Extracting structured information from unstructured histopathology reports using generative pre-trained transformer 4 (GPT-4).

Deep learning applied to whole-slide histopathology images (WSIs) has the potential to enhance precision oncology and alleviate the workload of experts. However, developing these models necessitates large amounts of data with ground truth labels, which can be both time-consuming and expensive to obtain. Pathology reports are typically unstructured or poorly structured texts, and efforts to implement structured reporting templates have been unsuccessful, as these efforts lead to perceived extra workload. In this study, we hypothesised that large language models (LLMs), such as the generative pre-trained transformer 4 (GPT-4), can extract structured data from unstructured plain language reports using a zero-shot approach without requiring any re-training. We tested this hypothesis by utilising GPT-4 to extract information from histopathological reports, focusing on two extensive sets of pathology reports for colorectal cancer and glioblastoma. We found a high concordance between LLM-generated structured data and human-generated structured data. Consequently, LLMs could potentially be employed routinely to extract ground truth data for machine learning from unstructured pathology reports in the future. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

19th International Xenopus Conference Meeting Report: Latest developments and future perspectives.

The African clawed frog, Xenopus laevis, and the Western clawed frog, Xenopus tropicalis, have been foundational model organisms for establishing key principles of embryonic development. Today, the utility of Xenopus has been greatly expanded for studying a wide range of biological processes both in health and disease. Here, we describe the latest advancements from the Xenopus community, which span the molecular, cellular, tissue, and organismal scales.

Chronic and Neurotropic: A Paradigm-Challenging Case of Dengue Virus Encephalitis in a Patient With Advanced HIV Infection.

A 32-year-old female with advanced human immunodeficiency virus infection presented to an Australian hospital with subacute, worsening symptoms of encephalitis. Metagenomic sequencing and Dengue NS3 antigen staining of brain tissue confirmed active dengue virus (DENV) encephalitis. The most recent possible DENV exposure was months prior in West Africa, indicating chronicity.

A single workflow for multi-species blood transcriptomics.

BACKGROUND: Blood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for applications in diagnostics and monitoring of the immune response to vaccines. However, multi-species transcriptomic analysis is still a challenge from a technological point of view and a standardized workflow is urgently needed to allow interspecies comparisons. RESULTS: Here, we propose a single and complete total RNA-Seq workflow to generate reliable transcriptomic data from blood samples from humans and from animals typically used in preclinical models. Blood samples from a maximum of six individuals and four different species (rabbit, non-human primate, mouse and human) were extracted and sequenced in triplicates. The workflow was evaluated using different wet-lab and dry-lab criteria, including RNA quality and quantity, the library molarity, the number of raw sequencing reads, the Phred-score quality, the GC content, the performance of ribosomal-RNA and globin depletion, the presence of residual DNA, the strandness, the percentage of coding genes, the number of genes expressed, and the presence of saturation plateau in rarefaction curves. We identified key criteria and their associated thresholds to be achieved for validating the transcriptomic workflow. In this study, we also generated an automated analysis of the transcriptomic data that streamlines the validation of the dataset generated. CONCLUSIONS: Our study has developed an end-to-end workflow that should improve the standardization and the inter-species comparison in blood transcriptomics studies. In the context of vaccines and drug development, RNA sequencing data from preclinical models can be directly compared with clinical data and used to identify potential biomarkers of value to monitor safety and efficacy.

Different concepts of neighborhood safety and child internalizing and externalizing behaviors.

Neighborhood safety is defined inconsistently across epidemiologic studies - a conceptual problem that results in incomparable measurements, hampering the design of health interventions. Using child behavior problems (measured via the Child Behavior Checklist) as the outcome of interest, this study directly compared four measures of neighborhood safety: two of experienced safety and two of perceived safety, with each one measured at family and community levels. These included children's direct experience of harm, parental perceptions, community crime statistics, and community perceptions. In a sample of 3291 ten-year-olds from the Generation R cohort (living in municipal Rotterdam, Netherlands, 2013), all four measures were correlated (χ2 ≥ 9.2, P < 0.002 in pairwise chi-square comparisons), but ultimately identified different levels of risk for behavioral health. Direct experiences of harm, parental perceptions, and community crime statistics were all associated with increased child internalizing behaviors (ß = 3.12, ß = 2.10, and ß = 1.77, respectively), while only experiences of harm and parental perceptions were associated with increased externalizing behaviors (ß = 2.75 and ß = 1.31, respectively). These results provide novel evidence that the conceptual distinctions underlying different measures of neighborhood safety are meaningful for child mental health and should be considered in intervention design.

The 14th International Podocyte Conference 2023: from podocyte biology to glomerular medicine.

The 14th International Podocyte Conference took place in Philadelphia, Pennsylvania, USA from May 23 to 26, 2023. It commenced with an early-career researchers' meeting on May 23, providing young scientists with a platform to present and discuss their research findings. Throughout the main conference, 29 speakers across 9 sessions shared their insights on podocyte biology, glomerular medicine, novel technologic advancements, and translational approaches. Additionally, the event featured 3 keynote lectures addressing engineered chimeric antigen receptor T cell- and mRNA-based therapies and the use of biobanks for enhanced disease comprehension. Furthermore, 4 brief oral abstract sessions allowed scientists to present their findings to a broad audience. The program also included a panel discussion addressing the challenges of conducting human research within the American Black community. Remarkably, after a 5-year hiatus from in-person conferences, the 14th International Podocyte Conference successfully convened scientists from around the globe, fostering the presentation and discussion of crucial research findings, as summarized in this review. Furthermore, to ensure continuous and sustainable education, research, translation, and trial medicine related to podocyte and glomerular diseases for the benefit of patients, the International Society of Glomerular Disease was officially launched during the conference.

Agreement of medical record abstraction and self-report of breast cancer treatment with an extended recall window.

BACKGROUND: Medical record abstraction (MRA) and self-report questionnaires are two methods frequently used to ascertain cancer treatment information. Prior studies have shown excellent agreement between MRA and self-report, but it is unknown how a recall window longer than 3 years may affect this agreement. METHODS: The Women's Environmental Cancer and Radiation Epidemiology (WECARE) Study is a multicenter, population-based case-control study of controls with unilateral breast cancer individually matched to cases with contralateral breast cancer. Participants who were diagnosed with a first primary breast cancer from 1985 to 2008 before the age of 55 years completed a questionnaire that included questions on treatment. First primary breast cancer treatment information was abstracted from the medical record from radiation oncology clinic notes for radiation treatment and from systemic adjuvant treatment reports for hormone therapy and chemotherapy. Agreement between MRA and self-reported treatment was assessed with the kappa statistic and corresponding 95% confidence intervals (CIs). RESULTS: A total of 2808 participants with MRA and self-reported chemotherapy treatment information, 2733 participants with MRA and self-reported hormone therapy information, and 2905 participants with MRA and self-reported radiation treatment information were identified. The median recall window was 12.5 years (range, 2.8-22.2 years). MRA and self-reported treatment agreement was excellent across treatment modalities (kappachemo, 98.5; 95% CI, 97.9-99.2; kappahorm, 87.7; 95% CI, 85.9-89.5; kapparad, 97.9; 95% CI, 97.0-98.7). There was no heterogeneity across recall windows (pchemo = .46; phorm = .40; prad = .61). CONCLUSIONS: Agreement between self-reported and MRA primary breast cancer treatment modality information was excellent for young women diagnosed with breast cancer and was maintained even among women whose recall window was more than 20 years after diagnosis.

Two models of mind blanking.

Mind blanking is a mental state in which attention does not bring any perceptual input into conscious awareness. As this state is still largely unexplored, we suggest that a comprehensive understanding of mind blanking can be achieved through a multifaceted approach combining self-assessment methods, neuroimaging and neuromodulation. In this article, we explain how electroencephalography and transcranial magnetic stimulation could be combined to help determine whether mind blanking is associated with a lack of mental content or a lack of linguistically or conceptually determinable mental content. We also question whether mind blanking occurs spontaneously or intentionally and whether these two forms are instantiated by the same or different neural correlates.

The assessment of emotion reactivity: The Italian validation of the Perth Emotional Reactivity Scale-Short Form (PERS-S).

Emotion reactivity refers to the activation, intensity and duration of emotional responses to internal or external stimuli. It can be differentiated from emotion regulation since the former is the very first response to an emotional trigger, and the latter can be defined as a tool for maintaining one's arousal in a window of tolerance. Since, to date, there are no Italian self-report measures able to evaluate individuals' emotional reactivity, this study aimed to contribute to the Italian validation of the Perth Emotional Reactivity Scale-Short Form (PERS-S). The PERS-S is an 18-item self-report measure answered on a 5-point Likert scale that generates six subscale scores and two composite scores, with higher scores indicating higher levels of reactivity. Data from 768 individuals showed that the PERS-S had good to excellent goodness of fit. The internal consistency was high, with an overall reliability coefficient (Cronbach's α) of .87 and .86 for the negative and positive general scales, respectively. The PERS-S also demonstrated appropriate convergent validity, showing significant correlations with conceptually related measures, and acceptable divergent validity, showing minimal correlations with unrelated constructs. Finally, we evaluated the Test-Retest Reliability by administering the PERS-S to the same sample twice, with a 2-week interval. The significant correlations between the two PERS-S administrations suggest temporal stability. The Italian version of the PERS-S will enrich the repertoire of self-report measures for investigating the development and risk factors of mental health disorders and may have practical applications in clinical settings.

ICTV Virus Taxonomy Profile: Fusariviridae 2024.

Fusariviridae is a family of mono-segmented, positive-sense RNA viruses with genome sizes of 5.9-10.7 kb. Most genomic RNAs are bicistronic, but exceptions have up to four predicted ORFs. In bicistronic genomes, the 5'-proximal ORF codes for a single protein with both RNA-directed RNA polymerase (RdRP) and RNA helicase (Hel) domains; little is known about the protein encoded by the second ORF. Fusarivirids do not appear to form virions. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Fusariviridae, which is available at ictv.global/report/fusariviridae.

ICTV Virus Taxonomy Profile: Phasmaviridae 2024.

Phasmaviridae is a family for negative-sense RNA viruses with genomes of about 9.7-15.8 kb. These viruses are maintained in and/or transmitted by insects. Phasmavirids produce enveloped virions containing three single-stranded RNA segments that encode a nucleoprotein (N), a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Phasmaviridae, which is available at ictv.global/report/phasmaviridae.

ICTV Virus Taxonomy Profile: Hantaviridae 2024.

Hantaviridae is a family for negative-sense RNA viruses with genomes of about 10.5-14.6 kb. These viruses are maintained in and/or transmitted by fish, reptiles, and mammals. Several orthohantaviruses can infect humans, causing mild, severe, and sometimes-fatal diseases. Hantavirids produce enveloped virions containing three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Hantaviridae, which is available at ictv.global/report/hantaviridae.

ICTV Virus Taxonomy Profile: Fimoviridae 2024.

Members of the family Fimoviridae are plant viruses with a multipartite negative-sense enveloped RNA genome (-ssRNA), composed of 4-10 segments comprising 12.3-18.5 kb in total, within quasi-spherical virions. Fimoviruses are transmitted to plants by eriophyid mites and induce characteristic cytopathologies in their host plants, including double membrane-bound bodies in the cytoplasm of virus-infected cells. Most fimoviruses infect dicotyledonous plants, and many cause serious disease epidemics. This is a summary of the ICTV Report on the family Fimoviridae, which is available at ictv.global/report/fimoviridae.

ICTV Virus Taxonomy Profile: Turriviridae 2024.

The family Turriviridae includes viruses with a dsDNA genome of 16-17 kbp. Virions are spherical with a diameter of approximately 75 nm and comprise a host-derived internal lipid membrane surrounded by a proteinaceous capsid shell. Members of the family Turriviridae infect extremophilic archaea of the genera Sulfolobus and Saccharolobus. Viral infection results in cell lysis for Sulfolobus turreted icosahedral virus 1 infection but other members of the family can be temperate. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Turriviridae, which is available at ictv.global/report/turriviridae.

ICTV Virus Taxonomy Profile: Nairoviridae 2024.

Nairoviridae is a family for negative-sense RNA viruses with genomes of about 17.2-21.1 kb. These viruses are maintained in and/or transmitted by arthropods among birds, reptiles and mammals. Norwaviruses and orthonairoviruses can cause febrile illness in humans. Several orthonairoviruses can infect mammals, causing mild, severe and sometimes, fatal diseases. Nairovirids produce enveloped virions containing two or three single-stranded RNA segments with open reading frames that encode a nucleoprotein (N), sometimes a glycoprotein precursor (GPC), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Nairoviridae, which is available at www.ictv.global/report/nairoviridae.

ICTV Virus Taxonomy Profile: Kolmioviridae 2024.

Kolmioviridae is a family for negative-sense RNA viruses with circular, viroid-like genomes of about 1.5-1.7 kb that are maintained in mammals, amphibians, birds, fish, insects and reptiles. Deltaviruses, for instance, can cause severe hepatitis in humans. Kolmiovirids encode delta antigen (DAg) and replicate using host-cell DNA-directed RNA polymerase II and ribozymes encoded in their genome and antigenome. They require evolutionary unrelated helper viruses to provide envelopes and incorporate helper virus proteins for infectious particle formation. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Kolmioviridae, which is available at ictv.global/report/kolmioviridae.

ICTV Virus Taxonomy Profile: Filoviridae 2024.

Filoviridae is a family of negative-sense RNA viruses with genomes of about 13.1-20.9 kb that infect fish, mammals and reptiles. The filovirid genome is a linear, non-segmented RNA with five canonical open reading frames (ORFs) that encode a nucleoprotein (NP), a polymerase cofactor (VP35), a glycoprotein (GP1,2), a transcriptional activator (VP30) and a large protein (L) containing an RNA-directed RNA polymerase (RdRP) domain. All filovirid genomes encode additional proteins that vary among genera. Several filovirids (e.g., Ebola virus, Marburg virus) are pathogenic for humans and highly virulent. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Filoviridae, which is available at www.ictv.global/report/filoviridae.

Complete response to capmatinib in a patient with metastatic lung adenocarcinoma harboring CD47-MET fusion: a case report.

Comprehensive genomic profiling is highly recommended for treatment decision in nonsquamous, non-small cell lung cancer (NSCLC). However, rare genomic alterations are still being unveiled, with scarce data to guide therapy. Herein, we describe the treatment journey of a 56-year-old, never-smoker Caucasian woman with a metastatic NSCLC harboring a CD47-MET fusion, initially classified as a variant of unknown significance. She had undergone 3 lines of therapy over the course of 3 years, including chemotherapy, immunotherapy, and anti-angiogenic therapy. After reanalysis of her next-generation sequencing data in our service, the fusion was reclassified as likely oncogenic. The patient was started with fourth-line capmatinib, with a good tolerance so far and a complete metabolic response in the active sites of disease, currently ongoing for 18 months. In conclusion, we highlight the sensitivity of a novel MET fusion to capmatinib and emphasize the need for comprehensive panels in NSCLC and molecular tumor board discussions with specialized centers when rare findings arise.

Assessing the growth, yield, and biochemical composition of greenhouse cherry tomatoes with special emphasis on the progressive growth report.

The growth of plants hinges on a complex interplay of biochemical and physiological activities across various growth stages. These intricate processes dynamically adapt to different environmental conditions, shaping both plant development and productivity. This study explores the impact of greenhouse climate on the growth, yield, and biochemistry of winter-grown cherry tomatoes 'Cheramy F1'. A randomized complete block design (RCBD) under split plot arrangements (3 Rows) with three replications (3 plants from each row) was adopted. The data were collected on various dates during the period extending from December to March of two consecutive growing seasons in 2022 and 2023, and presented as averages. An analysis of variance was applied to statistically analyze the collected data at a confidence level of p < 0.05. The climatic conditions in the greenhouse were calculated as temperature ranging from a minimum of 10.5 °C to the maximum of 41.3 °C by an average of 21.2 °C during the vegetative stage and from 8.2 °C to 32.3 °C by an average of 20.9 °C during the fruit-bearing stage, with an average CO2 concentration fluctuated within the range of 385.61 ppm to 510.30 ppm and an average light intensity of 94.62 to 240.45 W/m². This study assessed various growth parameters such as plant height, leaf growth, stem diameter, leaf spacing, leaf count, leaf area, and inflorescence count per plant, and suggested the optimum range of greenhouse conditions for each stage. The key results of this study revealed the Progressive Growth Report (PGR), predicting daily potential growth rates of plants: plant height, 2.86 to 3.81 cm/day; growth rate of mature older leaf: 0.003988 m2/day; middle younger leaf: 0.008733 m2/day; top nascent leaf: 0.010722 m2/day; three to five leaves per week; and one inflorescence per week. In our accidental observation, we noticed unusual plant growth and yield responses because of the various growing postures and positions that the plants adopted in the greenhouse. An exceedingly significant difference among the inflorescences was found in view of their growth, productivity and biochemical composition. A non-significant interaction was found between the fruit keeping quality (shelf days), fruit height, fruit diameter, and inflorescence number. The present study results highlight the possible responses of greenhouse-grown cherry tomatoes to different ranges of temperature, light intensity, and CO2 concentrations, offering valuable insights for optimizing greenhouse cherry tomatoes cultivation.

Laboratory approaches to determining blood culture contamination rates: an ASM Laboratory Practices Subcommittee report.

Blood culture contamination (BCC) is the presence of specific commensal and environmental organisms cultivated from a single blood culture set out of a blood culture series and that do not represent true bacteremia. BCC can impact quality of care and lead to negative outcomes, unnecessary antibiotic exposure, prolonged hospital stays, and substantial costs. As part of the laboratory's quality management plan, microbiology laboratory personnel are tasked with monitoring BCC rates, preparing BCC rate reports, and providing feedback to the appropriate committees within their healthcare system. The BCC rate is calculated by the laboratory using pre-set criteria. However, pre-set criteria are not universally defined and depend on the individual institution's patient population and practices. This mini-review provides practical recommendations on elaborating BCC rate reports, the parameters to define for the pre-set criteria, how to collect and interpret the data, and additional analysis to include in a BCC report.