Correlation of ER, PR, and HER2 at protein and mRNA levels in the Asian patients with operable breast cancer

Breast cancer is the most common cancer and the leading cause of cancer-related death in women. The estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are important biomarkers in the prognosis of breast cancer, and their expression is used to categorize breast cancer into subtypes. We aimed to analyze the concordance between ER, PR, and HER2 expression levels and breast cancer subtyping results obtained by immunohistochemistry (IHC, for protein) and reverse transcriptase-polymerase chain reaction (RT-PCR, for mRNA) and to assess the recurrence-free survival (RFS) of the different subtypes as determined by the two methods. We compared biomarker expression by IHC and RT-PCR in 397 operable breast cancer patients and categorized all patients into luminal, HER2, and triple-negative (TN) subtypes. The concordance of biomarker expression between the two methods was 81.6% (kappa = 0.4075) for ER, 87.2% (kappa = 0.5647) for PR, and 79.1% (kappa = 0.2767) for HER2. The kappa statistic was 0.3624 for the resulting luminal, HER2, and TN subtypes. The probability of a 5-year RFS was 0.78 for the luminal subtype versus 0.77 for HER2 and 0.51 for TN, when determined by IHC (p = 0.007); and 0.80, 0.71, and 0.61, respectively, when determined by the RT-PCR method (p = 0.008). Based on the current evidence, subtyping by RT-PCR performs similarly to conventional IHC with regard to the 5-year prognosis. The PCR method may thus provide a complementary means of subtyping when IHC results are ambiguous.

Performance evaluation of novel fluorescent-based lateral immune flow assay (LIFA) for rapid detection and quantitation of total anti-SARS-CoV-2 S-RBD binding antibodies in infected individuals

1.AbstractBackgroundThe vast majority of the commercially available LFIA is used to detect SARS-CoV-2 antibodies qualitatively. Recently, a novel fluorescence-based LIFA test was developed for quantitative measurement of the total binding antibody units (BAU/mL) against the receptor-binding domain of the SARS-CoV-2 spike protein (S-RBD).AimTo evaluate the performance of the fluorescence LIFA Finecare™ 2019-nCoV S-RBD test along with its reader (Model No.: FS-113).MethodsPlasma from 150 RT-PCR confirmed-positive individuals and 100 pre-pandemic samples were tested by FinCare™ to access sensitivity and specificity. For qualitative and quantitative validation of the FinCar™ measurements, the BAU/mL results of FinCare™ were compared with results of two reference assays: the surrogate virus-neutralizing test (sVNT, GenScript, USA), and the VIDAS®3 automated assay (BioMérieux, France).ResultsFinecare™ showed 92% sensitivity and 100% specificity compared to PCR. Cohen’s Kappa statistic denoted moderate and excellent agreement with sVNT and VIDAS®3, ranging from 0.557 (95% CI: 0.32-0.78) to 0.731 (95% CI: 0.51-0.95), respectively. A strong correlation was observed between Finecare™/sVNT (r=0.7, p<0.0001) and Finecare™/VIDAS®3 (r=0.8, p<0.0001).ConclusionFinecare™ is a reliable assay and can be used as a surrogate to assess binding and neutralizing antibody response post-infection or vaccination, particularly in none or small laboratory settings.

Assessing Spatiotemporal Built-up Dynamics in Chiang Mai City, Thailand using Entropy approach

The rates of urban dynamics affecting by industrialization, urban agglomeration, and large-scale migration turn its behaviour from monocentric to polycentric metropolitan resulting in unprecedented urban growth. Therefore, the present study incorporated an entropy-based approach to measure the degree of compactness and dispersiveness of urban development in Chiang Mai City. The Object-based machine learning was deployed for the image classifications with an overall accuracy above the minimum requirements (i.e., 90%) and kappa statistic of agreement above 0.85. The study reveals that Chiang Mai city has undergone urban development outskirts from the urban centre (CBD) and north and south-west direction from the CBD. A considerable increase in urban demographic and physical urban patches was observed in last 1998 to 2018. The research emphasized the significant role of Shannon Entropy to analyze the built-up growth supplemented by Remote Sensing and Geographic Information System (GIS) in respective zones and geographical directions.

Comparison of Morphological Similarities and Differences between Liquid-Based Cytology and Conventional Techniques of Serous Effusion Cytology Specimens

<b><i>Introduction:</i></b> The aim of this study is to discover a fast and efficient method for the diagnosis of serous effusion cytology specimens by comparing the cytomorphological features of SurePath (SP) smears and smears prepared by cytospin. After the macroscopic features of the incoming material were recorded, it was divided into 2 for conventional technique (CT) and liquid-based technique. Cytospin was used for CT and SurePath for liquid-based technique in this study. <b><i>Materials and Methods:</i></b> 243 serous effusions (33 thoracentesis and 92 paracentesis fluids, 118 peritoneal lavage fluids) were investigated. After shaking the effusion gently, it was centrifuged for 5 min at 1,250 rpm for cytospin smear. SP smear was prepared according to the “BD PrepStain slide processor”. Two smears were prepared with these 2 methods and then stained with Papanicolaou. The smears were examined under a light microscope in terms of fixation, background, cellularity, nucleus, and structural features. All statistical analysis of the data was performed using the SPSS 17.0 software. For each microscopic feature, the χ² test was used to assess the significance of the relationship between cytospin and SP, and level of agreement in between the methods was assessed using the kappa statistic. <b><i>Results:</i></b> A statistically significant difference was observed between the 2 methods in background (<i>p</i> &#x3c; 0.001), cellularity (<i>p</i> &#x3c; 0.001), nucleus features (<i>p</i> &#x3c; 0.001), and structural features (<i>p</i> &#x3c; 0.05). There was no significant difference in fixation. Low level of agreement was observed with the kappa statistic in fixation, background, and cellularity. Moderate level of agreement was observed in the nucleus and structural feature groups with the kappa statistic. <b><i>Discussion/Conclusion:</i></b> Although there are advantages of liquid-based technique such as standardized fixation and cleaner background, since the cellular and background components required for morphological analysis and diagnosis are better preserved in cytospin, it is considered to be better to use liquid-based technique not alone but together with CT.

QUERY EXPANSION RANKING PADA ANALISIS SENTIMEN MENGGUNAKAN KLASIFIKASI MULTINOMIAL NAÏVE BAYES (Studi Kasus : Ulasan Aplikasi Shopee pada Hari Belanja Online Nasional 2020)

Shopee is one of the e-commerce sites that has many users in Indonesia. Shopee provides various attractive promos on special days such as National Online Shopping Day on December 12. Shopee site was a complete error on December 12, 2020. Complaints and opinions of Shopee users were also shared through various media, one of them was Google Play Store. Sentiment analysis was used to see the user's response to the Shopee’s incident. Sentiment analysis results can be extracted to obtain information regarding positive or negative reviews from Shopee users. Sentiment analysis was performed using the Multinomial Naïve Bayes classification. the simplest method of probability classification, but it is sensitive to feature selection so that the amount of data is determined by the results of feature selection Query Expansion Ranking. The algorithm that has the highest accuracy and kappa statistic is the best algorithm in classifying Shopee’s users sentiment. The results showed that the classification performance using Multinomial Naïve Bayes with 80% of the features (terms) which have the highest Query Expansion Ranking value was obtained at the accuracy and kappa statistics values are 89% and 77.62%. This means that Multinomial Nave Bayes has a good performance in classifying reviews and the number of features used affects the performance results obtained.

Evaluation of YouTube videos for patients’ education on periradicular surgery

The aim of this study was to evaluate the content of periradicular surgery-related YouTube videos available for patients’ education. YouTube search was made for videos related to periradicular surgery using specific terms. After exclusions, 42 videos were selected, viewed and assessed by two independent observers. The videos were assessed in terms of duration, days since upload, country of upload, number of views, likes and dislikes, authorship source, viewing rate and interaction index. To grade the content of videos about periradicular surgery, a usefulness score was created with 10 elements based mainly on the American Association of Endodontists guidelines. Each element was given a score of 0 or 1. SPSS software (SPSS Inc, Chicago, IL, USA) was used to analyze data at a 95% confidence level. An inter-evaluator reliability analysis for the scoring system was performed using the Kappa statistic. The videos received an average of 35103.9 views (range: 9–652378) with an average duration of 338.71 seconds (range: 42–2081), respectively. Most videos were provided by individuals (57%). Half of the videos were posted by authors from the United States. The inter-evaluator reliability for usefulness scoring was 94.5%. No video covered the 10 scoring elements completely, presenting very low usefulness scores (mean: 3.2; range: 1–7). The most discussed elements were supporting media (100%) and steps of the procedure (90.5%) followed by indications and contraindications (45.2%) and symptoms (31%). None of the included videos discussed the procedure’s cost or prognosis. In terms of usefulness score, no significant difference was detected between different sources of upload (chi-square test, P > 0.05). Information on periradicular surgery in YouTube videos is not comprehensive and patients should not rely on YouTube as the only source of information. Dental professionals should enrich the content of YouTube with good quality videos by providing full and evidence-based information that will positively affect patients’ attitudes and satisfaction.

What evidence exists on the impact of anthropogenic radiofrequency electromagnetic fields on animals and plants in the environment? A systematic map protocol

Background Exposure to radiofrequency (RF) electromagnetic fields (EMF), particularly from telecommunications sources, is one of the most common and fastest growing anthropogenic factors on the environment. In many countries, humans are protected from excessive RF EMF exposure by safety standards that are based on guidelines by the International Commission on Non-Ionizing Radiation Protection (ICNIRP). The ICNIRP guidelines are based on knowledge of how RF EMF affects the human body, however, there are currently no recognised international guidelines to specifically protect animals and plants. Whether the ICNIRP guidelines for humans is adequate to provide protection to the environment is a subject of active debate. This systematic map will collate all the available evidence on whether anthropogenic RF EMF has a negative effect on plants and animals in the environment. The map will also identify gaps in knowledge, recommend future research and inform environmental and radiation protection authorities. Methods The proposed systematic map will include peer-reviewed and grey literature published in English. The EMF—Portal, PubMed and Web of Science databases will be searched using a search string prepared by the review team and tested for comprehensiveness against a list of known relevant reviews. Once duplicates are removed, retrieved articles will be screened in three stages: title, abstract, and full text. Studies will be selected with a subject population of all plants and animals, with exposures to anthropogenic RF EMF (frequency range 100 kHz–300 GHz) compared to no or lower-level exposure, and for all outcomes related to the studied populations. Kappa statistic tests will be conducted at each stage to ensure consistency of decision-making regarding the predefined inclusion/exclusion criteria. Eligible studies will then proceed to the data extraction phase, which will extract meta-data such as bibliographic information, taxonomic information, RF EMF exposure data, outcome(s), sample size, etc. The extracted data will then be organised into a systematic map and the findings summarised by cross-tabulating key meta-data variables in heat maps, charts or other data visualization methods. The systematic map will identify gaps in knowledge, priorities for future research and potential subtopics for further analysis and/or systematic review.

Superiority of Siriraj Stroke Score Over Guy’s Hospital Score in Diagnosing Acute Hemorrhagic Stroke at Bedside

Background: The clinical diagnosis of stroke in a patient admitted in the intensive care unit (ICU) is undeniably challenging. Several point-based risk scores have been developed to predict clinical outcomes after ischemic stroke. Objective: To assess the Siriraj stroke score and Guy’s Hospital stroke score in the clinical diagnosis of acute stroke. Materials and Methods: All patients were subjected to Computed tomography (CT) scan head within 72 hours of admission. The sensitivity, specificity, positive predictive value was calculated for both the scores. Comparability between the scores and CT scan head finding was determined with the help of Kappa statistic program. Results: Sensitivity of Guy’s Hospital stroke score for ischemic stroke is 100%, specificity is 96.4%, accuracy 97.1%, positive predictive value of 87.5% and negative predictive value 100%. The sensitivity of Guy’s Hospital stroke score for hemorrhage stroke is 96.4%, specificity is 100%, accuracy 97.1%, positive predictive value of 100% and negative predictive value 87.5% Conclusion: Siriraj stroke score as a simple method of screening patients for intracerebral hemorrhage, as it is easier to use at bedside and has a greater accuracy in diagnosing hemorrhage than Guy’s Hospital score. KYAMC Journal. 2021;12(3): 142-146

Intra- and inter-observer reproducibility of r-ASRM endometriosis classification system and its components, using edited videotaped laparoscopic procedures

Several classification systems have been proposed for endometriosis but the search for the ideal system is ongoing. While the most commonly used system has historically been r-ASRM, this system is not fit for purpose, particularly for deep endometriosis. In order to explore strategies to devise a new system and learn from problems with the existing ones, this study was designed to assess the reproducibility of each component in r-ASRM and its total score using videotaped laparoscopic procedures. Two surgeons independently scored 64 edited videos of laparoscopic endometriosis procedure, twice. Using the Kappa statistic, the agreement of the scores given was analyzed. r-ASRM showed a moderate inter-observer agreement (ƙ = 0.503) and good intra-observer agreement (ƙ = 0.774 and 0.682 for scorer 1 and 2 respectively) for overall disease staging. The agreement for each component of the system, however, was highly variable. The least agreement was observed for the peritoneum with ƙ = 0.157 and ƙ = 0.362 respectively for inter-observer and intra-observer. The lowest intra-observer agreement was seen for cul-de-sac for scorer 2 (ƙ = 0.382). Whilst the overall rASRM shows acceptable agreement between two scorers, this agreement seems to be the product of inconsistent scoring for each component.

Oesophageal IGRT considerations for SBRT of LA-NSCLC: barium-enhanced CBCT and interfraction motion

Background To determine the optimal volume of barium for oesophageal localisation on cone-beam CT (CBCT) for locally-advanced non-small cell lung cancers (NSCLC) and quantify the interfraction oesophageal movement relative to tumour. Methods Twenty NSCLC patients with mediastinal and/or hilar disease receiving radical radiotherapy were recruited. The first five patients received 25 ml of barium prior to their planning CT and alternate CBCTs during treatment. Subsequent five patient cohorts, received 15 ml, 10 ml and 5 ml. Six observers contoured the oesophagus on each of the 107 datasets and consensus contours were created. Overall 642 observer contours were generated and interobserver contouring reproducibility was assessed. The kappa statistic, dice coefficient and Hausdorff Distance (HD) were used to compare barium-enhanced CBCTs and non-enhanced CBCTs. Oesophageal displacement was assessed using the HD between consensus contours of barium-enhanced CBCTs and planning CTs. Results Interobserver contouring reproducibility was significantly improved in barium-enhanced CBCTs compared to non-contrast CBCTs with minimal difference between barium dose levels. Only 10 mL produced a significantly higher kappa (0.814, p = 0.008) and dice (0.895, p = 0.001). The poorer the reproducibility without barium, the greater the improvement barium provided. The median interfraction HD between consensus contours was 4 mm, with 95% of the oesophageal displacement within 15 mm. Conclusions 10 mL of barium significantly improves oesophageal localisation on CBCT with minimal image artifact. The oesophagus moves substantially and unpredictably over a course of treatment, requiring close daily monitoring in the context of hypofractionation.