Imagined speech classification exploiting EEG power spectrum features

Imagined speech recognition has developed as a significant topic of research in the field of brain-computer interfaces. This innovative technique has great promise as a communication tool, providing essential help to those with impairments. An imagined speech recognition model is proposed in this paper to identify the ten most frequently used English alphabets (e.g., A, D, E, H, I, N, O, R, S, T) and numerals (e.g., 0 to 9). A novel electroencephalogram (EEG) dataset was created by measuring the brain activity of 30 people while they imagined these alphabets and digits. As part of signal preprocessing, EEG signals are filtered before extracting delta, theta, alpha, and beta band power features. These features are used as input for classification using support vector machines, k-nearest neighbors, and random forest (RF) classifiers. It is identified that the RF classifier outperformed the others in terms of classification accuracy. Classification accuracies of 99.38% and 95.39% were achieved at the coarse-level and fine-level, respectively with the RF classifier. From our study, it is also revealed that the beta frequency band and the frontal lobe of the brain played crucial roles in imagined speech recognition. Furthermore, a comparative analysis against state-of-the-art techniques is conducted to demonstrate the efficacy of our proposed model.

Ecotoxicological effects of cypermethrin on indigenous climbing perch (Anabas testudineus)

Pesticides including cypermethrin (10% EC) are commonly used pesticide in tea gardens of Bangladesh possess distinct harmful effects on an aquatic community. The experiment was carried out to assess the ecotoxicological effects of cypermethrin (10%) concentrate on indigenous Climbing Perch (Anabas testudineus). A total of 120 A. testudineus (mean length 16 ± 2.67 cm and mean weight 31.6 ± 3.56 g) were exposed to the acute toxicity test when the lethal concentration 50 value (LC50) for 96 h was maintained at 1.00 ppm. Three different sub-lethal concentrations of 0.05 ppm (5%), 0.10 ppm (10%), and 0.20 ppm (20%) were used respectively as three treatments and a control of 0 ppm with three replicates each. Restlessness, erratic movement, increased opercular activities, loss of equilibrium, and irregular response to feeding were observed in all the treatments compared to control one. Concerning histopathological alterations, all the analyzed organs showed highest changes in the T3 (cypermethrin conc. 20%) compared to other treatments while T0 (0 ppm) had normal structure. The major changes in the gill were epithelial cell hyperplasia, necrosis, severe lamellar fusion and epithelial lifting; while necrotic proximal tubules, glomerular shrinkage, disrupted renal corpuscle of the kidney and nuclear pyknosis, degenerated hepatic cells and vacuolation were observed in the liver. Severe melanomacrophage centre (MMC), haemosiderosis and vacuolation were found in spleen. The effect of cypermethrin on the hematological parameters of experimental fish was also studied. Red blood cells, hemoglobin and hematocrit were decreased in the experimental groups and lowest value was in T3 while values of white blood cells were increased in the experimental groups compared to control one. Hence, the present observation revealed that pesticides even at low concentrations can cause harmful effects on A. testudineus.

Endoscopic Transnasal Repair of Cerebrospinal Fluid Leakage: Experience in BSMMU

Endoscopic transnasal repair of CSF rhinorrhoea is gaining popularity around the world because of its tremendous success rate but it depends on defect site, size, technique of repair, experiences of surgeon and also patient's profile. Aim of this study was to analysis of surgical outcome of endoscopic transnasal repair of CSF rhinorrhoea. A retrospective study carried out in the department of ENT and Head neck surgery at Bangabandhu Sheikh Mujib Medical University (BSMMU) from January 2018 to December 2019. Of the total of 24 patients 16(66.0%) were female and 8(33.0%) males. The commonest site of the leak was in the cribriform plate in 18(75.3%) followed by 5(20.8%) in the fovea ethmoidalis, and 1(4.0%) in the sphenoid sinus, the overall success rate of this series with first surgical procedure was 95.83% and 100.0% with a second procedure. Meticulous pre-operative evaluation, proper identification of leakage site, choice of graft materials and surgical technique are keys to attaining excellent results.

Complete Heparin Reversal by Protamine during Off-Pump Coronary Artery Bypass Surgery (OPCAB): A Necessity or Myth?

In our country majority of the coronary artery bypass surgery (CABG) are done off-pump and was reported having excellent clinical outcome along with cost efficiency by various investigators. Heparin is commonly used as most effective anticoagulant, and protamine sulfate is now generally used to reverse the anticoagulant action of heparin. While under dosing of protamine may result in incomplete heparin reversal and prolonged anticoagulation, protamine overdosing is associated with impaired clot formation exerted by the intrinsic anti-coagulation properties of protamine itself, moreover protamine administration is associated with mild to severe cardiovascular and pulmonary complications. Apart from traditional full neutralization of heparin now-a-days, half dose protamine was also introduced showing good outcome regarding lower activated clotting time (ACT), overall, less surgical bleeding with less transfusion. This comparative study was designed to detect differences between traditional and decreased protamine dosing in Off-Pump Coronary Artery Bypass (OPCAB) surgery. Four hundred (400) patients who underwent Off-Pump Coronary Artery Bypass Surgery (OPCAB) surgery at our institution over a period of 12 months were analyzed and were divided into two groups. Group A- received 0.5mg of protamine per 100 unit of heparin; Group B-received 1.0mg of protamine per 100 unit of heparin. ACT, blood loss, hemoglobin and platelet count units of blood and blood product transfusion requirements, clinical outcome and hospital stay were assessed in each patient. This study showed that 0.5mg of protamine per 100 unit of heparin was always able to reverse the anticoagulant effect of heparin with no significant difference in hemodynamic parameters, amount of blood loss and requirements of blood transfusion in between the groups. A standard protamine dosing formula (protamine-heparin at ratio of 1:1) adequate for on-pump cardiac surgical procedures significantly overestimates protamine requirements for OPCAB. Patients treated with decreased protamine do not appear to have adverse outcomes in terms of post-operative bleeding.

A Case Report of Porphyria Cutanea Tarda with Hepatitis-C Virus Co-infection

Porphyria cutanea tarda is a rare disorder of heme metabolism due to deficiency of the enzyme uroporphyrinogen decarboxylase which is manifested as some typical dermatological features and hepatic dysfunction. The Hepatitis-C virus co-infection is common and it can be aggravated by other environmental factors. We report a case of porphyria cutanea tarda in a 37-year-old woman, who presented with recurrent skin blisters and has concomitant Hepatitis-C virus infection. She was taking oestrogen containing oral contraceptive pill for a long duration. The diagnosis of porphyria cutanea tarda was considered on the basis of clinical features and high level of urine porphyrin level. She was put on hydroxychloroquine and combination drugs for Hepatitis-C virus with significant improvement after 3 months of therapy.

Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh

BACKGROUND

Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones.

RESULTS

Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes (CCs): the globally dominant CC1 and CC2, and CC10; one strain had a novel sequence type (ST). AMR phenotype-genotype agreement was observed and the genomes contained various beta-lactamase genes including bla_OXA-23 (n = 12), bla_OXA-66 (n = 6), and bla_NDM-1 (n = 3). All genomes displayed roughly similar virulomes, however some virulence genes such as the Acinetobactin bauA and the type IV pilus gene pilA displayed high genetic variability. CC2 strains carried highest levels of plasmidic gene content and possessed conjugative elements carrying AMR genes, virulence factors and insertion sequences.

CONCLUSION

This study presents the first comparative genomic analysis of XDR clinical Acinetobacter spp. from Bangladesh. It highlights the prevalence of different classes of beta-lactamases, mobilome-derived heterogeneity in genetic architecture and virulence gene variability in prominent Acinetobacter clonal complexes in the country. The findings of this study would be valuable in understanding the genomic epidemiology of A. baumannii clones and their association with closely related pathogenic species like A. nosocomialis in Bangladesh.

Residue level and health risk assessment of organophosphorus pesticides in country bean and bitter gourd collected from Cumilla, Bangladesh

Organophosphorus pesticides are one of the most commonly used pesticide classes in agriculture in the management of insect pests due to their high efficacy. The extensive use of organophosphorus pesticides can contaminate both the atmosphere and food, which may lead to health problems. In this study, the residue level of organophosphorus pesticides, and their health risk assessment was evaluated on country bean and bitter gourd. Out of forty analysed samples of the country bean, two samples contained multiple residues, seven samples contained single residue. On the other hand, out of forty samples of bitter gourd, one sample contained multiple residues and three samples contained single residue. Among the organophosphorus pesticides, diazinon was the most frequently detected organophosphorus pesticide in country bean and bitter gourd. The highest short-term risks or acute risk (aHI) was below 1.83%, and the highest long-term risk or chronic risk (HQs) was below 10.46% for the country bean and bitter gourd, respectively. Short- and long-term risk assessment results showed that the intake risks of country bean and bitter gourd were acceptable. The health hazard results showed that country bean and bitter gourd consumption in Cumilla, Bangladesh does not pose an acute or chronic risk to human health. However, a routine monitoring system must be established to control the contamination of vegetables with pesticides.

Whole genome sequencing provides genomic insights into three Morganella morganii strains isolated from bovine rectal swabs in Dhaka, Bangladesh

Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae tribe of the Morganellaceae family, is an unusual opportunistic pathogen mainly responsible for nosocomial and urinary tract infections. While cattle have long been established as a source of a few zoonotic pathogens, no such data has been recorded for M. morganii despite its ubiquitous presence in nature and a number of animal hosts. In this study, draft genomes were produced of three M. morganii isolates from Bangladeshi cattle. The three isolates, named B2, B3 and B5, possessed an average genome size of 3.9 Mp, a GC% of ∼51% and pan and core genomes of 4637 and 3812 genes, respectively. All strains were bearers of the qnrD1 carrying plasmid Col3M and possessed roughly similar virulence profiles and prophage regions. The strains also carried genes that were unique when compared with other publicly available M. morganii genomes. Many of these genes belonged to metabolic pathways associated with adaptation to environmental stresses and were predicted in silico to be borne in genomic islands. The findings of this study expand on the current understanding of M. morganii''s genomic nature and its adaptation in cattle.

Outcome of Management of Liver Abscess by Surgical Approach in a Tertiary Care Hospital

Liver abscess is a serious, life threatening condition. A recent development in the management of liver abscesses, facilitated by advances in diagnostic and interventional radiology, has decreased mortality rates. The purpose of this study is to search for the clinical presentations and surgical outcomes of liver abscess in our country. The markers of the outcome are mortality, duration of hospital stay and complications such as wound infection, residual disease following surgery, biliary leakage, intra abdominal abscess formation. This observational cross sectional study was conducted in Mymensingh Medical College & Hospital (MMCH), Bangladesh for 12 months from 1st January 2017 to 31st December 2017. Total 25 patients presenting with the features of liver abscess were included in this study by convenient and purposive sampling according to the inclusion and exclusion criteria. Surgical principles of liver abscess management were applied and outcomes were observed. The patients were diagnosed on the basis of clinical feature, findings of abdominal ultrasound and occasionally by doing CT scan. Most of the patients (28%) were in the age group of 51-60 years. Regarding sex distribution majority of the patients (64%) was male. Most of patients presented with fever (92%), anorexia and vomiting (32%), upper abdominal pain (84%). Hepatomegaly and reactive pleural effusion are the important findings present in 9(36%) and 8(32%) patients respectively. Size of the liver abscess was more than 5cm in 72% patients. Among the patients right lobe was predominantly involved. It was found during laparotomy that 4 patients (16%) had spontaneous rupture of abscess into peritoneal cavity. One (4%) patient developed biliary leakage after surgical drainage. No intra abdominal abscess or residual diseases was observed after surgery. Among the patients 24% developed wound infection. The overall mortality rate was 12%. The median length of hospital stay was 8 days (range: 1-15 days). Outcome of surgical drainage of liver abscess in tertiary care hospital of our country shows satisfactory result. So, patients with large multiple liver abscess, septic shock, failures of percutaneous drainage should be treated by early open surgical intervention.

Outcome of Closed Reduction and Internal Fixation by Titanium Elastic Nailing for Fracture Shaft of Femur in Children

Femoral fractures are frequent in the pediatric population. Treatment options are based on the patient's age, fracture pattern, type of trauma and associated soft tissue injury. The traditional treatment method for pediatric femoral shaft fracture has been traction and spica casting. The immediate spica cast is safe and effective for children up to 6 years of age with isolated femoral fracture and acceptable reduction. Patients between 6 and 10 years of age can also be treated with spica casting with or without traction. This prospective study was done in the department of Orthopaedics, Mymensingh Medical College Hospital, Mymensingh, Bangladesh form from July 2015 to June 2019 to evaluate the outcome of closed reduction and internal fixation by titanium elastic nailing for fracture shaft of femur. Twenty patients, all presenting with fresh diaphyseal fractures of femur, treated with closed reduction and internal fixation by titanium elastic nailing. These patients were prospectively evaluated over a period of at least 18 months. Fractures were classified according to Association of Orthopaedics (AO) classification of shaft of femur fractures. According to AO classification, all were A1, A2, A3 fractures. Average age of the patients was 11±2.7 years; range was 6 to 16 years. There were 15 males and 5 females. Out of 20 cases treated with this method, stable fixation and union was achieved in all of them. Radiological union was achieved at an average of 10±2.3 weeks (8-15 weeks). The results were excellent in twelve patients (60%), successful in five (25%) and poor in three patients (15%) as per the scoring criteria for TEN. The effective treatment of diaphyseal fractures of the femur is intramedullary fixation by titanium elastic nailing in patients of the 6-16 years age group.

Anterior Cruciate Ligament Reconstruction using Bone Patellar Tendon Bone Autograft in ACL Deficient Knee

More than 120,000 anterior cruciate ligament (ACL) injuries occur every year in the United States, mostly during the high school and college years. The incidence of these injuries is slowly increasing, especially in females. This is likely caused by their increasing participation in high school and other organized sports. In addition, several studies have shown that female athletes are at an increased risk of ACL injury in sex comparable sports. The goal of this study was to evaluate the functional outcome of Arthroscopic anterior cruciate ligament reconstruction using Bone-Patellar tendon- Bone autograft. 25 patients with chronic ACL deficient knee presenting to Mymensingh Medical College Hospital (MMCH), Mymensingh, Bangladesh from January 2018 to December 2019 were included in the study. The patients with severe osteoarthritis (OA) knee, local active infection and systemic disease, intraarticular fracture of knee that might influence the study results were excluded from the study. Bone patellar tendon bone graft was harvested from ipsilateral knee. The patient was followed till 6 months with specified program of rehabilitation. Results were evaluated by an independent examiner using radiography, subjective and objective evaluation. Assessment using Lysholm's score was 50 (42-63) preoperatively and 90.8 (63-97) at the latest follow up (p<0.005). No patient complained of instability at latest follow up. The quadriceps muscle showed atrophy at final follow-up. Five Patients complained of anterior knee pain. We found no graft displacement on follow up radiographs. Osteo-integration occurred in all cases. ACLR with a BPTB graft can stabilize the knee without loss of motion by closely mimicking the native ACL without any hazards and additional complications. It is useful in high demand patients and cost effective option with high patient satisfaction rate for reconstruction of ACL.

Fetuin B overexpression suppresses proliferation, migration, and invasion in prostate cancer by inhibiting the PI3K/AKT signaling pathway

Fetuin B (FETUB) is a glycoprotein that is a member of the cysteine protease inhibitor family, and it is associated with cancer. However, the role of FETUB in prostate carcinogenesis is unknown. In this study, we overexpressed FETUB in prostate cancer cells by using lentivirus and then studied the impacts on cell apoptosis, migration and invasion. We found that apoptosis was increased and the migration and invasion of prostate cancer cells were significantly inhibited after overexpression. Then, we performed experiments in vivo and found that there were fewer tumors in the overexpression groups than in the control groups. In addition, we demonstrated that overexpression of FETUB inactivates the PI3K/AKT signaling pathway. Rescue assays revealed that intervention of 740Y-P reversed the anti-tumor effect of FETUB on prostate cancer cells. Taken together, our results revealed that FETUB may act as a novel regulator to promote apoptosis and inhibit the migration and invasion of prostate cancer cells and that FETUB is related to the inactivation of the PI3K/AKT signaling pathway.

Genotype-phenotype correlation of β-lactamase-producing uropathogenic Escherichia coli (UPEC) strains from Bangladesh

Escherichia coli is a pathogen commonly encountered in clinical laboratories, and is capable of causing a variety of diseases, both within the intestinal tract (intestinal pathogenic strains) and outside (extraintestinal pathogenic E. coli, or ExPEC). It is associated with urinary tract infections (UTIs), one of the most common infectious diseases in the world. This report represents the first comparative analysis of the draft genome sequences of 11 uropathogenic E. coli (UPEC) strains isolated from two tertiary hospitals located in Dhaka and Sylhet, Bangladesh, and is focused on comparing their genomic characteristics to each other and to other available UPEC strains. Multilocus sequence typing (MLST) confirmed the strains belong to ST59, ST131, ST219, ST361, ST410, ST448 and ST4204, with one of the isolates classified as a previously undocumented ST. De novo identification of the antibiotic resistance genes bla_NDM-5, bla_NDM-7, bla_CTX-M-15 and bla_OXA-1 was determined, and phenotypic-genotypic analysis of virulence revealed significant heterogeneity within UPEC phylogroups.

Efficacy of Intra-peritoneal Tramadol Instillation for Postoperative Pain Management after Laparoscopic Cholecystectomy

Gall stone disease is one of the most common conditions encountered in general surgical practices in adult population. The gold standard treatment for symptomatic gall stone disease is laparoscopic cholecystectomy. It results in less post-operative pain as compared to open cholecystectomy but post-operative pain may be mild, moderate or even severe in some patients. This Randomized control trail was conducted to In-patient department of Surgery, Mymensingh Medical College & Hospital (MMCH), Mymensingh, Bangladesh from April 2018 to September 2018. It was undertaken to evaluate the analgesic effect of intra-peritoneal tramadol instillation in patients undergoing laparoscopic cholecystectomy. Total 70 patients with symptomatic gallstone disease undergoing laparoscopic cholecystectomy were randomized equally in two groups. Then patients were selected in according to the inclusion and exclusion criteria. In first group (Group A), patients were received intra-peritoneal tramadol 100mg (diluted in 20.0ml distilled water). Sprayed 10.0ml diluted tramadol into the sub diaphragmatic area, 5.0ml into the area of gall bladder bed and 5.0ml into the space between the liver and kidney under direct vision just before removal of trocars. In second group (Group B) the conventional operative procedure was followed. Postoperatively, patient was extubated and shifted to recovery room. Data recorded and analyzed, such as post-operative pain score at 1, 4, 8, and 24 hour; cumulative 1, 8 and 24 hour analgesic consumption. In addition that postoperative hospital period monitoring of heart rate, blood pressure, respiratory rate, temperature at 0, 4, 8, 24 hours was also analyzed. Intensity of pain was assessed by Visual Analogue Scale (VAS) scoring system. Patients showed a VAS ≥3 or patients who requested for analgesia was administrated a supplemental dose of analgesic. In the present study the mean pain scores in Group A were found to be low at1hourpost-operative was 0.60±0.56 and there was a gradual increase in score in respect of time interval with peak of 2.07±0.91 at 24 hours. Whereas, in Group B the mean pain scores immediate post-operative period were at its peak was, 2.50±0.82 which decreased to 1.30±0.84 at 1 hour and further there was rise at 4 hours (2.10±0.71) and 24 hours (2.33±0.0.71). But at any point of time the mean VAS remained significantly low (p<0.050) in patients with Group A compared to Group B except at 1st 24 hours (p=0.210). Intra-peritoneal instillation of tramadol for postoperative pain control in laparoscopic cholecystectomy has beneficial effect in terms of postoperative pain relief following laparoscopic cholecystectomy.

Isolation of pathogenic microorganisms and determination of their antibiotic resistance patterns collected from different bakery products of Dhaka city

Bakery products play an important part in the diet of daily life and provide vital nutrients to human. But pathogenic microorganisms may get entry to bakery items through improper handling and storage which may lead some disease to consumers. For this reason, the objective of this study was to detect pathogenic bacteria in different bakery products collected from different places of Dhaka city. In this study, commonly consumed bakery items such as sweets, biscuit, cake and bread samples were collected from different locations for the detection of pathogenic microorganism. Here, all the samples were found to be contaminated huge microbial count up to 106 CFU/g. Klebsiella spp. and Pseudomonas spp. were most predominate among all. On the other hand, Escherichia coli was totally absent in all the samples. This result indicated that bakery products prepared under unhygienic environments and which may serve as a reservoir of various pathogenic bacteria and most of them were showed resistance against common antibiotics. To ensure the health safety of consumer’s government should take necessary actions to educated food handlers.

Knowledge and Practice of Hepatitis B among Biological and Biomedical Sciences Students in a Public University of Bangladesh

A large numbers of biological and biomedical sciences students intricate themselves in health care professions, which makes them vulnerable to occupational exposure of Hepatitis B. This study aimed to determine the level of knowledge and practice of hepatitis B among biological and biomedical sciences students in a public university of Bangladesh. A cross-sectional study was conducted in Noakhali Science and Technology University (NSTU), Noakhali, Bangladesh from March 2017 to July 2017. Data was collected from students through purposive sampling technique using self-administered structured questionnaire and analyzed by using IBM SPSS 23.0. Out of the 303 participants, 213(70.3%) were within adequate knowledge range and 30(9.9%) of the students were in good practice range. Only 71(23.14%) of the students were fully vaccinated against Hepatitis B. Knowledge level of Participant's were significantly associated with their age and father's education. The practice level was significantly associated with age and all educational variables. Moreover, significant positive but weak linear correlations between knowledge and practice score were identified. The study indicates adequate knowledge, but poor practice of students towards HB. Thus, we recommend all students to implement their knowledge in real life and should be vaccinated prior to entry into health profession.

Plant growth promotion and suppression of bacterial leaf blight in rice by Paenibacillus polymyxa Sx3

The effects and mechanisms of Paenibacillus polymyxa Sx3 on growth promotion and the suppression of bacterial leaf blight in rice were evaluated in this study. The results from a plate assay indicated that Sx3 inhibited the growth of 20 strains of Xanthomonas oryzae pv. oryzae (Xoo). Rice seedling experiments indicated that Sx3 promoted plant growth and suppressed bacterial leaf blight. In addition, bacteriological tests showed that Sx3 was able to fix nitrogen, solubilize phosphate and produce indole acetic acid, indicating that various mechanisms may be involved in the growth promotion by Sx3. The culture filtrate of P. polymyxa Sx3 reduced bacterial growth, biofilm formation and disrupted the cell morphology of Xoo strain GZ 0005, as indicated by the transmission and scanning electron microscopic observations. In addition, MALDI-TOF MS analysis revealed that Sx3 could biosynthesize two types of secondary metabolites fusaricidins and polymyxin P. In summary, this study clearly indicated that P. polymyxa Sx3 has strong in vitro and in vivo antagonistic activity against Xoo, which may be at least partially attributed to its production of secondary metabolites. SIGNIFICANCE AND IMPACT OF THE STUDY: Antagonistic bacteria can grow well in their originating environment. However, it is unclear whether antagonistic bacteria were able to survive in different ecological environments. This study revealed that Paenibacillus polymyxa Sx3 isolated from rhizosphere soil of cotton significantly promoted the plant growth and suppressed bacterial leaf blight in rice. Therefore, it could be inferred that P. polymyxa Sx3 has the potential to be used as biocontrol agents in plants grown in different ecological environments.

Abstract P3-06-10: Multiscale modeling of omics data for precision breast cancer treatment

Introduction: The vast majority of cancer patients continue to receive treatments that are minimally informed by omics data. In the case of breast cancer, only ER and HER2 are routinely used for treatment selection. There is a particular need for personalized treatment in individuals with primary and secondary drug resistance or aggressive breast cancers. Emerging bioinformatics and statistical methods have made a fundamental impact on cancer research. However, challenges remains with regard to patient-centric data analysis and providing genomic data guidance to oncologists. There exists a large number of FDA approved anti-neoplastic drugs used to treat cancers other than breast and the development of innovative informatics methods and algorithms to repurpose those drugs should benefit breast cancer patients.

Methods and Results: We have developed precision care systems (such as PANOPLY and CORPUS) to identify personalized therapies for an individual patient and to deliver genomic reports in a standard, searchable format so that a researcher or an oncologist can quickly navigate through molecular data and obtain prioritized drugs and targets.The PANOPLY (Precision cancer genomics report: single sample inventory) algorithm applies machine learning and topology-based network analysis methods to integrate multi-omics profiles and clinical data; individual-specific molecular alterations are identified and compared with a set of matched-controls having similar clinical data. Since there is a lack of a “gold standard” dataset to test such algorithms, we simulated 500 case-control sets and evaluated drug predictions across multiple simulation scenarios. We applied the PANOPLY algorithm to The Cancer Genome Atlas (TCGA) breast cancer cohort, which consists of multi-omics data and clinical data. In addition, PANOPLY was also applied to an in-house neoadjuvant breast cancer study (BEAUTY) that consists of multi-omics data, clinical data, and patient-derived xenografts (PDXs). In the TCGA breast cancer study we obtained survival data to determine the cases and matched-controls; and in the BEAUTY, we used pathologic complete response (pCR) as an outcome to determine responders and non-responders. Recurrent targetable alterations were not enriched in patients without pCR in the BEAUTY study. We have applied the PANOPLY to non-responder patients to identify individual specific alterations, dysregulated networks, drug targets, and drugs for each patient and stored them as case reports in CORPUS (Computational Oncology Reports and Precision therapeUticS), a web-based repository that allows clinicians to review genomic reports. Using comprehensive “omic” data derived from a triple negative breast cancer patient who had pre and post-neoadjuvant chemotherapy PDXs, PANOPLY prioritized the PARP inhibitors as the top class of drug. Using the PDX models available from this patient, we tested olaparib and confirmed the in vivo antitumor activity (more effective than vehicle with a p-value &lt; 0.05 in the PDXs). Further studies to confirm PANOPLY findings are currently underway.

Conclusions: In summary, the PANOPLY and CORPUS systems incorporate molecular data together with clinical data to provide genomic reports with proposed drug targets to advance or enable precision breast cancer care.

Citation Format: Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Alaparthi T, Yu J, Vedell PT, Kalmbach MT, Bockol MA, Hossain A, Weinshilboum RM, Boughey JC, Wang L, Suman VJ, Goetz MP. Multiscale modeling of omics data for precision breast cancer treatment [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-10.