Automatic detection of fish scale circuli using deep learning.

Teleost fish scales form distinct growth rings deposited in proportion to somatic growth in length, and are routinely used in fish ageing and growth analyses. Extraction of incremental growth data from scales is labour intensive. We present a fully automated method to retrieve this data from fish scale images using Convolutional Neural Networks (CNNs). Our pipeline of two CNNs automatically detects the centre of the scale and individual growth rings (circuli) along multiple radial transect emanating from the centre. The focus detector was trained on 725 scale images and achieved an average precision of 99%; the circuli detector was trained on 40 678 circuli annotations and achieved an average precision of 95.1%. Circuli detections were made with less confidence in the freshwater zone of the scale image where the growth bands are most narrowly spaced. However, the performance of the circuli detector was similar to that of another human labeller, highlighting the inherent ambiguity of the labelling process. The system predicts the location of scale growth rings rapidly and with high accuracy, enabling the calculation of spacings and thereby growth inferences from salmon scales. The success of our method suggests its potential for expansion to other species.

Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype.

Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling. SIGNIFICANCE: The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.

Management of DOAC-related bleeding in cancer patients: a single center-case series.

Venous thromboembolism (VTE) and stroke carry significant mortality and morbidity in cancer patients. Direct oral anticoagulants (DOACs) have been demonstrated to be effective for the treatment of VTE and prevention of stroke in atrial fibrillation (AF). Bleeding rates are variable and are based on the cancer type and the patient's specific risk factors. There are approved specific antidotes for DOAC-associated bleeding. Other strategies are available for bleeding reversal, including the use of prothrombin complex concentrate (PCC). No randomized studies have compared head-to-head the efficacy and safety of reversal agents. We aim to examine the safety and effectiveness of hemostatic agents in cancer patients with DOAC-related major bleeding. A retrospective chart review study of patients at MD Anderson Cancer Center with DOAC-related major bleeding between 2014 and 2019. Bleeding severity and clinical hemostasis were described based on ISTH guidelines and the Sarode criteria, respectively. The rates of thrombotic complications and mortality at 30-day from the index bleeding event were described. We identified 23 patients with DOAC-related major bleeding; 14 patients received PCC and 9 patients received andexanet alfa. The most common sites of bleeding were the gastrointestinal tract and intracranial. Effective hemostasis and 30-day mortality were similar to reported results from other reports of outcomes of reversal agents for DOAC related-bleeding in non-cancer patients. One patient in each treatment group experienced a thrombotic event. Further larger scale studies are needed to confirm our findings in cancer patients.

Callose in leptoid cell walls of the moss Polytrichum and the evolution of callose synthase across bryophytes.

Introduction: Leptoids, the food-conducting cells of polytrichaceous mosses, share key structural features with sieve elements in tracheophytes, including an elongated shape with oblique end walls containing modified plasmodesmata or pores. In tracheophytes, callose is instrumental in developing the pores in sieve elements that enable efficient photoassimilate transport. Aside from a few studies using aniline blue fluorescence that yielded confusing results, little is known about callose in moss leptoids. Methods: Callose location and abundance during the development of leptoid cell walls was investigated in the moss Polytrichum commune using aniline blue fluorescence and quantitative immunogold labeling (label density) in the transmission electron microscope. To evaluate changes during abiotic stress, callose abundance in leptoids of hydrated plants was compared to plants dried for 14 days under field conditions. A bioinformatic study to assess the evolution of callose within and across bryophytes was conducted using callose synthase (CalS) genes from 46 bryophytes (24 mosses, 15 liverworts, and 7 hornworts) and one representative each of five tracheophyte groups. Results: Callose abundance increases around plasmodesmata from meristematic cells to end walls in mature leptoids. Controlled drying resulted in a significant increase in label density around plasmodesmata and pores over counts in hydrated plants. Phylogenetic analysis of the CalS protein family recovered main clades (A, B, and C). Different from tracheophytes, where the greatest diversity of homologs is found in clade A, the majority of gene duplication in bryophytes is in clade B. Discussion: This work identifies callose as a crucial cell wall polymer around plasmodesmata from their inception to functioning in leptoids, and during water stress similar to sieve elements of tracheophytes. Among bryophytes, mosses exhibit the greatest number of multiple duplication events, while only two duplications are revealed in hornwort and none in liverworts. The absence in bryophytes of the CalS 7 gene that is essential for sieve pore development in angiosperms, reveals that a different gene is responsible for synthesizing the callose associated with leptoids in mosses.

Methods: A bioinformatic protocol for rapid analysis of zebrafish embryo photo-motory responses (PMR) in neurotoxicity testing.

Chemobehavioural phenotyping presents unique opportunities for analyzing neurotoxicants and discovering behavior-modifying neuroceuticals in small aquatic model organisms such as zebrafish (Danio rerio). A recently popularized approach in this field involves the utilization of zebrafish embryos for a photo-motor response (PMR) bioassay. The PMR bioassay entails stimulating zebrafish embryos between 24 and 36 h post fertilization (hpf) with a high-intensity light stimulus, inducing a transient increase in the frequency of photo-induced embryo body flexions. These flexions can be computationally analyzed to derive behavioral signatures, enabling the categorization of neuromodulating chemicals. Despite the significant advantages of the PMR bioassay, its widespread implementation is hindered by lack of well described and straightforward high-throughput bioinformatic analysis of behavioral data. In this methods article, we present an easily implementable bioinformatics protocol specifically designed for rapid behavioral analysis of large cohorts of zebrafish specimens in PMR bioassays. We also address common pitfalls encountered during PMR analysis, discuss its limitations, and propose future directions for developing next-generation biometric analysis techniques in chemobehavioural assays utilizing zebrafish embryos.

An Open-Source Programmable Interface for Sensory-Motor Biotests with Zebrafish (Danio rerio).

Assessment of animals' sensory-motor functions requires precise and electronically controlled stimuli to induce and quantify specific behavioral phenotypes. However, accessible and inexpensive tools for conducting diverse sensory-motor biotests with fish are lacking. In this work, we present an open-source software and hardware interface that enables automated delivery of three independent and fully programmable stimuli for behavioral bioassays. We demonstrate the proof-of-concept application of this low-cost technology in establishing reproducible fear responses using a mechanical tap-startle stimulus in larval zebrafish. This response is characterized by a sudden burst of motion in response to a nondirectional mechanical stimulus delivered to the fish chamber. We propose that the simplicity and flexibility of this interface offer innovative opportunities for studying sensory-motor functions in various fields, including neurobiology, neuropharmacology, neurotoxicology, and aquatic ecotoxicology.

The impact of regional STEMI systems on protocol use and quality improvement initiatives in community hospitals without cardiac catheterization laboratories.

Study objective: Since the 1990s, national guidelines have recommended hospitals develop STEMI treatment protocols and monitor quality. A 2003 survey of Minnesota hospitals without cardiac catheterization laboratories (CCL) found <2/3 had STEMI protocols, <50% had a quality assessment (QA) process, and protocols in existence were incomplete. We evaluated temporal changes in STEMI processes in relationship to changes in mortality. Design setting and participants: Follow-up surveys were mailed to emergency departments at 108 Minnesota hospitals without CCL. Results: Among 87% of responding hospitals, 89% had formal protocols or guidelines for STEMI management compared to 63% in 2003 (p < 0.001). In 2010, 67% of hospitals had triage/transfer criteria and 15% of hospitals used protocols for transfer decisions, compared to only 8% (p < 0.001) and 1% (p = 0.098), respectively, in 2003. The percentage of hospitals transferring patients with STEMI from the emergency department increased from 23% in 2003 to 56% in 2010 (p < 0.001). During this time, age-adjusted acute MI mortality rate in Minnesota decreased 33% and was more pronounced in areas with regional STEMI systems. Conclusions: Since 2003, utilization of STEMI guidelines, protocols, and standing orders in Minnesota hospitals without CCL has markedly improved with <10% of hospitals lacking specific STEMI management protocols. The majority of hospitals routinely transfer patients with STEMI for primary PCI and have comprehensive QA processes. This improvement was stimulated by regional STEMI systems, further supporting the current class I recommendation for STEMI systems of care in current guidelines. The decline in Minnesota STEMI mortality paralleled the growth of regional STEMI systems.