The microorganisms used in this study were Candidia albicans (ATCC 10231), Candidia glabrata (ATCC 90030) and Candidia krusei (DSM 70079). This test was based on growth of microorganisms and turbidity measurement technique using a spectrophotometer. The direct contact test was conducted by direct and indirect methods. Multiple comparisons were carried out using analysis of variances (ANOVA) with repeated measures followed by Tukey's tests. RESULTS: The antifungal activity of both sealers was similar in the indirect method. The antifungal activity of both sealers in the direct method was similar against Candida albicans and higher for AH-26 sealer against Candida krusei and Candida glabrata. CONCLUSION: The total antifungal effect of MTA Fillapex sealer was significantly less than AH-26 sealer in direct method. The antifungal effect of both sealers was similar in indirect method.

In vitro evaluation of the sealing ability of three newly developed root canal sealers: A bacterial microleakage study.

BACKGROUND: The purpose of this study was to compare the sealing ability of MTA Fillapex, Apatite Root Canal Sealer and AH26 sealers. MATERIAL AND METHODS: The present in vitro study was carried out on 142 extracted single-rooted human mature teeth. The teeth were randomly divided into three experimental groups (n=44) and two control groups (n=5). Three root canal sealers were MTA Fillapex, Apatite Root Canal Sealer and AH26. The teeth in the control groups were either filled with no sealer or made completely impermeable. The root canals were prepared and obturated with gutta-percha and one of the sealers. The teeth were sterilized with ethylene oxide gas prior to the bacterial leakage assessment using Enterococcus faecalis. Leakage was evaluated every 24 hours for 90 days. Data were analyzed with descriptive statistical methods and chi-squared test. If the data were significant, a proper post hoc test was used. Statistical significance was set at P<0.05. RESULTS: The positive control specimens exhibited total bacterial penetration whilst the negative control specimens showed no evidence of bacterial penetration. At the end of the study, the analysis of microleakage with chi-squared test showed no significant differences between the experimental groups (P<0.05). The results of chi-squared test analyzing the pair-wise differences between the groups considering the numerical values for leakage day indicated the lowest leakage with AH26 and the highest with Apatite root sealer. CONCLUSIONS: According to the results of the present study, sealing ability of AH26 was significantly higher than that of MTA Fillapex and Apatite Root Canal Sealer. Key words:Mineral Trioxide aggregate, root canal obturation, dental seal.

Er,Cr:YSGG Laser as a Novel Method for Rebonding Failed Ceramic Brackets.

OBJECTIVE: Since there is no standard method for rebonding loose ceramic brackets, the aim of this study was to evaluate the possibility of using Er,Cr:YSGG laser to eliminate the remaining composite materials from the base of ceramic brackets and to compare the bond strength of rebonded brackets with the new ones. MATERIALS AND METHODS: Sixty-two extracted human premolars were mounted in acrylic cylinders. Thirty-one ceramic brackets were bonded, and shear bond strength was tested using Hounsfield testing machine. The remnants of the bonding material were removed from the bases of brackets using Er,Cr:YSGG laser. These brackets were rebonded to 31 fresh teeth and again shear bond strength was measured. Pattern of debonding was assessed in both cases under a stereomicroscope and graded according to ARI index. Data were analyzed with independent t-test and Fisher's exact test. RESULTS: Mean shear bond strength of the bond and rebond groups was 12.29 ± 5.46 and 10.58 ± 5.16 MPa, respectively. There were no significant differences between the two groups (p = 0.21). Pattern of bond failure was not statistically different between the two groups. CONCLUSIONS: Er,Cr:YSGG laser was effective in removing the remnants of bonding material from the base of ceramic brackets without any interference with the ceramic base itself, demonstrating that it might be a suitable method for rebonding ceramic brackets.

Antibacterial Activity of MTA Fillapex and AH 26 Root Canal Sealers at Different Time Intervals.

INTRODUCTION: The main goal of endodontic treatment is elimination of bacteria and their by-products from infected root canals. This study compared the antibacterial effect of two different sealers, AH 26 and MTA Fillapex, on 4 microorganisms 24, 48 and 72 h and 7 days after mixing. METHODS AND MATERIALS: The microorganisms used in this study consisted of Lactobacillus acidophilus (ATCC 4356), Lactobacillus casei (ATCC 39392), Staphylococcus aureus (ATCC 25923) and Enterococcus faecalis (ATCC 29212). This test is based on the growth of bacteria and turbidity measurement technique using a spectrophotometer, and direct contact was conducted. Multiple comparisons were carried out using repeated-measures ANOVA followed by Tukey's test and student's t-test. The level of significance was set at 0.05. RESULTS: The antibacterial activity in the indirect technique was more than the technique with both sealers. In the direct technique the antibacterial activity on all microorganisms were lower for MTA Fillapex sealer. In the indirect technique, both sealers exhibited similar antibacterial properties. CONCLUSION: The antibacterial effect of MTA Fillapex sealer was significantly less than that of AH 26 sealer in the direct technique. The antibacterial effects of both sealers were similar in the indirect technique.