Expertise In Biology Research Articles

Horizon scanning of potential threats to high-Arctic biodiversity, human health and the economy from marine invasive alien species: A Svalbard case study.

The high Arctic is considered a pristine environment compared with many other regions in the northern hemisphere. It is becoming increasingly vulnerable to invasion by invasive alien species (IAS), however, as climate change leads to rapid loss of sea ice, changes in ocean temperature and salinity, and enhanced human activities. These changes are likely to increase the incidence of arrival and the potential for establishment of IAS in the region. To predict the impact of IAS, a group of experts in taxonomy, invasion biology and Arctic ecology carried out a horizon scanning exercise using the Svalbard archipelago as a case study, to identify the species that present the highest risk to biodiversity, human health and the economy within the next 10 years. A total of 114 species, currently absent from Svalbard, recorded once and/or identified only from environmental DNA samples, were initially identified as relevant for review. Seven species were found to present a high invasion risk and to potentially cause a significant negative impact on biodiversity and five species had the potential to have an economic impact on Svalbard. Decapod crabs, ascidians and barnacles dominated the list of highest risk marine IAS. Potential pathways of invasion were also researched, the most common were found associated with vessel traffic. We recommend (i) use of this approach as a key tool within the application of biosecurity measures in the wider high Arctic, (ii) the addition of this tool to early warning systems for strengthening existing surveillance measures; and (iii) that this approach is used to identify high-risk terrestrial and freshwater IAS to understand the overall threat facing the high Arctic. Without the application of biosecurity measures, including horizon scanning, there is a greater risk that marine IAS invasions will increase, leading to unforeseen changes in the environment and economy of the high Arctic.

AHOD2131: A Randomized Phase 3 Response-Adapted Trial Comparing Standard Therapy with Immuno-Oncology Therapy for Children and Adults with Newly Diagnosed Stage I and II Classic Hodgkin Lymphoma

Background: Chemotherapy in combination with radiotherapy (RT) is the standard for early-stage (ES) Hodgkin lymphoma (cHL). Despite high cure rates (12-year overall survival (OS) >93%), there is room to improve short and long-term outcomes for children and adults with ES cHL. Incorporation of immunotherapy (IO) into front line treatment of ES cHL is an opportunity to both improve progression-free survival (PFS) and maintain OS, while minimizing long-term morbidity and mortality by reducing exposure to RT and high-dose chemotherapy. Study Design and Methods: HL leaders of the NCTN groups, expert HL researchers and physicians, and representatives from the Cancer Therapy Evaluation Program (CTEP) formed a working group in April 2020 with the goals of harmonizing treatment approaches for ES cHL across pediatric and adult patients and reaching consensus regarding the optimal study design for incorporating IO therapy into frontline treatment. Study champions identified from each of the North American cooperative groups [Children's Oncology Group (COG), SWOG, ECOG-ACRIN, Alliance, NRG] and experts in imaging, radiation oncology, lymphoma biology and patient-reported outcomes (PROs) were included. The resulting COG-led clinical trial, AHOD2131, represents the largest ES cHL trial in the history of North American cooperative groups and the first to enroll patients across the age continuum. AHOD2131 (NCT05675410; Figure) is a randomized, phase 3 trial enrolling patients ages 5 to 60 years with newly diagnosed, previously untreated stage I and II cHL and will investigate the addition of the CD30-antibody drug conjugate brentuximab vedotin (Bv) with PD-1 blockade (nivolumab) compared to standard chemotherapy +/- RT. Since the April 2023 activation, 97 North American sites have activated the trial, and 21 participants have enrolled. Target enrollment is 1875 patients over 5 years of accrual, for an estimated 1782 eligible and evaluable patients. The primary objective is to compare the 3-year PFS of patients with ES cHL treated through a response-adapted, superiority design with either standard therapy or with an IO approach (BV + nivolumab). All patients will be stratified as favorable or unfavorable based on disease risk features at enrollment. Based on initial response assessment by PET/CT (via central review) after 2 cycles of ABVD, patients were classified to PET2 positive (SER, defined as 5 Point Score 4 or 5, ~15% of patients) and PET negative (RER). Those who are PET positive will receive involved site RT (ISRT). The SER and RER patients will be randomized to standard chemotherapy vs. IO therapy respectively. In addition to the primary outcome of PFS, there are 11 secondary and 10 exploratory aims. The secondary aims focus on OS, PFS of subgroups, and event-free survival at 12 years, physician-reported treatment-related adverse event (AE) rates, patient-reported AE using pediatric and adult versions of Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE), and the capture of representation by self-report and the use of electronic PRO data collections. The exploratory aims include the assessment of imaging central review as compared to local institutional review and the use of convolutional neural networks through artificial-intelligence machine learning. The study will examine the effect of therapy on acute and long-term adverse effects including health-related quality of life (HRQoL) and OS for up to 12 years. The study will compare patient self-report and provider AE reports and evaluate the associations of self-reported race/ethnicity and social determinants of health (SDOH)and post-progression/post-relapse OS. AHOD2131 strengthens the effort between the North American cooperative groups to conduct collaborative clinical trials and aims to harmonize an improved standard of care for ES cHL across the age continuum.

Technological Pedagogical Content Knowledge (TPACK) for Preservice Biology Teachers: Two Insights More Promising

TPACK questionnaires have been extensively developed, but measurements considering biological content insights still need to be explored. This study aimed to develop and validate TPACK questionnaires by assessing core competencies, core content, and interdisciplinary biology knowledge for preservice biology teachers. We performed development and validation through focus group discussions with biological education experts, and survey studies. The survey was conducted in three phases with a total number of 732 preservice biology teachers. In phase 1, descriptive analysis was calculated based on 232 participants. In Phase 2, Exploratory Factor Analysis (EFA) was calculated based on 250 participants. In phase 3, Confirmatory Factor Analysis (CFA) was calculated to validate and confirm the final dimension of the instrument recently developed based on 250 participants. This series of analyses resulted in 44 items with eight dimensions: Technological Pedagogical Biological Content Knowledge of Biology (TPACKB) comprises 12 items; Technological Knowledge (TK) of biology, Biological Knowledge (BK), and Technological Pedagogical Knowledge (TPK) of the biology consist of 6 items respectively; Technological Biological Knowledge (TBK) comprises of 5 items; Pedagogical Knowledge (PK) of biology, Pedagogical Biological Knowledge (PBK), and Biological Context Knowledge (BCxK) comprise of 3 items respectively. Our study recommended a TPACK questionnaire to assess preservice biology teachers' holistically interdisciplinary understanding, core content, and core competencies as necessary steps to empower biological resolution for their students.

Examination of the Texts Examination of the Texts and Visuals in the “Cell Divisions” Unit in the 10th Grade Science High School Biology Text-Book in Terms of Scientific Content

In this study, it was aimed to examine the visual content and expressions in the texts in the “Cell Divisions” unit in the 10th Grade Biology textbook of the Ministry of National Education, Secondary Science High School, taught in the 2022-2023 academic year, in terms of scientific content. The data sources of the research, in which the case study design and document analysis data collection technique, which are among the qualitative research designs, are used, constitute the relevant textbook. National and international reference books were used to evaluate the scientific conformity of the expressions and images in the texts in the relevant unit in the textbook, which was examined by descriptive analysis by three field experts in Biology and Science. According to the results of the research, it was determined that the scientific content of the texts and images in the “Cell Divisions” unit in the MoNE Secondary Science High School 10th Grade Biology textbook could not be created in full compliance with the required qualifications, and there were missing, incorrect expressions and representations. Since this situation will cause wrong learning and misconceptions in students, it is recommended to rearrange the relevant texts and visuals.

Abstract IA03: Head and Neck Cancer Takes a Nerve, Cancer neuroscience: emerging hallmark of cancer

Abstract Over the past decade, emerging technologies have enabled investigators to begin to bridge the gap between cancer and neuroscience research to unveil the interactive roles of nerves in cancer. We are now beginning to define how the nervous system contributes to cancer initiation, growth, spread, recurrence, and even resistance to oncologic therapeutic strategies. Indeed, neuromodulation with both genetic and pharmacological approaches has been shown to affect not only tumor growth but also antitumor immune response. Collectively, studies have demonstrated a significant and pressing need to recognize cancer neuroscience interplay as a hallmark of cancer to 1) establish the neoneurogenic process as a highly relevant therapeutic target for both the prevention and treatment of cancer, 2) foster interdisciplinary cross-talk among experts in cancer biology and neuroscience, which have traditionally progressed along parallel paths, and 3) integrate human variables such as biological sex, age, race, and gender as underlying factors that can impact cancer neuroscience. Citation Format: Moran Amit. Head and Neck Cancer Takes a Nerve, Cancer neuroscience: emerging hallmark of cancer [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr IA03.

Prediction of multiple types of RNA modifications via biological language model.

It has been demonstrated that RNA modifications play essential roles in multiple biological processes. Accurate identification of RNA modifications in the transcriptome is critical for providing insights into the biological functions and mechanisms. Many tools have been developed for predicting RNA modifications at single-base resolution, which employ conventional feature engineering methods that focus on feature design and feature selection processes that require extensive biological expertise and may introduce redundant information. With the rapid development of artificial intelligence technologies, end-to-end methods are favorably received by researchers. Nevertheless, each well-trained model is only suitable for a specific RNA methylation modification type for nearly all of these approaches. In this study, we present MRM-BERT by feeding task-specific sequences into the powerful BERT (Bidirectional Encoder Representations from Transformers) model and implementing fine-tuning, which exhibits competitive performance to the state-of-the-art methods. MRM-BERT avoids repeated de novo training of the model and can predict multiple RNA modifications such as pseudouridine, m6A, m5C, and m1A in Mus musculus, Arabidopsis thaliana, and Saccharomyces cerevisiae. In addition, we analyse the attention heads to provide high attention regions for the prediction, and conduct saturated in silico mutagenesis of the input sequences to discover potential changes of RNA modifications, which can better assist researchers in their follow-up research. MRM-BERT is freely accessible at http://csbio.njust.edu.cn/bioinf/mrmbert/.

Brain organoid data synthesis and evaluation.

Datasets containing only few images are common in the biomedical field. This poses a global challenge for the development of robust deep-learning analysis tools, which require a large number of images. Generative Adversarial Networks (GANs) are an increasingly used solution to expand small datasets, specifically in the biomedical domain. However, the validation of synthetic images by metrics is still controversial and psychovisual evaluations are time consuming. We augment a small brain organoid bright-field database of 40 images using several GAN optimizations. We compare these synthetic images to the original dataset using similitude metrcis and we perform an psychovisual evaluation of the 240 images generated. Eight biological experts labeled the full dataset (280 images) as syntetic or natural using a custom-built software. We calculate the error rate per loss optimization as well as the hesitation time. We then compare these results to those provided by the similarity metrics. We test the psychovalidated images in a training step of a segmentation task. Generated images are considered as natural as the original dataset, with no increase of the hesitation time by experts. Experts are particularly misled by perceptual and Wasserstein loss optimization. These optimizations render the most qualitative and similar images according to metrics to the original dataset. We do not observe a strong correlation but links between some metrics and psychovisual decision according to the kind of generation. Particular Blur metric combinations could maybe replace the psychovisual evaluation. Segmentation task which use the most psychovalidated images are the most accurate.

An Insight into the Behaviour of Recalcitrant Seeds by Understanding Their Molecular Changes upon Desiccation and Low Temperature

Systems biology is an interdisciplinary study that involves a combination of expertise in biology, chemistry, mathematics, physics, and engineering to unravel the biology of complex living systems by incorporating multiple kinds of quantitative molecular computations by using sophisticated mathematical models. This interdisciplinary study can be applied to identify and understand molecular and metabolic changes in recalcitrant plant species. Many tropical plants with recalcitrant seeds have difficulty with long-term seed storage and preservation due to their intolerance to desiccation and low temperatures. The aim of this review was to explore and discuss how omics analyses can assist in elucidating molecular responses and metabolic changes of recalcitrant seed species. Genomics and transcriptomics analyses identified genes, such as late embryogenesis abundant (LEA), that were highly expressed after exposure to desiccation and low temperatures. Meanwhile, proteomic analysis using 2D gel electrophoresis, MALDI-TOF MS, or MS/MS analysis revealed dehydrins induced from recalcitrant seeds upon exposure to desiccation and low temperatures. Metabolomic analysis using liquid chromatography–mass spectrometry (LC–MS) and gas chromatography–mass spectrometry (GC–MS) profiling of recalcitrant seeds has discovered metabolites such as sugar and organic acid changes in recalcitrant seeds at different developmental stages. This information may contribute to comprehending the behaviour of recalcitrant seeds and provide insight into how crop management can be improved in terms of seed storage for conservation in order to maintain plant biodiversity.

Use of a hybrid intelligence decision tree to identify mature B-cell neoplasms.

Mature B-cell neoplasms are challenging to diagnose due to their heterogeneity and overlapping clinical and biological features. In this study, we present a new workflow strategy that leverages a large amount of flow cytometry data and an artificial intelligence approach to classify these neoplasms. By combining mathematical tools, such as classification algorithms and regression tree (CART) models, with biological expertise, we have developed a decision tree that accurately identifies mature B-cell neoplasms. This includes chronic lymphocytic leukemia (CLL), for which cytometry has been extensively used, as well as other non-CLL subtypes. The decision tree is easy to use and proposes a diagnosis and classification of mature B-cell neoplasms to the users. It can identify the majority of CLL cases using just three markers: CD5, CD43, and CD200. This approach has the potential to improve the accuracy and efficiency of mature B-cell neoplasm diagnosis.

Northeast Regional Center for Excellence in Vector-Borne Diseases' Master of Science training program: a curriculum to support future capacity in public health entomology.

A major lack of expertise in vector biology, surveillance, and control for public health professionals has been acknowledged over the past several decades, especially in light of the introduction of West Nile and Zika viruses to the United States. To address this growing need, the Northeast Regional Center for Excellence in Vector-Borne Diseases (NEVBD) designed a unique educational program to cross-train students in the fundamentals of vector biology and public health. Here, we summarize the formation, evaluation, and outcomes of NEVBD's Master of Science in Entomology: Vector-Borne Disease Biology program and provide details on core competencies to enable adoption and adaptation of the program to other institutions and contexts. A discussion of major barriers to filling the nation's need for public health personnel with medical entomology training, such as financial barriers and recruitment of underrepresented students, is presented. We conclude with considerations for administering these training programs.

Assessing the Impact of Climate Change on the Biodeterioration Risk in Historical Buildings of the Mediterranean Area: The State Archives of Palermo

The growing sensitivity towards environmental sustainability, particularly in the light of climate change, requires a reflection on the role that historical buildings can play in heritage conservation. This research proposed an interdisciplinary approach combining climate and biological expertise to evaluate the biodeterioration risk associated with different IPCC outdoor climate scenarios. Conduction heat transfer functions and dose–response functions were used to model the indoor climate of a historical building and the related climate-induced risk of mould and pest proliferation. The approach was applied to a case study in the Mediterranean area, i.e., the State Archives of Palermo (Italy) housed in a 15th-century convent. In 2018, a survey conducted by ICPAL-MiC experts warned about past infestations and risks deriving from climate conditions. An environmental monitoring campaign conducted in 2021 allowed for the characterisation of the buffering effect in a historical building in response to the outdoor climate and the simulation of future indoor climate. Since indoor temperature and mixing ratio are expected to raise in future scenarios, it was found that there is an increased risk of insects’ proliferation, combined with a decreased risk of spore germination and mould growth. Such evidence-based evaluation allows for the design of tailored preventive conservation measures to enhance the durability of both the archival collections and the building.

Lessons Learned from the Design, Construction, and Commissioning of a Retrofitted Arthropod Containment Level 3 Insectary.

Arthropods are vectors for many pathogens that significantly harm human and animal health globally, and research into vector-borne diseases is of critical public health importance. Arthropods present unique risks for containment, and therefore insectary facilities are essential to the safe handling of arthropod-borne hazards. In 2018, the School of Life Sciences at Arizona State University (ASU) began the process to build a level 3 arthropod containment (ACL-3) facility. Even with the COVID-19 pandemic, it took more than 4 years for the insectary to be granted a Certificate of Occupancy. At the request of the ASU Environmental Health and Safety team, Gryphon Scientific, an independent team with biosafety and biological research expertise, studied the project lifecycle through the design, construction, and commissioning of the ACL-3 facility with the goal of identifying lessons learned from the delayed timeline. These lessons learned convey insight into best practices for assessing potential facility sites, anticipating challenges with retrofitted construction, preparing for commissioning, equipping the project team with necessary expertise and expectations, and supplementing the gaps in available containment guidance. Several unique mitigations designed by the ASU team to address research risks not specifically addressed in the American Committee of Medical Entomology Arthropod Containment Guidelines are also described. Completion of the ACL-3 insectary at ASU was delayed, but the team thoroughly assessed potential risks and enabled appropriate practices for the safe handling of arthropod vectors. These efforts will enhance future ACL-3 construction by helping to avoid similar setbacks and streamlining progress from concept to operation.

P72 Development of a novel platform trial evaluating systemic therapies in adult atopic eczema with parallel mechanistic studies (BEACON and BEACONomics): a UK-wide interdisciplinary collaboration

Abstract Atopic eczema is common and profoundly impacts on the quality of life, and psychological and social function. More severe disease often requires systemic (standard or targeted) immune-modifying therapy; however, drug response and tolerability vary in practice. As the molecular effects of the drugs used have not been characterized in detail, the causes of such variability remain poorly understood. There remains equipoise as to which drug is best, with no active comparator data for standard vs. targeted therapies. We have designed a global first trial in atopic eczema to directly compare the effectiveness and tolerability of standard and targeted drugs. The platform design, building on expertise in cancer and COVID (Medical Research Council Clinical Trials Unit), allows incorporation of additional comparator arms as new treatments emerge. We used multistakeholder input from patients [partnership with National Eczema Society, patient coapplicants, national patient survey (> 90 participants), public and patient involvement webinar feedback], clinicians [UK Dermatology Clinical Trials Network, national surveys (> 50 clinicians)], health economics and qualitative researchers. We partnered with experts in skin biology and single-cell methods, exploiting high-throughput analytic pipelines of the Human Cell Atlas, to design embedded studies to dissect mechanisms underlying drug effects. The trial (BEACON), which commenced in February 2023, is funded through the NIHR Health Technology Assessment programme. This 12-month multiarm trial involves > 400 adults with moderate-to-severe eczema requiring systemic therapy from > 30 UK sites. It is designed around real-world practice and incorporates inclusive recruitment strategies and remote data capture. BEACON will establish the comparative clinical effectiveness, tolerability and cost-effectiveness of methotrexate, ciclosporin and dupilumab. It will transition to a multiarm, multistage platform trial, enabling additional treatment arms. The primary outcome is EASI at 6 months, with key Harmonising Outcome Measures for Eczema outcome measures incorporated. Dose increases and treatment switching (6 months) are possible, mirroring standard practice. BEACON-omics is funded through the National Institute for Health and Care Research Efficacy and Mechanism Evaluation and Open Targets (public–private partnership). This longitudinal cohort study will profile serial skin and blood samples at scale (150 participants) using single-cell multiome and spatial transcriptome approaches, to investigate mechanisms of treatment effects and provide a foundational resource for new target discovery. This world-first platform trial for systemic therapies in adult atopic eczema, and one of the first in chronic inflammatory disease, will provide comparative data on commonly used systemic treatments and incorporate novel therapies as they emerge. Integrated cutting-edge discovery science will maximize the potential of the platform.

Formative assessment and student understanding of structure-function.

The structure and function relationship is a core concept identified by physiology faculty. Prior research has shown this may be a difficult concept for students to understand. Formative written assessments, such as short answer essay questions, allow students to demonstrate their thinking by encouraging students to use their diverse ideas to construct their responses. Varying the context of a question, such as the inclusion of a scenario, may be used to provide insight into the different stages of students' emerging biological expertise. Short answer questions based on the core concept structure↔function were administered to students in a junior level General Physiology course and a sophomore level Human Anatomy and Physiology course at a large southeastern public university. Questions were based on the integumentary, muscular, digestive and cardiovascular systems. Student responses were scored with a conceptual rubric developed for each question prompt as well as each organ system represented in the question prompts. Students were interviewed to determine if their responses to the short answer questions accurately reflected their thinking. Less than half of the student responses in this study demonstrated conceptual understanding of the structure-function relationship. Students demonstrated different conceptual understanding of structure↔function concepts depending on the question prompt with a scenario versus question prompt without a scenario. The question prompts with scenarios versus non-scenarios provided a different context which may have influenced student explanations. These results suggest that instructors should provide students with questions in varying contexts to allow students to demonstrate their heterogeneous ideas about a concept.Formative.

Detection and differentiation of herbicide stresses in roses by Raman spectroscopy.

Herbicide application is a critical component of modern horticulture. Misuse of herbicides can result in damage to economically important plants. Currently, such damage can be detected only at symptomatic stages by subjective visual inspection of plants, which requires substantial biological expertise. In this study, we investigated the potential of Raman spectroscopy (RS), a modern analytical technique that allows sensing of plant health, for pre-symptomatic diagnostics of herbicide stresses. Using roses as a model plant system, we investigated the extent to which stresses caused by Roundup (Glyphosate) and Weed-B-Gon (2, 4-D, Dicamba and Mecoprop-p (WBG), two of the most commonly used herbicides world-wide, can be diagnosed at pre- and symptomatic stages. We found that spectroscopic analysis of rose leaves enables ~90% accurate detection of Roundup- and WBG-induced stresses one day after application of these herbicides on plants. Our results also show that the accuracy of diagnostics of both herbicides at seven days reaches 100%. Furthermore, we show that RS enables highly accurate differentiation between the stresses induced by Roundup- and WBG. We infer that this sensitivity and specificity arises from the differences in biochemical changes in plants that are induced by both herbicides. These findings suggest that RS can be used for a non-destructive surveillance of plant health to detect and identify herbicide-induced stresses in plants.

Examining expertise: Synthetic biology experts' perceptions of risk, benefit, and the public for research and applications regulation.

Scientific experts can play an important role in decision-making surrounding policy for technical and value-laden issues, often in contexts that directly affect lay publics. Yet little is known about what characterizes scientific experts who want lay public involvement in decision-making. In this study, we examine how synthetic biology experts' perceptions of risks, benefits, and ambivalence for synthetic biology relate to views of lay publics, deference to scientific authority, and regulations. We analyzed survey data of researchers in the United States, who published academic articles relating to synthetic biology from 2000 to 2015. Scientific experts who see less risk and are more deferent to scientific authority appear to favor a more closed system in which regulations are sufficient, citizens should not be involved, and scientists know best. Conversely, scientific experts who see more potential for risk and see the public as bringing a valuable perspective appear to favor a more open, inclusive system.

Overcoming Challenges and Innovations in Orthopedic Prosthesis Design: An Interdisciplinary Perspective.

Recent advances in the orthopedic prostheses design have significantly improved the quality of life for individuals with orthopedic disabilities. However, there are still critical challenges that need to be addressed to further enhance the functionality of orthopedic prostheses improving biocompatibility to promote better integration with natural tissues, enhancing durability to withstand the demands of daily use, and improving sensory feedback for better control of movement are the most pressing issues. To address these challenges, promising emerging solutions such as smart prosthetics, 3D printing, regenerative medicine, and artificial intelligence have been developed. These innovative technologies hold the potential to significantly enhance the functionality of orthopedic prostheses. Realizing the full potential of these next-generation orthopedic prostheses requires addressing several critical factors. These include interdisciplinary collaboration between experts in orthopedics, materials science, biology, and engineering, increased investment in research and development, standardization of components to ensure quality and reliability, and improved access to prosthetics. A comprehensive review of these challenges and considerations for future orthopedic prosthesis design is s provided in this paper addressing the further advances to the field. By addressing these issues, we can continue to improve the lives of individuals with orthopedic disabilities and further enhance the field of orthopedic prosthetics.

Back to Basics in Cancer Research: A Message from the Incoming Editor-In-Chief.

Back to Basics in Cancer Research: A Message from the Incoming Editor-In-Chief.

Classification of Highly Divergent Viruses from DNA/RNA Sequence Using Transformer-Based Models.

Viruses infect millions of people worldwide each year, and some can lead to cancer or increase the risk of cancer. As viruses have highly mutable genomes, new viruses may emerge in the future, such as COVID-19 and influenza. Traditional virology relies on predefined rules to identify viruses, but new viruses may be completely or partially divergent from the reference genome, rendering statistical methods and similarity calculations insufficient for all genome sequences. Identifying DNA/RNA-based viral sequences is a crucial step in differentiating different types of lethal pathogens, including their variants and strains. While various tools in bioinformatics can align them, expert biologists are required to interpret the results. Computational virology is a scientific field that studies viruses, their origins, and drug discovery, where machine learning plays a crucial role in extracting domain- and task-specific features to tackle this challenge. This paper proposes a genome analysis system that uses advanced deep learning to identify dozens of viruses. The system uses nucleotide sequences from the NCBI GenBank database and a BERT tokenizer to extract features from the sequences by breaking them down into tokens. We also generated synthetic data for viruses with small sample sizes. The proposed system has two components: a scratch BERT architecture specifically designed for DNA analysis, which is used to learn the next codons unsupervised, and a classifier that identifies important features and understands the relationship between genotype and phenotype. Our system achieved an accuracy of 97.69% in identifying viral sequences.

Bilateral Thoracic Cytoreductive Surgery for Pseudomyxoma Peritonei of Appendiceal Origin.

Pleural spread occurs in pseudomyxoma peritonei (PMP) in less than 10% of the patients and is treated by thoracic cytoreductive surgery with or without hyperthermic intrathoracic chemotherapy (HITOC). It is performed both for symptom palliation and disease control and includes pleurectomy and decortication and wedge and segmental lung resections. So far, only unilateral spread treated with a thoracic cytoreductive surgery (CRS) has been reported in literature. We report a patient with bilateral thoracic PMP following a complete abdominal CRS and hyperthermic intraperitoneal chemotherapy (HIPEC) who was treated with bilateral staged thoracic CRS and subsequently had a 4th CRS for abdominal disease. The staged procedure was performed as she was symptomatic due to the thoracic disease and there was disease on all pleural surfaces. HITOC was not performed. Both procedures were uneventful with no major morbidity. The patient is currently disease free nearly 84months after the first abdominal CRS and 60months after the second thoracic CRS. Thus, an aggressive CRS in the thorax in patients with PMP can result in a prolongation of survival while preserving the quality of life if the abdominal disease is controlled. A thorough understanding of the disease biology and surgical expertise are both essential for selecting the right patients for these complex procedures and achieving good short- and long-term outcomes.