Text mining for contexts and relationships in cancer genomics literature.

MOTIVATION: Scientific advances build on the findings of existing research. The 2001 publication of the human genome has led to the production of huge volumes of literature exploring the context-specific functions and interactions of genes. Technology is needed to perform large-scale text mining of research papers to extract the reported actions of genes in specific experimental contexts and cell states, such as cancer, thereby facilitating the design of new therapeutic strategies. RESULTS: We present a new corpus and Text Mining methodology that can accurately identify and extract the most important details of cancer genomics experiments from biomedical texts. We build a Named Entity Recognition model that accurately extracts relevant experiment details from PubMed abstract text, and a second model that identifies the relationships between them. This system outperforms earlier models and enables the analysis of gene function in diverse and dynamically evolving experimental contexts. AVAILABILITY AND IMPLEMENTATION: Code and data are available here: https://github.com/cambridgeltl/functional-genomics-ie.

Virtual Clinics: A Student-Led, Problem-Based Learning Approach to Supplement Veterinary Clinical Experiences.

The COVID-19 pandemic created an abrupt need for effective remote clinical experiences for senior clinical veterinary students. Subsequently, the authors created virtual clinics. This activity was derived from a problem-based learning (PBL) model wherein students designed clinical cases and participated through virtual role play as clients and clinicians. The purpose of this article is to describe virtual clinics and to report data from focus groups of participating students and faculty facilitators from two institutions regarding the positive and negative aspects of the shift in practice. A few common emerging themes included that case rounds were fun and engaging, students could learn at their own pace, and peer-to-peer learning opportunities had perceived value. Themes are reflected against the pedagogical literature to draw out areas that resonated. Students felt this activity was more engaging than listening to a discussion of a case they had no ownership of, and facilitators agreed that the peer-to-peer interactions added to student engagement. Additionally, students developed deeper knowledge about the underlying disease process and clinical presentation of their case, which required independent and self-directed learning, enabling students to think about a case from a client's perspective. By participating in these activities, students developed skills of classroom-to-clinic transitional value. While virtual clinics should not replace in-person clinical experiences, this activity might be useful to facilitate students' transition from a structured classroom setting to a less-structured clinical experience.

LPCAT4 Knockdown Alters Barrier Integrity and Cellular Bioenergetics in Human Urothelium.

Urothelium is a transitional, stratified epithelium that lines the lower urinary tract, providing a tight barrier to urine whilst retaining the capacity to stretch and rapidly resolve damage. The role of glycerophospholipids in urothelial barrier function is largely unknown, despite their importance in membrane structural integrity, protein complex assembly, and the master regulatory role of PPARγ in urothelial differentiation. We performed lipidomic and transcriptomic characterisation of urothelial differentiation, revealing a metabolic switch signature from fatty acid synthesis to lipid remodelling, including 5-fold upregulation of LPCAT4. LPCAT4 knockdown urothelial cultures exhibited an impaired proliferation rate but developed elevated trans-epithelial electrical resistances upon differentiation, associated with a reduced and delayed capacity to restitute barrier function after wounding. Specific reduction in 18:1 PC fatty acyl chains upon knockdown was consistent with LPCAT4 specificity, but was unlikely to elicit broad barrier function changes. However, transcriptomic analysis of LPCAT4 knockdown supported an LPC-induced reduction in DAG availability, predicted to limit PKC activity, and TSPO abundance, predicted to limit endogenous ATP. These phenotypes were confirmed by PKC and TSPO inhibition. Together, these data suggest an integral role for lipid mediators in urothelial barrier function and highlight the strength of combined lipidomic and transcriptomic analyses for characterising tissue homeostasis.

Veterinary and Pharmacy Students' Expectations Before and Experiences After Participating in an Interdisciplinary Access to Care Veterinary Clinic, WisCARES.

This pilot survey study describes student expectations and experiences at WisCARES, a low-cost veterinary medical teaching clinic where students from multiple disciplines collaborate. We hypothesized that prior to the workday, students would describe different expectations of working in an interdisciplinary access to care clinic than what they ultimately experienced. We surveyed 62 students from the School of Veterinary Medicine (46) and pharmacy (16) who spent a clinic day at WisCARES. Before introductory rounds, students completed a short survey consisting of four open-ended questions about their learning expectations; at the end of the day, they reviewed their initial responses and added what they actually learned. Qualitative information was categorized and analyzed using descriptive statistics. Thirteen major themes emerged: diversity, confidence, communication, case lead/case management, financial experience, helping people, teamwork, technical skills, inter-professional experience, mentoring, non-specific positive regard, appreciation for resources, and rounds. Students reported improved confidence in managing and leading cases with specific positive outcomes in communicating with clients, particularly regarding leading financial conversations. Developing greater insight into diversity was a common theme expressed in students' expectations but was less frequently noted as an end-of-day outcome. Veterinary students less frequently described the value of the inter-professional environment and collaboration, but this was a major theme noted among pharmacy students. Student feedback was positive overall. The current study is useful in identifying areas for improving collaborative instruction and access to care professional student learning opportunities.

Teaching Tip Using Play-Doh to Enhance the Perceived Learning of Veterinary Medicine.

Teaching anatomy to veterinary students is challenging, and using two-dimensional (2D) representations may limit the opportunity for learners to make the connections required to fully appreciate the complex structures involved and the relationships between them. This research considered the implementation of three-dimensional (3D) modeling using Play-Doh with learners to consider whether they were able to make effective representations that may then support further learning. The evidence from teacher observations and student feedback suggests that, despite some initial hesitation surrounding the use of what some might perceive as a toy in the higher education classroom, the learners believed that the approach allowed improvement in terms of their understanding, knowledge retention and recall. They reported that the approach enabled greater visualization of the structures they were representing. For teachers, the approach has the advantage that the material is cheap, readily available, easily manipulated, can be reused, and needs no sophisticated technology.

How to Approach Cultural Humility Debriefing within Clinical Veterinary Environments.

Cultural humility debriefing provides learners with the opportunity to consider how they engage with clients and patients while keeping their own identities and biases in mind. In this article, we invite a deeper understanding of the cultural humility debrief by reviewing its history and uses, describing the state of mind and communication skills required for successful facilitation, and providing a step-by-step process as a framework for veterinary educators to implement effective cultural humility debriefing in practice. This teaching technique is rooted in established communication tools-specifically, permission seeking, open-ended questions, reflective listening, and empathy. Drawing on experience from an inter-professional clinic that serves people who live at or below the national poverty level, this article offers insights to veterinary educators so they can use the cultural humility debrief. By utilizing the outlined debriefing strategies in a clinical setting, it is possible to augment any existing veterinary curriculum and strengthen education around cultural topics.

LION LBD: a literature-based discovery system for cancer biology.

MOTIVATION: The overwhelming size and rapid growth of the biomedical literature make it impossible for scientists to read all studies related to their work, potentially leading to missed connections and wasted time and resources. Literature-based discovery (LBD) aims to alleviate these issues by identifying implicit links between disjoint parts of the literature. While LBD has been studied in depth since its introduction three decades ago, there has been limited work making use of recent advances in biomedical text processing methods in LBD. RESULTS: We present LION LBD, a literature-based discovery system that enables researchers to navigate published information and supports hypothesis generation and testing. The system is built with a particular focus on the molecular biology of cancer using state-of-the-art machine learning and natural language processing methods, including named entity recognition and grounding to domain ontologies covering a wide range of entity types and a novel approach to detecting references to the hallmarks of cancer in text. LION LBD implements a broad selection of co-occurrence based metrics for analyzing the strength of entity associations, and its design allows real-time search to discover indirect associations between entities in a database of tens of millions of publications while preserving the ability of users to explore each mention in its original context in the literature. Evaluations of the system demonstrate its ability to identify undiscovered links and rank relevant concepts highly among potential connections. AVAILABILITY AND IMPLEMENTATION: The LION LBD system is available via a web-based user interface and a programmable API, and all components of the system are made available under open licenses from the project home page http://lbd.lionproject.net. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Teaching Cultural Humility and Implicit Bias to Veterinary Medical Students: A Review and Recommendation for Best Practices.

Cultural humility, with its concomitant understanding of the importance of the influences of diversity and inclusion, improves health outcomes in the human medical field. Recent changes to the American Veterinary Medical Association Council on Education requirements in veterinary medicine include teaching the impact of implicit bias on the delivery of veterinary medical services. Because overt enhancement of self-awareness is not fodder for traditional veterinary medical education delivery systems, in this article we review existing literature on the impact of recognition of implicit bias on health care and offer insights on ways to help veterinary students learn this skill, drawing on evidence from an inter-professional intervention called WisCARES (Wisconsin Companion Animal Resources, Education, and Social Services).

Differential transcription factor expression by human epithelial cells of buccal and urothelial derivation.

Identification of transcription factors expressed by differentiated cells is informative not only of tissue-specific pathways, but to help identify master regulators for cellular reprogramming. If applied, such an approach could generate healthy autologous tissue-specific cells for clinical use where cells from the homologous tissue are unavailable due to disease. Normal human epithelial cells of buccal and urothelial derivation maintained in identical culture conditions that lacked significant instructive or permissive signaling cues were found to display inherent similarities and differences of phenotype. Investigation of transcription factors implicated in driving urothelial-type differentiation revealed buccal epithelial cells to have minimal or absent expression of PPARG, GATA3 and FOXA1 genes. Retroviral overexpression of protein coding sequences for GATA3 or PPARy1 in buccal epithelial cells resulted in nuclear immunolocalisation of the respective proteins, with both transductions also inducing expression of the urothelial differentiation-associated claudin 3 tight junction protein. PPARG1 overexpression alone entrained expression of nuclear FOXA1 and GATA3 proteins, providing objective evidence of its upstream positioning in a transcription factor network and identifying it as a candidate factor for urothelial-type transdifferentiation or reprogramming.

Evaluation of Perceived Technical Skill Development by Students During Instruction in Dental Extractions in Different Laboratory Settings-A Pilot Study.

In veterinary general practice, dental extractions are common procedures that require a specific set of surgical skills. Veterinary medical educators are tasked with preparing students for general practice, equipping them with medical knowledge and surgical skills. Results of this pilot study demonstrate students' preference for circle-based laboratory setup, a perceived high value of immediate feedback when performing laboratory exercises, and a lack of preference for timing of the laboratory relative to the relevant material provided in lecture. The impact of lecture, supplemental information, and laboratory setup on development of these surgical skills are explored.