Should BRAFV600E be Incorporated into Treatment Recommendations for Thyroid Cancer?

Around 90% of all well-differentiated thyroid cancers are papillary thyroid carcinomas (PTC). PTCs have a recurrence rate of around 20% and a low mortality rate of around 5%. Within PTCs, around 60% of them have the BRAFV600E mutation. Currently, there is a debate on whether BRAFV600E is an independent predictor of tumor aggressiveness and recurrence. This study looks at whether BRAFV600E is an independent predictor of recurrence and outcomes in PTC. Tissue microarrays (TMA) were made from well-differentiated thyroid tumors and stained for the BRAFV600E mutation. BRAFV600E expression was calculated using an H-score: the staining intensity (0-3) multiplied by the amount of tumor that stained positive. A univariate analysis showed that BRAFV600E was significantly associated with age (p=0.0259), gender (p=0.019), extrathyroidal extension (p=0.049), positive margins (p=0.033), lymph node ratio (p=0.0106), N stage (p=0.015), AJCC 8 stage (p=0.0042), ATA risk category (p=0.018), and time to recurrence (p=0.0487). A multivariable analysis found that only extrathyroidal extension was an independent predictor of recurrence. Overall, BRAFV600E was not an independent predictor of recurrence in this cohort. Current treatment plans based on risk of recurrence appear to be appropriate, and it is not recommended that BRAFV600E be included as an independent variable.https://digitalcommons.unmc.edu/surp2021/1058/thumbnail.jp

BanLec, a banana lectin, is a potent inhibitor of Middle East respiratory syndrome coronavirus in in vitro assays

Poster Abstract Session - Viral Infections: Treatment and Prevention: no. 1159BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) continues to cause human infections with multiple clusters two years after the onset of the epidemic. Though mild cases have been recognized, the infection is severe in those with co-morbidities and >30% of patients die from the infection. Our recent structure-based development of a fusion inhibitor is one of the few treatment options for MERS and it led us to hypothesize that other existing antivirals that block cellular entry may also be active against MERS-CoV. BanLec is a jacalin-related banana lectin that has potent anti-HIV activity through binding to glycosylated viral envelope proteins and blocking cellular entry. We assessed the anti-MER-CoV activity of BanLec in cell culture assays. METHODS: The anti-MERS-CoV activity of BanLec was assessed by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction (PRA) assays in Vero, Calu-3, and/or HK2 cells. The cytotoxicity of BanLec was also assessed. RESULTS: The CC50 of BanLec was >10 nM in Vero and Calu-3 cells. CPE was completely absent in Vero and HK2 cells infected with MERS-CoV on 3 dpi with 30.00 nM of BanLec. In Calu-3 cells, CPE was completely absent at 90.00 nM of the drug. The EC50 of BanLec ranged from 3.99-4.82 nM (Table 1). The mean viral loads reduced by 7.13, 3.40, and 3.63 log10 copies/ml in Vero, Calu-3, and HK2 cells respectively (Fig. 1A to C). The highest percentage of plaque reduction at a concentration of >10 nM of BanLec were 100% and 59.5% in Vero cells and HK2 cells respectively (Fig. 2A & B). CONCLUSION: BanLec exhibits potent in vitro anti-MERS-CoV activity. The detailed mechanism and in vivo correlation of its antiviral activity should be further tested in animal models. The potential advantages of using BanLec for MERS include its high stability and the prospect of using it as a topical treatment or prophylaxis for exposed patients. (Table see attachment)BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) continues to cause human infections with multiple clusters two years after the onset of the epidemic. Though mild cases have been recognized, the infection is severe in those with co-morbidities and >30% of patients die from the infection. Our recent structure-based development of a fusion inhibitor is one of the few treatment options for MERS and it led us to hypothesize that other existing antivirals that block cellular entry may also be active against MERS-CoV. BanLec is a jacalin-related banana lectin that has potent anti-HIV activity through binding to glycosylated viral envelope proteins and blocking cellular entry. We assessed the anti-MER-CoV activity of BanLec in cell culture assays. METHODS: The anti-MERS-CoV activity of BanLec was assessed by cytopathic effect (CPE) inhibition, viral yield reduction, and plaque reduction (PRA) assays in Vero, Calu-3, and/or HK2 cells. The cytotoxicity of BanLec was also assessed. RESULTS: The CC50 of BanLec was >10 nM in Vero and Calu-3 cells. CPE was completely absent in Vero and HK2 cells infected with MERS-CoV on 3 dpi with 30.00 nM of BanLec. In Calu-3 cells, CPE was completely absent at 90.00 nM of the drug. The EC50 of BanLec ranged from 3.99-4.82 nM (Table 1). The mean viral loads reduced by 7.13, 3.40, and 3.63 log10 copies/ml in Vero, Calu-3, and HK2 cells respectively (Fig. 1A to C). The highest percentage of plaque reduction at a concentration of >10 nM of BanLec were 100% and 59.5% in Vero cells and HK2 cells respectively (Fig. 2A & B). CONCLUSION: BanLec exhibits potent in vitro anti-MERS-CoV activity. The detailed mechanism and in vivo correlation of its antiviral activity should be further tested in animal models. The potential advantages of using BanLec for MERS include its high stability and the prospect of using it as a topical treatment or prophylaxis for exposed patients

Investigating Immune Profiles in Differentiated Thyroid Cancer by Multiplex Immunofluorescence

BACKGROUND: As the most common endocrine malignancy in the United States (U.S.), differentiated thyroid cancer (DTC) accounts for 3.8% of all cancers in the U.S., with roughly 10% of cases progressing to distant metastatic DTC, which is associated with a poor five year survival outcome despite conventional management, including surgery and radioactive iodine ablation. Recently, novel immunotherapies have garnered attention as a viable therapeutic resource for patients with advanced DTC. However, the response to therapy has been variable and unpredictable, which may be associated with an immune suppressive circulating phenotype. Nonetheless, the intra-tumoral immune infiltrate remains to be elucidated, demonstrating a critical need to address the gap in understanding in order to better prognosticate the disease. OBJECTIVE: To identify and compare tumor-infiltrating immune markers with those present in the adjacent normal thyroid tissue, and collate these immune infiltrates with tumor characteristics. METHODS: Twenty-nine adult tissue samples containing tumor and stromal regions were collected from patients with DTC. The samples were analyzed using multiplex immunofluorescence (MxIF) with antibodies against cell-surface molecules CD56, PD-1, PD-L1, FOXP3, CD3, CD8, CD4, CD45, CD68, CD163, INOS, HLA-DR, CD33, and CD19. 17 of the specimens were analyzed using HALO and a positive threshold was assigned based on review by a trained researcher. RESULTS: In evaluating the immune profiles, important differences in the immune infiltrates between different stages of the cancer were observed. Generally, PD-1 and PD-L1 were highly expressed within the tumor, despite variability in lymphocyte infiltration, indicating the importance of PD-1 and PD-L1 as potential predictive biomarkers for the aggressiveness of thyroid cancer. Tumor from patients with distant metastases demonstrated higher T cell infiltration, T regulatory cells, macrophages and PD-L1 positive cells as compared to localized tumor. CONCLUSION: Immune profiling demonstrated significant differences between tumor and adjacent healthy regions, particularly in terms of PD-1 and PD-L1 expression and lymphocyte infiltration, indicating that higher intratumor infiltration of T regulatory cells, macrophages and PD-1/PD-L1 positive cells may be associated with advanced thyroid cancer. Therefore, the data demonstrates the efficacy of MxIF in gathering valuable information regarding the tumor microenvironment, which will have major implications in guiding the selection of patients for immunotherapy.https://digitalcommons.unmc.edu/surp2021/1042/thumbnail.jp

MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge

<p>Abstract</p> <p>Background</p> <p>Since Swanson proposed the Undiscovered Public Knowledge (UPK) model, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections and are mainly applied to disease-effect relation. With the advancement in biomedical science, it has become imperative to extract and combine information from multiple disjoint researches, studies and articles to infer new hypotheses and expand knowledge.</p> <p>Methods</p> <p>We propose MKEM, a Multi-level Knowledge Emergence Model, to discover implicit relationships using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language System (UMLS) MetaMap. The contribution of MKEM is as follows: First, we propose a flexible knowledge emergence model to extract implicit relationships across different levels such as molecular level for gene and protein and Phenomic level for disease and treatment. Second, we employ MetaMap for tagging biological concepts. Third, we provide an empirical and systematic approach to discover novel relationships.</p> <p>Results</p> <p>We applied our system on 5000 abstracts downloaded from PubMed database. We performed the performance evaluation as a gold standard is not yet available. Our system performed with a good precision and recall and we generated 24 hypotheses.</p> <p>Conclusions</p> <p>Our experiments show that MKEM is a powerful tool to discover hidden relationships residing in extracted entities that were represented by our Substance-Effect-Process-Disease-Body Part (SEPDB) model. </p

Cerebral Blood Volume Changes During Radiotherapy May Predict Pseudoprogression versus Disease Progression for Patients with High Grade Glioma

https://openworks.mdanderson.org/sumexp21/1040/thumbnail.jp

Simultaneous storage of medical images in the spatial and frequency domain: A comparative study

BACKGROUND: Digital watermarking is a technique of hiding specific identification data for copyright authentication. This technique is adapted here for interleaving patient information with medical images, to reduce storage and transmission overheads. METHODS: The patient information is encrypted before interleaving with images to ensure greater security. The bio-signals are compressed and subsequently interleaved with the image. This interleaving is carried out in the spatial domain and Frequency domain. The performance of interleaving in the spatial, Discrete Fourier Transform (DFT), Discrete Cosine Transform (DCT) and Discrete Wavelet Transform (DWT) coefficients is studied. Differential pulse code modulation (DPCM) is employed for data compression as well as encryption and results are tabulated for a specific example. RESULTS: It can be seen from results, the process does not affect the picture quality. This is attributed to the fact that the change in LSB of a pixel changes its brightness by 1 part in 256. Spatial and DFT domain interleaving gave very less %NRMSE as compared to DCT and DWT domain. CONCLUSION: The Results show that spatial domain the interleaving, the %NRMSE was less than 0.25% for 8-bit encoded pixel intensity. Among the frequency domain interleaving methods, DFT was found to be very efficient

Walking through volcanic mud : the 2,100 year-old Acahualina footprints (Nicaragua) II: the Acahualina people, environmental conditions and motivation

We analyzed bare human footprints in Holocene tuff preserved in two pits in the Acahualinca barrio in the northern outskirts of Managua (Nicaragua). Lithology, volcanology, and age of the deposits are discussed in a companion paper (Schmincke et al. Bull Volcanol doi: 10.1007/s00445-008-0235-9, 2008). The footprint layer occurs within a series of rapidly accumulated basaltic–andesitic tephra that is regionally correlated to the Masaya Triple Layer Tephra. The people were probably trying to escape from a powerful volcanic eruption at Masaya Caldera 20 km farther south that occurred at 2.1 ka BP. We subdivided the swath of footprints, up to 5.6 m wide, in the northern pit (Pit I) into (1) a central group of footprints made by about six individuals, the total number being difficult to determine because people walked in each other’s footsteps one behind the other and (2) two marginal groups on either side of the central group with more widely spaced tracks. The western band comprises tracks of three adjacent individuals and an isolated single footprint farther out. The eastern marginal area comprises an inner band of deep footprints made by three individuals and, farther out, three clearly separated individuals. We estimate the total number of people as 15–16. In the southern narrow and smaller pit (Pit II), we recognize tracks of ca. 12 individuals, no doubt made by the same group. The group represented in both pits probably comprised male and female adults, teenagers and children based on differences in length of footprints and of strides and depth of footprints made in the soft wet ash. The smallest footprints (probably made by children) occur in the central group, where protection was most effective. The footprint layer is composed of a lower 5–15-cm thick, coarse-grained vesicle tuff capped by a medium to fine-grained tuff up to 3 cm thick. The surface on which the people walked was muddy, and the soft ash was squeezed up on the sides of the foot imprints and between toes. Especially, deep footprints are mainly due to local thickening of the water-rich ash, multiple track use, and differences in weight of individuals. The excellent preservation of the footprints, ubiquitous mudcracks, sharp and well-preserved squeeze-ups along the margins of the tracks and toe imprints, and the absence of raindrop impressions all suggest that the eruption occurred during the dry season. The people walked at a brisk pace, as judged from the tight orientation of the swath and the length of the strides. The directions of a major erosional channel in the overlying deposits that probably debouched into Lake Managua and the band of footprints are strictly parallel, indicating that people walked together in stride along the eastern margin of a channel straight toward the lake shore, possibly a site with huts and/or boats for protection and/or escape

Machine Learning Analyses of Highly-Multiplexed Immunofluorescence Identifies Distinct Tumor and Stromal Cell Populations in Primary Pancreatic Tumors

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a formidable challenge for patients and clinicians. OBJECTIVE: To analyze the distribution of 31 different markers in tumor and stromal portions of the tumor microenvironment (TME) and identify immune cell populations to better understand how neoplastic, non-malignant structural, and immune cells, diversify the TME and influence PDAC progression. METHODS: Whole slide imaging (WSI) and cyclic multiplexed-immunofluorescence (MxIF) was used to collect 31 different markers over the course of nine distinctive imaging series of human PDAC samples. Image registration and machine learning algorithms were developed to largely automate an imaging analysis pipeline identifying distinct cell types in the TME. RESULTS: A random forest algorithm accurately predicted tumor and stromal-rich areas with 87% accuracy using 31 markers and 77% accuracy using only five markers. Top tumor-predictive markers guided downstream analyses to identify immune populations effectively invading into the tumor, including dendritic cells, CD4+ T cells, and multiple immunoregulatory subtypes. CONCLUSIONS: Immunoprofiling of PDAC to identify differential distribution of immune cells in the TME is critical for understanding disease progression, response and/or resistance to treatment, and the development of new treatment strategies

Quantifying and filtering knowledge generated by literature based discovery

Background Literature based discovery (LBD) automatically infers missed connections between concepts in literature. It is often assumed that LBD generates more information than can be reasonably examined. Methods We present a detailed analysis of the quantity of hidden knowledge produced by an LBD system and the effect of various filtering approaches upon this. The investigation of filtering combined with single or multi-step linking term chains is carried out on all articles in PubMed. Results The evaluation is carried out using both replication of existing discoveries, which provides justification for multi-step linking chain knowledge in specific cases, and using timeslicing, which gives a large scale measure of performance. Conclusions While the quantity of hidden knowledge generated by LBD can be vast, we demonstrate that (a) intelligent filtering can greatly reduce the number of hidden knowledge pairs generated, (b) for a specific term, the number of single step connections can be manageable, and (c) in the absence of single step hidden links, considering multiple steps can provide valid links

Symptoms associated with victimization in patients with schizophrenia and related disorders

Background: Patients with psychoses have an increased risk of becoming victims of violence. Previous studies have suggested that higher symptom levels are associated with a raised risk of becoming a victim of physical violence. There has been, however, no evidence on the type of symptoms that are linked with an increased risk of recent victimization. Methods: Data was taken from two studies on involuntarily admitted patients, one national study in England and an international one in six other European countries. In the week following admission, trained interviewers asked patients whether they had been victims of physical violence in the year prior to admission, and assessed symptoms on the Brief Psychiatric Rating Scale (BPRS). Only patients with a diagnosis of schizophrenia or related disorders (ICD-10 F20–29) were included in the analysis which was conducted separately for the two samples. Symptom levels assessed on the BPRS subscales were tested as predictors of victimization. Univariable and multivariable logistic regression models were fitted to estimate adjusted odds ratios. Results: Data from 383 patients in the English sample and 543 patients in the European sample was analysed. Rates of victimization were 37.8% and 28.0% respectively. In multivariable models, the BPRS manic subscale was significantly associated with victimization in both samples. Conclusions: Higher levels of manic symptoms indicate a raised risk of being a victim of violence in involuntary patients with schizophrenia and related disorders. This might be explained by higher activity levels, impaired judgement or poorer self-control in patients with manic symptoms. Such symptoms should be specifically considered in risk assessments