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Annotations enrich text corpora and provide necessary labels for natural language processing studies. To reason and infer underlying implicit knowledge captured by labels, an ontology is needed to provide a semantically annotated corpus with structured domain knowledge. Utilizing a corpus of adverse event documents annotated for sepsis-related signs and symptoms as a use case, this paper details how a terminology and corresponding ontology were developed. The Annotated Adverse Event NOte TErminology (AAENOTE) represents annotated documents and assists annotators in annotating text. In contrast, the complementary Catheter Infection Indications Ontology (CIIO) is intended for clinician use and captures domain knowledge needed to reason and infer implicit information from data. The approach taken makes ontology development understandable and accessible to domain experts without formal ontology training.

In the cancer population, patients diagnosed with venous thromboembolism (VTE) are considered to have a threefold increased risk of mortality compared with those without VTE. With the advent of modern computed tomography (CT), the rate of diagnosis of subsegmental pulmonary embolism (SSPE) has increased, likely as a result of improved visualization of the peripheral pulmonary arteries. The clinical significance of SSPE remains unclear because of the lack of randomized controlled clinical trials. The aim of this study was to identify the incidence and risk factors of recurrent proximal PE within 12 months of diagnosis of SSPE in cancer. We performed a retrospective analysis of 206 adult cancer patients who were diagnosed with SSPE from 2014 to 2016 at the University of Texas MD Anderson Cancer Center. At the time of SSPE diagnosis, the majority had metastatic cancer, 108 patients (53.2%) were undergoing chemotherapy, and 23 patients (11.2%) had a history of VTE. Most patients had an Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 2. Sixty-seven percent of SSPE was discovered incidentally on restaging CT scans, with the majority being a single and isolated event (70.9%). Within 12 months of SSPE diagnosis, 18 patients (8.7%) were found to have a recurrent PE. The patients treated with anticoagulation had a lower rate of PE recurrence (8% vs 13% in those not treated with anticoagulation). Treatment with anticoagulation did not appear to have a significant impact on overall survival (P = .48) when adjusted for ECOG performance status and cancer stage.

In the cancer population, patients diagnosed with venous thromboembolism (VTE) are considered to have a threefold increased risk of mortality compared with those without VTE. With the advent of modern computed tomography (CT), the rate of diagnosis of subsegmental pulmonary embolism (SSPE) has increased, likely as a result of improved visualization of the peripheral pulmonary arteries. The clinical significance of SSPE remains unclear because of the lack of randomized controlled clinical trials. The aim of this study was to identify the incidence and risk factors of recurrent proximal PE within 12 months of diagnosis of SSPE in cancer. We performed a retrospective analysis of 206 adult cancer patients who were diagnosed with SSPE from 2014 to 2016 at the University of Texas MD Anderson Cancer Center. At the time of SSPE diagnosis, the majority had metastatic cancer, 108 patients (53.2%) were undergoing chemotherapy, and 23 patients (11.2%) had a history of VTE. Most patients had an Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 2. Sixty-seven percent of SSPE was discovered incidentally on restaging CT scans, with the majority being a single and isolated event (70.9%). Within 12 months of SSPE diagnosis, 18 patients (8.7%) were found to have a recurrent PE. The patients treated with anticoagulation had a lower rate of PE recurrence (8% vs 13% in those not treated with anticoagulation). Treatment with anticoagulation did not appear to have a significant impact on overall survival (P= .48) when adjusted for ECOG performance status and cancer stage.

Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously showed that human preimplantation embryos encapsulate missegregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N= 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping showed that these chromosome-containing cellular fragments (CCFs) can be maternally or paternally derived and display double-stranded DNA breaks. DNA breakage was further indicated by reciprocal subchromosomal losses/gains between blastomeres and large segmental errors primarily detected at the terminal ends of chromosomes. By combining time-lapse imaging with scDNA-seq, we determined that multipolar divisions at the zygote or two-cell stage were associated with CCFs and generated a random mixture of chromosomally normal and abnormal blastomeres with uniparental or biparental origins. Despite frequent chromosome missegregation at the cleavage-stage, we show that CCFs and nondividing aneuploid blastomeres showing extensive DNA damage are prevented from incorporation into blastocysts. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination via cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.

Background:Acute pulmonary embolism (PE) is a leading cause of morbidity in the cancer population. The availability of computed tomographic (CT) scans and CT-pulmonary angiography (CT-PA) has allowed for better visualization of the peripheral pulmonary arteries and assessment of PE, resulting in greater detection of subsegmental pulmonary embolism (SSPE). The clinical outcomes and the factors determining PE recurrence are not clear in the cancer related-SSPE population.