Expertise In Biology Research Articles

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.

Best Practices to Promote Field Science Safety.

Interventions are necessary to address the ongoing epidemic of sexual harassment and assault in field settings. An evidence-based approach to identifying specific interventions will be most effective at promoting the safety of scientists. We present the results of a workshop conducted by experts in field biology and the study of sexual harassment and assault that identified a comprehensive set of best practices for individuals and organizations. These recommendations are grounded in peer-reviewed scholarship and are separated into four topics: culture change, accountability, policy development, and reporting. The resulting report of the workshop recommends 44 practices, categorized by the resources required for implementation, the time frame of implementation, and the level of organization responsible for implementation. The best practices that we present are designed to support individuals and organizations in the development of field safety plans.

Converging on a Cure: The Roads to Predictive Immunotherapy.

Convergence science teams integrating clinical, biological, engineering, and computational expertise are inventing new forecast systems to monitor and predict evolutionary changes in tumor and immune interactions during early cancer progression and therapeutic response. The resulting methods should inform a new predictive medicine paradigm to select adaptive immunotherapeutic regimens personalized to patients' tumors at a given time during their cancer progression for durable patient response.

2022 Winners: Kathleen Scheffler, Federica Giannini and Tom Lemonnier

2022 Winners: Kathleen Scheffler, Federica Giannini and Tom Lemonnier

Abstract PL03-02: When to intervene along the breast cancer continuum?

Abstract Advances in epidemiology and cancer biology have clearly established that the group of diseases currently deemed “cancers” in fact encompasses many conditions with enormous variation in biologic behavior. Decades of cancer screening have preferentially diagnosed early, asymptomatic, indolent lesions. This trend will only increase as screening technologies become ever more sensitive, leading to an epidemic of overtreatment in completely asymptomatic individuals. The treatment of many of these conditions often has uncertain benefit on cancer mortality, while coming at the clear cost of treatment-related morbidity. Multi-omic testing plays a role in refining treatment recommendations based upon risk of progression. Genomic profiling of accurately annotated longitudinal case control datasets have provided insights into breast lesions termed “ductal carcinoma in situ” (DCIS), which are thought to be precursors to invasion and metastases. Both transcriptomics as well spatially resolved proteomic characterization of DCIS have uncovered novel biology of the epithelial cells that make up DCIS, as well as the heterogeneous precancer ecosystems which can be either permissive or inhibitory for invasion. Recent work has uncovered a clonal evolution pathway characterized by multiclonal invasion, and has helped to build risk stratification tools to refine treatment recommendations. In addition to molecular characterization, risk modeling may yield insights about which patients derive greatest benefit from intervention. For asymptomatic tumors at low risk of cancer progression, there may be little to no benefit to treatment, whereas for more high-risk lesions, progression to invasion and metastasis may be rapid and deadly. Given the lead-time between the development of precancer and progression to invasive disease, there may also be a case for tailoring intervention of screen detected cancer by age and the presence of competing comorbidities. The decision of whether and when to intervene for screen-detected cancers will require a multidisciplinary effort including expertise in cancer biology, mathematical modeling, psychology, health policy, decision science and communication, as well as thoughtful engagement from patients and health care providers to identify the optimal time to intervene along the cancer progression continuum. Citation Format: E. Shelley Hwang. When to intervene along the breast cancer continuum?. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr PL03-02.

Drug-delivery research and much more: interview with Dan Peer.

Drug-delivery research and much more: interview with Dan Peer.

Anzalone Prime: An Interview with Prime Editing Developer Andrew Anzalone

Anzalone Prime: An Interview with Prime Editing Developer Andrew Anzalone

Validity analysis of digital module based on generic science skills on environmental pollution topic for 10th grade students

The development of digital modules based on interesting generic science skills can be integrated in biology learning. Generic science skills (GSS) are related to skills through application and biological context. The factual and procedural knowledge obtained by students can be explored in the environmental pollution material because of various concepts and solve various real problems. This research is a descriptive study that explains the stages of digital module validation analysis based on generic science skills on environmental pollution for grade 10 high school students. Digital module validation test refers to five aspects such as (1) suitability of material, (2) presentation, (3) language, (4) generic science skills, and (5) visual/appearance. The subjects in the research at the initial review stage were three validators consisting of practitioners who are experts in learning biology and learning media. Based on the results of the study, it is known that the module developed as a whole is very valid in reference to aspects, namely the feasibility of the content aspect, the feasibility of the presentation aspect, the feasibility of the language aspect, the feasibility of the GSS aspect and the appearance, this shows that the digital module produced can be continued at the next stage.

How tracking technology is transforming animal ecology: epistemic values, interdisciplinarity, and technology-driven scientific change

Tracking technology has been heralded as transformative for animal ecology. In this paper I examine what changes are taking place, showing how current animal movement research is a field ripe for philosophical investigation. I focus first on how the devices alter the limitations and biases of traditional field observation, making observation of animal movement and behaviour possible in more detail, for more varied species, and under a broader variety of conditions, as well as restricting the influence of human presence and observer bias. I reconstruct these as shifts in scope, objectivity, accuracy and fruitfulness. The second transformation is slightly less obvious but equally significant for animal ecology. Tracking devices generate complex data that demands both statistical and biological expertise, which has led to increasingly frequent and intensive collaborations between statisticians and biologists. Based on interviews, I examine how researchers in these interdisciplinary collaborations negotiate the collection, analysis and interpretation of movement data, integrating research interests, methodological constraints, previous field observations, and background theory. Tracking technology is therefore also shifting which disciplinary considerations are brought to bear on research into animal movement and behaviour and how this research is conducted.

A Few Words about Modern Genetics

The human organism is composed of cells that have their own building blocks, among which the most important role is played by the nucleus, which contains the genetic material that we inherit from our parents, and which carries information about the way the human organism should function. This genetic material is found on DNA molecules, and DNA molecules are packaged in the form of chromosomes, which are formed by wrapping DNA molecules around proteins. Hereditary diseases are caused by mutations of one or more genes, which we inherited from one or both parents. Hereditary diseases are not the same as genetic diseases because some mutations and gene damage can occur after fertilization and later in a person’s life. Some genetic defects can be manifested by congenital malformations or diseases, but the defects of some genes will lead to disease symptoms only in adulthood or only under the influence of environmental factors. Through research in the field of molecular biology, the method of analyzing genetic markers is continuously improved, the sensitivity threshold of the method is lowered, and thus the analysis of increasingly scarce biological samples is enabled. The ultimate goal of biological expertise is to establish the identity of the person from whom the disputed trace originates, and for this purpose, the DNA profile of the disputed trace is compared with the DNA profile of an undisputed sample of the person. Non-disputable samples are blood samples or samples of oral cavity epithelium that are taken from a person of known identity. The match of the DNA profile of the disputed trace with the DNA profile of the undisputed sample confirms that the disputed trace originates from a certain person.

Isocyanide-based multi-component reactions for carrier-free and carrier-bound covalent immobilization of enzymes.

Strategies for the covalent immobilization of enzymes depend on the type of functional group selected to perform the coupling reaction, and on the relative importance of selectivity, loading capacity, immobilization time and activity/stability of the resulting immobilized preparation. However, no single strategy is applicable for all covalent immobilization methods or can meet all these criteria, exemplifying the challenge of introducing a versatile process broadly compatible with the residues on the surface of proteins and the functional groups of common linkers. Here, we describe the use of isocyanide-based multi-component reactions for the carrier-bound and carrier-free covalent immobilization of enzymes. Isocyanide-based multi-component reactions can accept a wide variety of functional groups such as epoxy, acid, amine and aldehyde, as well as many commercially available bi-functional linkers, and are therefore suitable for either covalent coupling of enzymes on a solid support or intermolecular cross-linking of enzymes. In this strategy, an isocyanide is directly added to the reaction medium, the enzyme supplies either the exposed amine or carboxylic acid groups, and the support (in carrier-bound immobilization) or the bi-functional cross-linking agent (in carrier-free immobilization) provides another reactive functional group. The protocol offers operational simplicity, high efficiency and a notable reduction in time over alternative strategies, and can be performed by users with expertise in chemistry or biology. The immobilization reactions typically require 1-24 h.

DL-m6A: Identification of N6-Methyladenosine Sites in Mammals Using Deep Learning Based on Different Encoding Schemes.

N6-methyladenosine (m6A) is a common post-transcriptional alteration that plays a critical function in a variety of biological processes. Although experimental approaches for identifying m6A sites have been developed and deployed, they are currently expensive for transcriptome-wide m6A identification. Some computational strategies for identifying m6A sites have been presented as an effective complement to the experimental procedure. However, their performance still requires improvement. In this study, we have proposed a novel tool called DL-m6A for the identification of m6A sites in mammals using deep learning based on different encoding schemes. The proposed tool uses three encoding schemes which give the required contextual feature representation to the input RNA sequence. Later these contextual feature vectors individually go through several neural network layers for shallow feature extraction after which they are concatenated to a single feature vector. The concatenated feature map is then used by several other layers to extract the deep features so that the insight features of the sequence can be used for the prediction of m6A sites. The proposed tool is firstly evaluated on the tissue-specific dataset and later on a full transcript dataset. To ensure the generalizability of the tool we assessed the proposed model by training it on a full transcript dataset and test on the tissue-specific dataset. The achieved results by the proposed model have outperformed the existing tools. The results demonstrate that the proposed tool can be of great use for the biology experts and therefore a freely accessible web-server is created which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/DL-m6A/.

Criteria for preclinical models of cholangiocarcinoma: scientific and medical relevance.

Cholangiocarcinoma (CCA) is a rare malignancy that develops at any point along the biliary tree. CCA has a poor prognosis, its clinical management remains challenging, and effective treatments are lacking. Therefore, preclinical research is of pivotal importance and necessary to acquire a deeper understanding of CCA and improve therapeutic outcomes. Preclinical research involves developing and managing complementary experimental models, from in vitro assays using primary cells or cell lines cultured in 2D or 3D to in vivo models with engrafted material, chemically induced CCA or genetically engineered models. All are valuable tools with well-defined advantages and limitations. The choice of a preclinical model is guided by the question(s) to be addressed; ideally, results should be recapitulated in independent approaches. In this Consensus Statement, a task force of 45 experts in CCA molecular and cellular biology and clinicians, including pathologists, from ten countries provides recommendations on the minimal criteria for preclinical models to provide a uniform approach. These recommendations are based on two rounds of questionnaires completed by 35 (first round) and 45 (second round) experts to reach a consensus with 13 statements. An agreement was defined when at least 90% of the participants voting anonymously agreed with a statement. The ultimate goal was to transfer basic laboratory research to the clinics through increased disease understanding and to develop clinical biomarkers and innovative therapies for patients with CCA.

Current challenges and future directions for engineering extracellular vesicles for heart, lung, blood and sleep diseases.

Extracellular vesicles (EVs) carry diverse bioactive components including nucleic acids, proteins, lipids and metabolites that play versatile roles in intercellular and interorgan communication. The capability to modulate their stability, tissue-specific targeting and cargo render EVs as promising nanotherapeutics for treating heart, lung, blood and sleep (HLBS) diseases. However, current limitations in large-scale manufacturing of therapeutic-grade EVs, and knowledge gaps in EV biogenesis and heterogeneity pose significant challenges in their clinical application as diagnostics or therapeutics for HLBS diseases. To address these challenges, a strategic workshop with multidisciplinary experts in EV biology and U.S. Food and Drug Administration (USFDA) officials was convened by the National Heart, Lung and Blood Institute. The presentations and discussions were focused on summarizing the current state of science and technology for engineering therapeutic EVs for HLBS diseases, identifying critical knowledge gaps and regulatory challenges and suggesting potential solutions to promulgate translation of therapeutic EVs to the clinic. Benchmarks to meet the critical quality attributes set by the USFDA for other cell-based therapeutics were discussed. Development of novel strategies and approaches for scaling-up EV production and the quality control/quality analysis (QC/QA) of EV-based therapeutics were recognized as the necessary milestones for future investigations.

Visual Literacy of Molecular Biology Revealed through a Card-Sorting Task.

Visual literacy, which is the ability to effectively identify, interpret, evaluate, use, and create images and visual media, is an important aspect of science literacy. As molecular processes are not directly observable, researchers and educators rely on visual representations (e.g., drawings) to communicate ideas in biology. How learners interpret and organize those numerous diagrams is related to their underlying knowledge about biology and their skills in visual literacy. Furthermore, it is not always obvious how and why learners interpret diagrams in the way they do (especially if their interpretations are unexpected), as it is not possible to "see" inside the minds of learners and directly observe the inner workings of their brains. Hence, tools that allow for the investigation of visual literacy are needed. Here, we present a novel card-sorting task based on visual literacy skills to investigate how learners interpret and think about DNA-based concepts. We quantified differences in performance between groups of varying expertise and in pre- and postcourse settings using percentages of expected card pairings and edit distance to a perfect sort. Overall, we found that biology experts organized the visual representations based on deep conceptual features, while biology learners (novices) more often organized based on surface features, such as color and style. We also found that students performed better on the task after a course in which molecular biology concepts were taught, suggesting the activity is a useful and valid tool for measuring knowledge. We have provided the cards to the community for use as a classroom activity, as an assessment instrument, and/or as a useful research tool to probe student ideas about molecular biology.

Broadening the Taxonomic Breadth of Organisms in the Bio-Inspired Design Process.

(1) Generating a range of biological analogies is a key part of the bio-inspired design process. In this research, we drew on the creativity literature to test methods for increasing the diversity of these ideas. We considered the role of the problem type, the role of individual expertise (versus learning from others), and the effect of two interventions designed to increase creativity-going outside and exploring different evolutionary and ecological "idea spaces" using online tools. (2) We tested these ideas with problem-based brainstorming assignments from a 180-person online course in animal behavior. (3) Student brainstorming was generally drawn to mammals, and the breadth of ideas was affected more by the assigned problem than by practice over time. Individual biological expertise had a small but significant effect on the taxonomic breadth of ideas, but interactions with team members did not. When students were directed to consider other ecosystems and branches of the tree of life, they increased the taxonomic diversity of biological models. In contrast, going outside resulted in a significant decrease in the diversity of ideas. (4) We offer a range of recommendations to increase the breadth of biological models generated in the bio-inspired design process.

Reduced volume of diabetic pancreatic islets in rodents detected by synchrotron X-ray phase-contrast microtomography and deep learning network

The pancreatic islet is a highly structured micro-organ that produces insulin in response to rising blood glucose. Here we develop a label-free and automatic imaging approach to visualize the islets in situ in diabetic rodents by the synchrotron radiation X-ray phase-contrast microtomography (SRμCT) at the ID17 station of the European Synchrotron Radiation Facility. The large-size images (3.2mm×15.97mm) were acquired in the pancreas in STZ-treated mice and diabetic GK rats. Each pancreas was dissected by 3000 reconstructed images. The image datasets were further analysed by a self-developed deep learning method, AA-Net. All islets in the pancreas were segmented and visualized by the three-dimension (3D) reconstruction. After quantifying the volumes of the islets, we found that the number of larger islets (=>1500 μm3) was reduced by 2-fold (wt 1004±94 vs GK 419±122, P<0.001) in chronically developed diabetic GK rat, while in STZ-treated diabetic mouse the large islets were decreased by half (189±33 vs 90±29, P<0.001) compared to the untreated mice. Our study provides a label-free tool for detecting and quantifying pancreatic islets in situ. It implies the possibility of monitoring the state of pancreatic islets in vivo diabetes without labelling.

An Infectious Bursal Disease Virus (IBDV) Reverse Genetics Rescue System and Neutralization Assay in Chicken B Cells

Infectious bursal disease virus (IBDV) is a major threat to the productivity of the poultry industry due to morbidity, mortality, and immunosuppression that exacerbates secondary infections and reduces the efficacy of vaccination programs. Field strains of IBDV have a preferred tropism for chicken B cells, the majority of which reside in the bursa of Fabricius (BF). IBDV adaptation to adherent cell culture is associated with mutations altering amino acids in the hypervariable region (HVR) of the capsid protein, which affects immunogenicity and virulence. Until recently, this has limited both the application of reverse genetics systems for engineering molecular clones, and the use of in vitro neutralization assays, to cell-culture-adapted strains of IBDV. Here, we describe the rescue of molecular clones of IBDV containing the HVR from diverse field strains, along with a neutralization assay to quantify antibody responses against the rescued viruses, both using chicken B cells. These methods are readily adaptable to any laboratory with molecular biology expertise and negate the need to obtain wild-type strains. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: A chicken B-cell rescue system for IBDV Basic Protocol 2: A chicken B-cell neutralization assay for IBDV.

Acute Myeloid Leukemia Multi-classification using Enhanced Few-shot Learning Technique

Acute Myeloid Leukemia (AML) is a form of the condition that is fatal and has a high mortality rate. It is characterised by abnormal cells growing rapidly inside the human body. The conventional method for detecting AML seems to be examining the blood sample manually under a microscope, which is a manual and cumbersome task that also requires well-trained medical expertise for efficient identification. On the other hand, considering medical diagnosis, the capacity to classify medical images faster and accurate is essential. The classification of medical images my currently be accomplished using a range of methodologies including Machine Learning (ML), Deep Learning (DL) and Transfer Learning (RL). While these approaches are effective for large datasets, they can take a while and~not ideal for small datasets. In recent years, advances in Deep Convolutional Neural Networks (DCNN) have made it possible and produce more accurate and promising outcome while processing a~medical image. However, the paradigm that DCNN~use for training includes a large number of annotations in order to prevent overfitting and produce promising results. Obtaining large-scale semantic annotations in clinical operations might be problematic in some cases, particularly biological expertise knowledge is needed. It is also regular occurrence in scenarios where only a small number of annotated classes are accessible in some circumstances. At this context, in order overcome the drawback of traditional approach a framework has been developed which comprises of Enhanced Few-Shot Learning Technique integrated Base Classifier (Feature Encoder)-EFLTBC. The proposed model has built using base classifier and meta-learning block, and it optimized the better results. To diagnose AML, the doctor must count the number of white blood cells and red blood cells and see if there are any abnormal health conditions in that using a microscope. However, obtaining an accurate result takes time and effort. To address these issues, the proposed Novel AML detection model employing is used in this study. Base classifier utilizing ResNet-18 pretrained model and meta learning block has computed using the average feature of every samples. Also, the dataset that we used consisting of three classes includes Normal monocytes, Abnormal monocytes, Lymphocyte and Experimental results outperform various existing deep learning technique with the accuracy of 97%, recall of 96.55% F1-Score of 96.65% and precision of 96.60.

Long-term High Resolution Image Dataset of Antarctic Coastal Benthic Fauna

Antarctica is a remote place, the continent is covered by ice and its surrounding coastal areas are frozen for the majority of the year. Due to its peculiarity the observation of the underwater organisms is particularly difficult, complicated by logistic factors. We present a long-term dataset consisting of 755 images acquired by using a non-invasive, autonomous imaging device and encompassing both the Antarctic daylight and dark periods, including the corresponding transition phases. All images have the same field of view showing the benthic fauna and part of the water column above, including fishes present in the monitored period. All the images are manually annotated after a visual inspection performed by expert biologists. The extended monitoring period and the annotated images make the dataset a valuable benchmark suitable for studying the dynamics of the long-term Antarctic underwater fauna as well as for developing and testing algorithms for automated image analysis focused on the recognition and classification of the Antarctic organisms and the automated analysis of their long-term dynamics.