Process identification and discrimination in the environmental dose rate time series of a radiopharmaceutical facility using machine learning techniques

Multi-facility nuclear sites with research reactors have several environmental area gamma monitors in a network as a part of their surveillance capability. However, the routine release of low levels of ⁴¹Ar gas from the reactor is prone to interfere with the recorded gamma dose rate and mask the genuine processes being monitored at the network's central control room. As a potential solution, machine learning techniques have been used in this study to autonomously identify and discriminate the genuine processes, viz., the radioactive consignment loading and its movement, at an interim radiopharmaceutical facility located close to a research reactor. To increase the richness of the recorded univariate dose rate time series, several additional features were created. A labelled dataset of process and non-process dose rate sub-sequences or segments was generated by subject matter experts, based on practical knowledge of the facility, and aided by k-means clustering algorithm. The labelled dataset was used to train several supervised classification models and the random forest class of models gave superior performance. The optimised random forest model was able to identify process sub-sequences with a precision of 82.35% and a specificity of 97.11%. The overall balanced accuracy of the model was 91% with a f1 score of 82%. This machine learning approach proved useful to autonomously identify genuine process driven sub-sequences in the univariate dose rate time series. It has an application in reducing the false alarms at exit portal monitors, especially at those sites where there is a potential for external interference in the monitored dose rate.

Estimation and sensitivity analysis of operational intervention levels for the early phase of radiological emergencies involving radioactive releases

Radiological emergencies involving any likely atmospheric release of radioactive material in the public domain are quite a challenge to respond to and manage. Such conditions require a quick and confident response. One such response involves using pre-planned operational intervention levels (OILs) to trigger certain protective actions or groups of actions. OILs are typically derived for nuclear emergencies, whose values cannot always be directly used in a radiological incident. Therefore, in this study, OILs were derived for the early phase of a radiological emergency involving ground- and skin-deposition exposure scenarios. The methodology is an adaptation of an internationally recommended method for nuclear emergencies, with modifications to suit radiological incidents. The derived OILs for the radiological emergency were compared against the internationally recommended values to attest their adaptability. Nominal range sensitivity analysis was performed over 14 factors used in the methodology, which provided broad insights into their influence. Moreover, exhaustive sampling of the extreme values of these factors helped to derive operational margins for the OILs to cover all possible scenario variations. Based on this analysis, generic OILs for the early phase of a radiological emergency are proposed, such that the projected doses are well below the respective generic criteria, ensuring justification on radiological grounds.

397 Seasonal Variation in Acute Cholecystitis; An Analysis to Predict Resources Allocation

Background

Acute cholecystitis accounts for 20% of Emergency General Surgical admissions. The concept of seasonal variation is still a developing concept in surgical literature. Whether acute cholecystitis also follows a seasonal trend remains to be established.

Aim

Given the struggle healthcare system has been facing towards resource and staff allocation to deliver best possible patient care, we thought this may be a step forward to predict North Wales demand of resources seasonally and make appropriate arrangements ahead of time.

Method

We performed a retrospective analysis of patients across North Wales who had a discharging diagnosis of acute cholecystitis from January 2010 to December 2019. Chi-square goodness-of-fit test was used to analyse seasonality of acute cholecystitis adjusting for variation in number of days between seasons. The number of days for seasons were taken as 92, 92, 91, and 90.25 for spring, summer, fall, and winter, respectively.

Results

Overall, 4100 patients presented to the three hospitals across North Wales with acute cholecystitis during the study period. The frequency of hospital admissions varied between months (minimum February n = 302, maximum July n = 373) and seasons (minimum winter n = 971, maximum spring n = 1067). After applying chi-square goodness-of-fit test to check significant seasonality, we did not find any significant seasonal variation in acute cholecystitis (p-value = 0.262).

Conclusions

Our data failed to show any significant seasonal variation in patients presenting with acute cholecystitis in North Wales. We recommend prospective collection of data at national level to validate our results.

Comparative genomic analysis of sifakas (Propithecus) reveals selection for folivory and high heterozygosity despite endangered status

Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.

Rapid diagnosis of SARS-CoV-2 using potential point-of-care electrochemical immunosensor: Toward the future prospects

Coronavirus disease (COVID-19) is an emerging and highly infectious disease making global public health concern and socio-economic burden. It is caused due to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). It has the tendency to spread rapidly through person-to-person. Currently, several molecular diagnostic platforms such as PCR, qRT-PCR, reverse transcription loop-mediated isothermal amplification (RT-LAMP), CRISPR are utilized for the diagnosis of SARS-CoV-2. These conventional techniques are costly, time consuming and require sophisticated instrumentation facility with well trained personnel for testing. Hence, it is tough to provide testing en-masse to the people in developing countries. On the other hand, several serological biosensors such as lateral flow immunosensor, optical, electrochemical, microfluidics integrated electrochemical/fluorescence is currently utilized for the diagnosis of SARS-CoV-2. In current pandemic situation, there is an urgent need of rapid and efficient diagnosis on mass scale of SARS-CoV-2 for early stage detection. Early monitoring of viral infections can help to control and prevent the spreading of infections in large chunk of population. In this review, the SARS-CoV-2 and their biomarkers in biological samples, collection of samples and recently reported potential electrochemical immunosensors for the rapid diagnosis of SARS-CoV-2 are discussed.

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements

Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (-4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.

Abstract P4-10-18: Patterns of failure in a predominately black, inner city cohort of triple negative breast cancer patients at a single institution

Introduction: Triple negative breast cancer (TNBC) accounts for 12-17% of breast cancer (BC) in the US, but behaves much more aggressively. It occurs more commonly in younger, black women and death within two years of diagnosis is more common in this subset of BC compared to hormone receptor positive BC. At the University of Maryland Greenebaum Comprehensive Cancer Center, we see a higher proportion of TNBC and present our comprehensive evaluation of the patterns of failure in women with TNBC treated at our urban breast center.

Materials/Methods: A retrospective review of TNBC patients treated from 2005-2017 identified 198 patients with Stage I (33%), Stage II (47%), Stage III (16%) and Stage IV (4%) TNBC. The patients were all female, median age of 54 years (range 22-86 years), 64% black, 40% married, 7% BRCA mutated, and 3% HIV positive. Tumor characteristics revealed 93% infiltrating ductal carcinoma, 68% grade 3, and 18% with lymphovascular space invasion. Self-palpation of the lesion occurred in 76% of women, and the lesion was in the upper outer quadrant 62% of the time. Thirty percent of pts had neoadjuvant and 67% adjuvant chemotherapy. Ninety-eight percent of pts underwent surgical resection, 55% had lumpectomy and 61% sentinel lymph node biopsy. Adjuvant radiation was given in 56% of patients with a median dose of 60 Gy (range 16-70 Gy). Chi-square testing was used to compare variables, while logistic regression with Kaplan-Meier estimate was used to calculate overall survival (OS) and freedom from recurrence (FFR).

Results: With a median follow up of 45 months, 33 (17%) documented failures occurred. At time of first documented failure, 30% were local (L), 6% regional (R), 22% distant (D), 6% combination of L/R, 12% combination of L/R/D, 9% L/D, and 15% R/D, with a total combined failure pattern in 42% of pts. There was no significant difference in failure patterns between white and black pts (p=0.50, Table 1). The 2 and 5 year OS was 88% and 80%, respectively. Median survival was not reached in our cohort. The 2 and 5-year FFR was 90% and 84%, respectively with a median time to any failure of 16 months after initiation of therapy and median OS of 29 months for these pts.

Conclusion: Our work shows that with modern BC therapies treatment outcomes for pts with TNBC are improved and 84% are free of disease at 5 yrs after the initial diagnosis. The patterns of failure in TNBC are complex, did not vary by race, and showed the largest proportion of our pts (58%) failing in distant and locoregional sites simultaneously, while an additional 30% of pts fail locally only. These failure patterns did not differ significantly based on race. Future efforts will identify pts most at risk for treatment failure for consideration of treatment intensification, as salvage options are limited when treatment failure occurs.

Comparison of Failure Patterns Between White and Black PatientsFailure PatternWhite (n,%)Black (n,%)p-valueLocal only2 (22.5)8 (33) Regional only1 (11)1 (4) Distant only2 (22.5)5 (21)p=0.496Local and Regional0 (0)2 (8) Local and Distant0 (0)3 (13) Regional and Distant3 (33)2 (8) Local, Regional and Distant1 (11)3 (13) 

Citation Format: Rice SR, Cherng H-R, Hamza M, Murali S, Rosenblatt P, Bellavance E, Cheston S, Amin N, Nichols EM. Patterns of failure in a predominately black, inner city cohort of triple negative breast cancer patients at a single institution [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 P4-10-18.

Deciphering foot-and-mouth disease (FMD) virus-host tropism

The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp ¹⁴³RGD¹⁴⁵ and at domain ⁶⁷⁶SIPLQ⁶⁸⁰ in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma.

FisOmics: A portal of fish genomic resources

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics/, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements.

The comparative genomics and complex population history of Papio baboons

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

High-resolution comparative analysis of great ape genomes

Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Optimization of Rice Bran Oil Encapsulation Using Jackfruit Seed Starch – Whey Protein Isolate Blend as Wall Material and Its characterization

Response surface methodology (RSM) was used to optimize rice bran oil encapsulation using jackfruit seed starch – whey protein isolate blend as wall material by spray drying technique. Oil concentration (20, 25 and 30 %), wall material (Jackfruit seed starch & whey protein isolate) starch-protein ratio (1:1, 3:1 and 5:1) and spray drying inlet air temperature (140, 150 and 160 °C) were considered as process variables for optimization. A three-factor, three-level Box-Behnken design of RSM was used to conduct the experiments with the aim of maximizing encapsulation efficiency and minimizing peroxide value in the encapsulated powder. A polynomial regression model was fitted using design expert software, and the optimum conditions obtained were 20 % oil concentration, 3:1 starch-protein ratio and 140 °C spray drying inlet air temperature. The encapsulated rice bran oil powers obtained at optimized conditions offered 85.90 % of encapsulation efficiency and 1.18 meq/kg oil of peroxide value. The characterization study revealed that powder particles size (diameter) varied from 3.40 to 300.51 µm and most of the particles were smooth spheres with little appendages.