Date Of Collection Research Articles

Responsibilities and perception of course coordinating professors of the curso de Licenciatura em Matemática no IFSP regarding the scope of the function

This article, an excerpt from the author's thesis, presents the responsibilities and impressions of the teachers who served as Coordination of Degree in Mathematics, at the Federal Institute of Education, Science and Technology of São Paulo (IFSP), between 2008 (the first institutional offer of the course) and 2021 (date of data collection), regarding the exercise of the function. With the central objective of identifying how the function demands pedagogical and educational management dimensions, we started with institutional documents and qualitative research data, obtained in a questionnaire sent to all (former) coordinators of the aforementioned period. By opting to categorize the data, two dimensions were obtained: pedagogical and educational management. This movement resulted in the characterization of the function as articulating, formative and transformative, from the point of view of the pedagogical dimension. As well as educational management consisting of leadership, democratic processes, participatory management and organizational culture and climate. (In)directly impacting the initial training of future mathematics teachers.

Herbarium data accurately predict the timing and duration of population‐level flowering displays

Forecasting the impacts of changing climate on the phenology of plant populations is essential for anticipating and managing potential ecological disruptions to biotic communities. Herbarium specimens enable assessments of plant phenology across broad spatiotemporal scales. However, specimens are collected opportunistically, and it is unclear whether their collection dates – used as proxies of phenological stages – are closest to the onset, peak, or termination of a phenophase, or whether sampled individuals represent early, average, or late occurrences in their populations. Despite this, no studies have assessed whether these uncertainties limit the utility of herbarium specimens for estimating the onset and termination of a phenophase. Using simulated data mimicking such uncertainties, we evaluated the accuracy with which the onset and termination of population‐level phenological displays (in this case, of flowering) can be predicted from natural‐history collections data (controlling for biases in collector behavior), and how the duration, variability, and responsiveness to climate of the flowering period of a species and temporal collection biases influence model accuracy. Estimates of population‐level onset and termination were highly accurate for a wide range of simulated species' attributes, but accuracy declined among species with longer individual‐level flowering duration and when there were temporal biases in sample collection, as is common among the earliest and latest‐flowering species. The amount of data required to model population‐level phenological displays is not impractical to obtain; model accuracy declined by less than 1 day as sample sizes rose from 300 to 1000 specimens. Our analyses of simulated data indicate that, absent pervasive biases in collection and if the climate conditions that affect phenological timing are correctly identified, specimen data can predict the onset, termination, and duration of a population's flowering period with similar accuracy to estimates of median flowering time that are commonplace in the literature.

First Report of Bacterial Leaf Spot Disease on Sesame (Sesamum indicum L.) Caused by Pseudomonas syringae pv. sesami in North Carolina.

In July 2022, dark brown to black, angular, water-soaked lesions were observed on sesame leaves (Sesamum indicum L.) in a research plot established to assess yield potential for eight varieties at the North Carolina (NC) Sandhills Research Station (Chavez 2023). Symptoms were indicative of a bacterial leaf spot (BLS). At early flowering stage, leaf spots were present on scattered plants; varieties ES108, SS3301, and ES201 exhibited up to 75% disease prevalence, with lower frequency in ES103, S39, S4302, S3251, and S3276. Symptomatic leaves from 3-4 plants were collected on four different dates from July through September. A section of symptomatic tissue was excised and macerated in sterile deionized water (SDW). A 10 µL aliquot was streaked onto SPA medium (15 g sucrose, 5.0 g proteose peptone, 0.50 g MgSO4 7H2O, 0.25 g K2HPO4, 15 g agar per liter of SDW) and incubated at 28ºC. After 72 h, numerous, smooth, white-cream colored, convex-shaped, colonies were individually isolated. Five randomly selected isolates from the different collection dates, designated as AHP108-AHP111 and AHP116, were genotyped. The 16S rRNA, gyrB, rpoD, and gapA genes were sequenced (Heuer et al. 1997; Hwang et al. 2005) and deposited to NCBI (GenBank Accessions: P213467- PP213470; OQ628040-OQ628042; PP214983-PP214994; and PP255798). These five isolates shared 100% sequence identity for gyrB and rpoD. AHP108-AHP111 shared 100% sequence identity for 16S rRNA and gapA, with 99.7% and 90.8% identity, respectively, for AHP116. A phylogenetic tree was inferred from a maximum-likelihood analysis of concatenated gyrB, rpoD, and gapA sequences of the five isolates and the top 11 hts from a blastn search of the NCBI nucleotide database. Those hits included closely related sequences from Pseudomonas syringae pv. sesami type strains ICMP 763T and ICMP 7459T. Based on this phylogenetic analysis AHP108-AHP111 and AHP116 are P. syringae pv. sesami. Recent genomic analysis suggests this pathovar is part of P. amygdali (Gomila et al. 2017), but an official name change has not been proposed. Each of the five isolates were infiltrated into leaves of sesame varieties ES108, ES103, and S327, consistently resulting in similar symptoms. Thus, strain AHP116, as a representative, was used to fulfill Koch's postulates using five, 30-day-old potted sesame plants (var. S3301). Plants were spray-inoculated with a bacterial suspension of ~108 CFU/ml until runoff; plants were incubated in moist chambers 24 h pre and post inoculation at 28ºC with 80% relative humidity and a 12 h photoperiod. At 13 days post inoculation, symptoms resembling those on plants at the Sandhills Research Stations in 2022 were evident. Reisolated bacteria were confirmed to be AHP116 through 16S rRNA and gyrB amplification and sequencing. No symptoms were observed on the five water-inoculated plants. BLS of sesame has been reported in Asia and is thought to be seedborne (Firdous et al. 2009; Prathuangwong and Yowabutra 1997). To our knowledge, this is the first report of P. syringae pv. sesami causing BLS on sesame in North Carolina. Sesame cultivation in the state increased from approximately 2,000 acres in 2022 to 13,000 acres in 2023 and there is interest in cultivating sesame as a rotational and alternative crop because it requires minimal input costs. Potential outbreaks of BLS in this warm, humid region could negatively affect sesame production, where little is known about the economic impact of the disease.

Designing formative feedback in collaborative online international learning

BACKGROUND: The adequate delivery of formative feedback in higher education is vigorously discussed to support the development of students’ learning activities. Most of the literature refers to individual feedback to students in the context of web-based training and teaching in higher education. However, concrete design recommendations are scarce, especially regarding collaborative online international learning modules. OBJECTIVE: This paper aims to identify and systematize the need for formative feedback from students in Virtual Exchange modules and concludes with implications for the design of formative feedback activities. METHODS: The research employs a two-step sequential explorative mixed methods and longitudinal approach. A quantitative pre-test is followed by a qualitative self-reflective journal survey with two data collection dates using a thematic co-occurrence analysis. RESULTS: Based on 11 abductively coded themes, findings include the effects of agents on students and barriers and prerequisites for implementing formative Feedback in COIL modules. CONCLUSIONS: The effects of feedback can vary depending on the agent. While e-tutors need to build trust and give orientation, teachers support reflection, and peers affect motivation. Applicable and quick responses are fundamental for a positive perception of formative feedback. Peer feedback can potentially improve learning and reduce the teacher’s workload.

Abstract LB345: Correlating the blood immune repertoire and clinical features of del17p CLL patients

Abstract Introduction: Deletion in the short arm of chromosome 17 (del17p) is a strong, negative prognostic biomarker found in about eight percent of patients with untreated chronic lymphocytic leukemia (CLL). CLL patients with del17p exhibit resistance to therapy, accelerated disease progression, and global immunodeficiency. It is unclear the extent to which global immunodeficiency impacts disease course and therapy outcomes. The goal of this study was to document the blood immune repertoire of patients with untreated CLL who have del17p and associate with clinical features, time to first treatment (TFT), and overall survival (OS). Methods: Biobanked blood samples from treatment-naïve del17p CLL patients (n = 58) and age-matched controls (n = 5) were obtained. B cells and T cells were analyzed with comprehensive, cell type-specific flow cytometry panels and visualized with unbiased dimensionality reduction. Lab values were log-transformed and compared using t-tests and one-way ANOVAs. TFT was calculated from date of sample collection to date of first CLL-directed therapy or last known untreated date; OS was calculated from date of sample collection to death or last known alive status. Cox proportional hazards regression analyses (results reported as hazard ratio [HR] and 95% confidence interval [CI]) were employed to identify associations of lab values with OS and TFT. Results: Patients with del17p CLL had increased proportions of T regulatory cells (Tregs) among total CD4+ T cells compared to controls (CLL 11.1%, control 5.7%, p = 0.05). A higher proportion of CD8+ T cells was associated with longer TFT (HR 0.57, 95%CI 0.36-0.89); in contrast, higher proportions of TIGIT+ (HR 1.83, 95%CI 1.03-3.28) and TIM3+ conventional (non-Treg) CD4+ T cells were associated with shorter TFT (HR 1.70, 95%CI 1.02-2.84). A higher proportion of PD1+ CD8+ T cells was associated with shorter OS (HR 1.79, 95%CI 1.05-3.06), in addition to PD1+ conventional CD4+ T cell proportion (HR 2.21, 95%CI 1.06-4.60). CLL B cells expressed PD-1 and inducible T cell costimulator (ICOS) at significantly lower median fluorescence intensities (MFIs) than control B cells (p < 0.0001 for both). The CXCR5+ MFI (HR 1.0002, 95%CI 1.0001-1.003) and CD23+ MFI (HR 1.88, 95%CI 1.01-3.50) of CLL B cells were associated with shorter TFT. Discussion: In this cohort of treatment-naïve del17p CLL patients, we determined that patients with higher proportions of exhausted CD4+ and CD8+ T cell phenotypes had significantly shorter OS. Cytotoxic T cell proportion positively associated with TFT, whereas proportions of CD4+ T cell exhaustion phenotypes negatively associated with TFT. Higher CXCR5+ and CD23+ MFIs of CLL B cells also associated with shorter TFT. The preliminary findings from our study suggest that the blood immune repertoire has strong associations with clinically relevant outcomes such as time to first treatment and overall survival in patients with untreated del17p CLL. Citation Format: Ethan J. Katcher, Kim A. Gwin, Sameer A. Parikh, Kari G. Rabe, Petra K. Lothert, Preeti Trisal, Esteban Braggio, Susan L. Slager, Nicholas Strong, Daniel L. Van Dyke, Zhiquan Wang, C. Chris Huang, Anita K. Gandhi, Kay L. Medina, Neil E. Kay. Correlating the blood immune repertoire and clinical features of del17p CLL patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB345.

Estimation of world seroprevalence of SARS-CoV-2 antibodies

In this paper, we estimate the seroprevalence against COVID-19 by country and derive the seroprevalence over the world. To estimate seroprevalence among adults, we use serological surveys (also called the serosurveys) conducted within each country. When the serosurveys are incorporated to estimate world seroprevalence, there are two issues. First, there are countries in which a serological survey has not been conducted. Second, the sample collection dates differ from country to country. We attempt to tackle these problems using the vaccination data, confirmed cases data, and national statistics. We construct Bayesian models to estimate the numbers of people who have antibodies produced by infection or vaccination separately. For the number of people with antibodies due to infection, we develop a hierarchical model for combining the information included in both confirmed cases data and national statistics. At the same time, we propose regression models to estimate missing values in the vaccination data. As of 31st of July 2021, using the proposed methods, we obtain the 95 % credible interval of the world seroprevalence as [ 35.5 % , 56.8 % ] .

Association between Fine Particulate Matter Exposure and Cerebrospinal Fluid Biomarkers of Alzheimer's Disease among a Cognitively Healthy Population-Based Cohort.

Epidemiological evidence suggests air pollution adversely affects cognition and increases the risk of Alzheimer's disease (AD), but little is known about the biological effects of fine particulate matter (, particulate matter with aerodynamic diameter ) on early predictors of future disease risk. We investigated the association between 1-, 3-, and 5-y exposure to ambient and traffic-related and cerebrospinal fluid (CSF) biomarkers of AD. We conducted a cross-sectional analysis using data from 1,113 cognitively healthy adults (45-75 y of age) from the Emory Healthy Brain Study in Georgia in the United States. CSF biomarker concentrations of , tTau, and pTau, were collected at enrollment (2016-2020) and analyzed with the Roche Elecsys system. Annual ambient and traffic-related residential concentrations were estimated at a and resolution, respectively, and computed for each participant's geocoded address, using three exposure time periods based on specimen collection date. Associations between and CSF biomarker concentrations, considering continuous and dichotomous (dichotomized at clinical cutoffs) outcomes, were estimated with multiple linear/logistic regression, respectively, controlling for potential confounders (age, gender, race, ethnicity, body mass index, and neighborhood socioeconomic status). Interquartile range (IQR; ) increases in 1-y [; 95% confidence interval (CI): , ] and 3-y (; 95% CI: , ) ambient exposures were negatively associated with CSF concentrations. Associations between ambient and were similar for 5-y estimates (; 95% CI: , 0.005). Dichotomized CSF variables revealed similar associations between ambient and . Associations with traffic-related were similar but not significant. Associations between exposures and tTau, pTau , or levels were mainly null. In our study, consistent trends were found between 1-y exposure and decreased CSF , which suggests an accumulation of amyloid plaques in the brain and an increased risk of developing AD. https://doi.org/10.1289/EHP13503.

45 Evaluation of Drug-Resistant Tuberculosis Guidelines and Outcomes by Treatment Site in South Africa

OBJECTIVES/GOALS: DR-TB care in South Africa includes decentralized treatment with shorter, all-oral regimens. Treatment guidelines direct regular clinical and laboratory evaluation to assess patient improvement. We therefore measured sputum collection frequency and follow-up time to assess fidelity to these guidelines in Gauteng Province, South Africa. METHODS/STUDY POPULATION: We included Rifampicin-resistant (RR) sputum specimens from the South African National Health Laboratory Service, which provides pathology services to 80% of the population, submitted between August 2022-September 2023. Patient data were obtained from a DR-TB registry and additional sputum specimen data were collected from follow-up laboratory worksheets. Follow-up spanned from first sputum collection date (baseline) to patient outcome date (e.g., completion, lost) or study closure date (if still on treatment). Monthly sputum submission rate was measured for those with ≥1 additional sputum submitted. We compared patient data by treatment site: at the specialized hospital vs. any other site, using Wilcoxon ranksum and χ2 tests. RESULTS/ANTICIPATED RESULTS: Baseline RR-TB specimens were available for 142 patients, of whom 28 (20%) had specimens submitted from the specialized hospital. Patients at the specialized hospital were older (median age 41 vs. 35.5 years, p=0.03), had higher baseline fluoroquinolone resistance (10% vs. 1%, p=0.01), and longer follow-up (median 5.2 vs. 3.5 months, p=0.01) compared to patients elsewhere. Further, 43 (30%) patients had ≥1 additional sputum submitted during follow-up. Among these, monthly sputum collection rates did not differ by site (0.3 vs. 0.3 sputum per month, p=0.89). We anticipate that increased sputum frequency will be associated with successful TB treatment outcomes based on preliminary findings. DISCUSSION/SIGNIFICANCE: These findings highlight ongoing challenges with routine laboratory follow-up according to DR-TB guidelines across treatment sites in South Africa. Future research is needed to determine reasons for low sputum collection rates, such as low patient adherence, variation in practice of healthcare workers, loss to follow-up, and clinical challenges.

Synergistic effects of L-glutamine and inorganic nitrogen molar ratios enhance the induction of somatic embryogenesis of Pinus maximinoi H.E. Moore

Clonal breeding programs of Pinus maximinoi require the establishment of a robust somatic embryogenesis (SE) protocol to produce enough cell lines to accelerate the effective continuous deployment of elite planting stocks to research and commercial compartments. Somatic embryogenesis was induced from immature zygotic embryo explants enclosed in megagametophytes of P. maximinoi collected from two plantations located in different climatic conditions. Cones were collected during the winter months from July to August and the influence of seed family, cone collection date and culture medium formulation, with emphasis on the organic and inorganic nitrogen supply, were studied. Ammonium to nitrate molar ratios of 1:1 and 1:2 in modified Litvay’s medium (mLV) produced the highest numbers of extrusions, while a 1:4 ratio mostly produced unhealthy, non-embryogenic extrusions. The formation of a tissue showing a rapidly-proliferating, spiky morphotype was produced in a medium supplemented with 1.5 g/L of L-glutamine. Morphologically advanced cultures with nodular structures were produced in megagametophytes from both plantations in a 1:2 NH4+:NO3− medium regardless of L-glutamine supplementation levels. The optimal medium for P. maximinoi SE induction contained a 1:2 NH4+:NO3− molar ratio with 1.5 g/L L-glutamine. The synergy between the molar ratio of NH4+:NO3− and L-glutamine resulted in the highest numbers of extrusions. The overall inductive competence window for somatic embryogenic response in P. maximinoi was determined to be from the second week of July to the first week of August for both plantations. The “peak” period was in the fourth week of July 2022. The success of the SE technology in P. maximinoi seed families is determined by the optimal inductive competence window of the immature megagametophytes enclosing zygotic embryos and the chemical composition of the induction medium in terms of the ammonium to nitrate molar ratio and the concentration of the L-glutamine used.

Evaluation of CoVid-19 infection among vaccinated and unvaccinated individuals using biochemical markers

The evaluation of infection rate for CoVid-19 cases among vaccinated and unvaccinated individuals using haematological parameters is of interest. Data such as age, gender, occupation, location, signs and symptoms, length of symptoms, date of sample collection and report generation, status of vaccinations, and outcome available in the database was used in this analysis. Ferritin levels, D-dimer values, CRP, troponin-1 levels and platelet count of each CoVid-19 patient were recorded and analysed. Data shows that maximum number of cases was reported during the second wave 143 (51.07%). The common age group affected was 31-40 years 28.56%. The common symptom identified was weakness in arms and legs among the unvaccinated group of CoVid-19 positive group. However, common symptom identified was fatigue (87%) among those who received only the first dose of CoVid vaccine. Nonetheless, the symptom identified was hair loss (68%) among those who received both the doses of CoVid vaccine. Thus, data shows that people do experience severe and life-threatening COVID-19 infection despite receiving the vaccination. Nonetheless, the infection is mild and very few individuals require hospitalization. No deaths are reported in the group that received the vaccination. This is in contrast to the unvaccinated group, which had a severe CoVid-19 infection with few deaths reported.

Amanita vidua: A NEW RECORD FOR TURKISH Amanita Section Phalloideae BASED ON MORPHOLOGICAL AND MOLECULAR DATA

The study involved collecting fungal specimens from Yeşildere village in Uşak province, Türkiye, on June 2, 2023. These specimens underwent detailed examination through both morphological and DNA (nrITS rDNA region and TEF1a gene) sequence-based phylogenetic analysis. Based on the evaluation of micro- and macromorphological characteristics, along with a high sequence similarity (over 99%) with Amanita vidua Gasch, G. Moreno & P.-A. Moreau, the specimen (labeled ANK Akata & Kaya 007) was identified as A. vidua. This identification marks A. vidua as a new record for the Turkish Amanita Sect. Phalloideae. The report describes this newly recorded species, including specific details such as its location, habitat observations, geographical coordinates, collection date, and photographs showcasing its macro and micromorphological features. Additionally, the report includes illustrations of microscopic and some microscopic structures of the species. The study is further enriched with images from a scanning electron microscope (SEM), offering a detailed view of the species' complex characteristics, and these findings are discussed briefly.

SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction–based assays in Addis Ababa, Ethiopia

ObjectivesThis study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)–based variant detection in Addis Ababa, Ethiopia. MethodsA cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. ResultsA total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. ConclusionsThe study data demonstrated that reverse transcription-PCR–based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.

Abstract 2502: Identification of poor responders to trastuzumab-deruxtecan with a multi-modal HER2-status predictor

Abstract Trastuzumab deruxtecan (TDXD) is approved for HER2 low or positive metastatic breast cancer. HER2-status is assessed through HER IHC and ERBB2 FISH assays. HER2-status has been shown to be correlated to RNA expression. This study aimed to assess if the addition of DNA to an RNA-based model can improve HER2-status prediction performance. Furthermore, to investigate the relationship between model score and outcomes for TDXD patients according to their overall survival (OS). Training and test sets of breast cancer samples were collected for HER2 status prediction (n = 1275, n = 397 respectively). HER2 status was reported positive: 11%, 12%, low: 61%, 60%, negative: 28%, 29% for each set respectively. HER2 testing and NGS were performed on samples with the same collection date. A TDXD discovery cohort of 284 patients included patients who received TDXD after RNA/DNA collection and had at least a 30-day follow-up. Metastatic disease was reported for 98% of the TDXD cohort. Receptor status was HR+/HER2- 39%, HR-/HER2- 17%, HR+/HER2+ 16%, HR-/HER2+ 9%, unknown 19%, and HER2-status was negative 11%, low 42%, and positive 27%, unknown 20%. OS was measured from medication start date. We trained a 12-gene linear model based on RNA expression and DNA copy number to predict HER2-positivity. The genes were selected by stepwise-selection on RNA and DNA features when predicting HER2-positivity using a random forest model. A baseline model consisting only of ERBB2 RNA expression was compared. Setting a HER2-positivity score threshold and allowing for an indeterminate group of 15% of the validation cohort, the RNA-DNA model achieved 91% PPA and 91% PPV in validation, whereas the RNA-only model achieved 83% PPA and 85% PPA. This indicates that the addition of DNA data improved the RNA-only HER2 predictor. The Concordance index of the RNA-DNA model score and OS for TDXD was 0.64. Characterizing this relationship, we partitioned the TDXD cohort to three equal sized sub-cohorts (33 1/3%) ordered by model score: low, intermediate, and high. Median OS in months for groups was: low 13.6, intermediate 18.5, and high 20.4. High-group patients had significantly better OS on TDXD compared to the low-group (HR = 0.39, log-rank p-value &amp;lt; 0.002). For patients with reported status, HER2-positivity rate in each group respectively was 6%, 16%, 85% (n=78), and HR-positivity in each group was 70%, 68%, 67% (n=156). Together, these findings indicate that HER2 status prediction improved by adding DNA to an RNA base predictor, and the predicted score was positively correlated with OS for TDXD. Citation Format: Kaveri Nadhamuni, Talal Ahmed, Mark Carty, Ben Terdich, Whitney L. Hensing, Timothy Taxter, Calvin Chao, Raphael Pelossof. Identification of poor responders to trastuzumab-deruxtecan with a multi-modal HER2-status predictor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2502.

Abstract 2318: Multimodal machine learning for the automatic classification of recurrent cancers

Abstract The National Cancer Institute’s (NCI) Surveillance, Epidemiology, and End Results (SEER) registries maintain and organize cancer incidence information allowing researchers to derive valuable insights into cancer epidemiology. While significant attention has been devoted to identifying cancers either from clinical text or through tabular data collected by SEER registries, there has been less emphasis on integrating these distinct modes of data. In our multimodal deep learning approach, we use longitudinal tabular data from the Consolidated Tumor Case (CTC) database that encompass a patient’s past diagnoses. This tabular information can augment clinical text to aid in the classification of pathology reports indicative of recurrent cancers. Four NCI SEER registries (Louisiana, New Jersey, Seattle and Utah) have manually labeled 61,150 pathology reports with one of six categories, which we refine into a four-class classification problem. Each pathology report is identified as either positive for recurrence, negative for recurrence/not disease free, new tumor, or an “other” (no malignancy/uncertain) class. Natural Language Processing techniques can extract meaningful information from clinical pathology reports, aiding in the identification of subtle indicators of recurrence by using relevant context. We use a hierarchical self-attention model (HiSAN) to construct document embeddings and classify the pathology report. To further enhance the predictive accuracy of our modeling approach we fuse the textual information from a pathology report with categorical data about patient’s cancer history. For each report, we create a patient context vector that encapsulates tumor-level information from patient’s previous cancer(s). The selected CTC records are associated with cancers diagnosed more than 120 days before the date of biospecimen collection stated in the pathology report. The patient context vector is crafted based on diverse categorical features; including cancer staging, patient age, treatment and sites of metastasis at the time of diagnosis. Features are represented using a combination of one-hot encoding and binning. Additionally, we employ patient and feature-level normalization to maintain proportional significance of features for individuals with multiple past diagnoses. We present preliminary results corresponding to different approaches for classifying cancer recurrence; first, we observe that using only the pathology reports as input yields an accuracy of 68%. Secondly, when using only CTC features with an XGBoost model, we achieve an accuracy of 49%. Finally we show that leveraging multiple data modalities, i.e. HiSAN generated pathology report embeddings and CTC data, significantly improves the model’s predictive accuracy to 76%. This research demonstrates a promising path forward in enhancing classification of clinical text by incorporating longitudinal patient history data. Citation Format: Patrycja Krawczuk, Zachary Fox, Dakota Murdock, Jennifer Doherty, Antoinette Stroupe, Stephen M. Schwartz, Lynne Penberthy, Elizabeth Hsu, Serban Negoita, Valentina Petkov, Heidi Hanson. Multimodal machine learning for the automatic classification of recurrent cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2318.

Abstract 225: Integration of patient-derived tumor organoids and patient clinical multimodal data to investigate the role of organoids in predicting treatment response

Abstract Introduction: Patient-derived organoids (PDOs) enable the ex vivo study of tumor heterogeneity and its effect on response to treatment. Our previous work demonstrated that our robust pan-cancer organoid platform shows genetic and transcriptomic concordance with clinical tumor samples and can be deployed for high-throughput drug response screening. Here, we ran a standard of care (SOC) panel on PDOs with paired de-identified clinically curated data to enable a comparison of patient response to the same drugs ex vivo and exploration of potentially more effective treatment alternatives. Methods: Patient tumor samples were cultivated into tumor PDOs in extracellular matrix + chemically defined media. PDOs underwent pathological review to ensure development of malignant tissue. PDOs were identified by clusters of Hoechst-positive cells and live and dead cell counts for each PDO were determined using fluorescent stains. The median number of cells per PDO in the well was calculated, excluding PDOs with &amp;lt;3 cells and the top 1% of PDOs by area. Drug screens were run with 6 doses of the compound and the inverse area under the curve of ToPro3 live cell measurements was calculated to quantify response. Tempus xT DNA-seq and xR whole-transcriptome assays were used to perform NGS on organoids and patient samples where available. Data was processed through our standard pipeline to identify targetable mutations, neoantigens, copy number variants (CNVs) and fusions. Results: We analyzed 38 PDOs with paired patient data across 9 different cancer types comprising mostly lung (n=14) and colorectal (n=12); 17 PDOs had responses associated with treatment given close to the biopsy collection date. Across the full PDO cohort, we observed a range of responses to SOC compounds, providing a platform to better understand biomarkers and mechanisms of response. Treatment response in PDOs correlated with patient response in many cases. In the 3 patients with progression-free survival &amp;gt;1 year and outcomes of either complete response or stable disease, all showed strong responses to the corresponding drugs in the SOC panel. For most patients with progressive disease recorded after treatment the corresponding PDO cluster showed limited response to treatment. The SOC panel includes several targeted therapies that provide insight into how patients respond to treatment beyond chemotherapy. For two patients with limited response to treatment in both patient and PDO, we identified targeted therapies relevant to their clinico-genomic landscape. One patient showed improved clinical outcomes to a later line of therapy with a similar mechanism of action to the drug that showed response in the organoid. Conclusion: These results suggest that PDOs may serve as a powerful tool for predicting patient response to treatment and aid the development of new therapies. Citation Format: Kathleen A. Burke, Brian Larsen, Yi-Hung Carol Tan, Jessica Barbeau, Curtis Brinkman, Elle Moore, Nick Callamaras, Jonathan R. Dry, Iker Huerga, Kate Sasser, Jeffrey A. Borgia. Integration of patient-derived tumor organoids and patient clinical multimodal data to investigate the role of organoids in predicting treatment response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 225.

Abstract 3432: Blood metabolomic profile of glioma risk: A pooled, multi-cohort analysis in COMETS

Abstract Although gliomas are relatively rare, they are among the most lethal malignancies. Yet, with the exception of ionizing radiation and family history, their etiologic factors remain largely unknown. We conducted an untargeted metabolomics investigation pooling nested case-control studies from 9 prospective cohorts (median age 63 years, 59% women) in the Consortium of Metabolomics Studies (COMETS). One cancer-free control was individually matched to each of the 803 glioma cases based on age, sex, self-identified race/ethnicity, and blood collection date. Using an ultrahigh-performance LC-MS/MS platform (Metabolon, Inc.), we identified 874 known metabolites in pre-diagnostic serum or plasma, and logistic regression models conditioned on the matching factors) estimated odds ratios (ORs) and 95% confidence intervals for the associations between 1-SD increases in circulating metabolites and glioma risk (Bonferroni corrected significance threshold P=5.7 × 10−5). A total of 58 metabolites were associated with glioma (P&amp;lt;0.05), with the top three being 3-methylglutarylcarnitine (OR=1.19; P=0.001), cholate (OR=0.85; P=0.001) and a sphingomyelin (SM) (d18:2/21:0, d16:2/23:0, OR=1.19; P=0.002). Analysis restricted to cases diagnosed &amp;gt;5 years after blood collection showed 51 metabolites associated with risk (P&amp;lt;0.05), including SM d18:2/23:1 (OR=1.32; P=5.2 × 10−5), and two other SMs (d18:2/21:0, d16:2/23:0 and d17:1/24:1(15Z)) (ORs=1.27 and 1.26, respectively; P&amp;lt;5.6 × 10−4). Our findings were not materially altered with further adjustment for smoking, BMI, height and diabetes. Analysis restricted to high-grade glioma cases (n=595) showed similar associations, whereas low-grade glioma (n=207) showed fewer metabolites related to risk (top signals of sphingosine, sphinganine and L-glutamic acid, each inversely associated). We did, however, observe that the 2-hydroxyglutarate/alpha-ketoglutarate ratio was significantly associated with low-grade disease (OR=2.9; P=0.0008), which was most pronounced among cases diagnosed &amp;gt;10 years following blood collection (OR=9.99; P=0.003). Glioblastoma (n=485) showed similar positive risk estimates including for 3-methylglutarylcarnitine which achieved Bonferroni significance (OR=1.35; P=3 × 10−5) and several SMs. In contrast, the top metabolite for astrocytoma risk (n=88) was tyrosine (OR=0.55; P=0.002). Gene-set and principal components analyses confirmed that the sub-pathways of SM, dihydro-SM, fatty acid, and dihydroceramide metabolism were significantly associated with overall glioma risk, and dihydro-SM, dihydroceramide, SM, lactosylceramide, glutathione, and purine metabolism were associated with high-grade glioma (all P values &amp;lt;0.05). These novel findings regarding altered metabolic pathways/dysregulation occurring years before glioma diagnoses may be related to etiologic factors or subclinical disease. Citation Format: Jiaqi Huang, Bin Zhao, Stephanie J. Weinstein, Marian L. Neuhouser, Steve C. Moore, Heather Eliassen, David J. Cote, Loic Le Marchand, Lorelei Mucci, Ying Yang, Victoria Stevens, Wei Zheng, Xiao-Ou Shu, Demetrius Albanes. Blood metabolomic profile of glioma risk: A pooled, multi-cohort analysis in COMETS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3432.

Circulating vaccine derived polio virus type 2 outbreak and response in Yemen, 2021–2022, a retrospective descriptive analysis

BackgroundThe outbreaks of circulating Vaccine Derived Polio Viruses (cVDPVs) have emerged as a major challenge for the final stage of polio eradication. In Yemen, an explosive outbreak of cVDPV2 was reported from August 2021 to December 2022. This study aims to compare the patterns of cVDPV2 outbreak, response measures taken by health authorities, and impacts in southern and northern governorates.MethodA retrospective descriptive study of confirmed cases of VDPV2 was performed. The data related to cVDPV2 as well as stool specimens and environmental samples that were shipped to WHO-accredited labs were collected by staff of surveillance. Frequencies and percentages were used to characterize and compare the confirmed cases from the southern and northern governorates. The average delayed time as a difference in days between the date of sample collection and lab confirmation was calculated.ResultsThe cVDPV2 was isolated from 227 AFP cases reported from 19/23 Yemeni governorates and from 83% (39/47) of environmental samples with an average of 7 months delayed from sample collection. However, the non-polio AFP (NPAFP) and adequate stool specimen rates in the north were 6.7 and 87% compared to 6.4 and 87% in the south, 86% (195) and 14%(32) out of the total 227 confirmed cases were detected from northern and southern governorates, respectively. The first and second cases of genetically linked isolates experienced paralysis onset on 30 August and 1st September 2021. They respectively were from Taiz and Marib governorates ruled by southern authorities that started vaccination campaigns as a response in February 2022. Thus, in contrast to 2021, the detected cases in 2022 from the total cases detected in the south were lower accounting for 22% (7 of 32) of compared to 79% (155 of 195) of the total cases the north.ConclusionA new emerging cVDPV2 was confirmed in Yemen. The result of this study highlighted the impact of vaccination campaigns in containing the cVDPV2 outbreak. Maintaining a high level of immunization coverage and switching to nOPV2 instead of tOPV and mOPV2 in campaigns are recommended and environmental surveillance should be expanded in such a risky country.

Quality methods in virtual and augmented reality with a focus on education: a systematic literature review

AbstractWith the goal of developing a unified approach for implementation of training for quality methods—with the help of innovative assistance systems—the current state of research is determined within the scope of this work. These quality methods include Quality Management Systems such as Lean Management and Six Sigma. A systematic literature search is conducted to determine the current state of research on Augmented and Virtual Reality data glasses, which are considered here as innovative assistance systems. This search extends without restriction to the date of data collection at the beginning of the year 2022, as Augmented and Virtual Reality data glasses are considered to be particularly immersive technologies. Based on the databases Scopus and Web of Science, an extended systematic literature review was used for the research. By answering the research question and classifying the implemented research work, an overview of the current state of virtual and augmented reality research will be given. This makes it clear that further research is needed, especially with regard to the training of quality methods, to develop specific models and action guidelines.

Comprehensive study on in vitro propagation of some imported peach rootstocks: in vitro explant surface sterilization and bud proliferation

The present study was conducted in the Laboratory of Tissue Culture, Horticulture Department, Faculty of Agriculture, Damietta University, Egypt. The objective of this study was to establish a micropropagation protocol suitable for three imported peach rootstocks: Okinawa (P. persica), Nemared (P. persica × P. davidiana) × P. persica), and Garnem (P. dulcis × P. persica) in vitro. The results showed that soaking the explants in sodium hypochlorite (NaOCl) at 20% for 15 min produced the highest responsiveness (82.81%), survival (96.61%), with the lowest mortality (3.14%) and contamination (0.24%). Explants of the Garnem genotype had the best response (89.12%), survival (90.62%), lowest mortality (0.00%), and highest contamination (9.37%) when compared to the other genotypes. In comparison with axillary buds, the shoot tip displayed the highest responsiveness, survival, and death (100, 87.40, and 12.59%, respectively), as well as the least significant contamination (0.00%). Additionally, the percentages of responsive, survived, dead, and contaminated explants at the various collection dates varied significantly. The 6-benzylaminopurine (BAP) concentrations used (3 to 5.0 mg/L) demonstrated similar behavior in terms of in vitro proliferation, with rates of 3.77 to 6.11, 4.33 to 8.88, and 3.33 to 7.44 shoot numbers per explant for the Okinawa, Nemared, and Garnem peach rootstocks, respectively, indicating that the number of shoot proliferations is genotype-dependent. Additionally, using 5.0 mg/L BAP in combination with 0.2 mg/L IBA significantly increased average shoot proliferation (96.29%), number of shoots per explant (7.48), and average leaf number/explant (16.33) compared to the other treatments. Based on these results, adventitious bud development was enhanced during in vitro multiplication of the Okinawa, Nemared, and Garnem peach rootstocks by the synergistic interaction of indole-butyric acid (IBA) and 6-benzylaminopurine (BAP).

A Survey and Analysis of the History of Ernest Henry Wilson’s Specimen Collections in China

Since the mid-17th century, Western plant collectors have explored Asia, particularly China, to collect native species for economic and botanical development. Ernest Henry Wilson (1876–1930) stands among the foremost figures in this pursuit. He conducted five plant collections in China between 1899 and 1918, gaining recognition for numerous valuable ornamental species. However, precise details such as the total number of specimens, a comprehensive species list, and the collection locations remained elusive, hindering a thorough assessment of his scientific contributions. To address this gap, we compiled data from various online databases and relevant publications, constructing a comprehensive dataset encompassing species names, collection dates, locations, and additional pertinent information. Employing Python, we organized and translated the species names and locations, facilitating analysis of families, genera, species, and the completeness and preferences of his collection. The conclusions drawn from the available data include 19,218 specimens, with 11,884 collection numbers, belonging to 200 families, 1046 genera, and 3794 species (including 342 infraspecific taxa). Wilson exhibited a preference for woody and flowering plants, resulting in a collection completeness of 25%. His collection spanned seven provinces, 28 prefecture-level cities, and 38 county-level areas, underscoring his significant contributions to the global dissemination of Chinese plant knowledge. This study conducts a comprehensive analysis of the plant specimens collected by Wilson in China, investigating their taxonomy, distribution, and historical context and evaluating Wilson’s contribution to plant dissemination. The findings serve as a valuable reference for subsequent biodiversity research endeavors.