Application of Machine Learning to the Prediction of Cancer-Associated Venous Thromboembolism

Venous thromboembolism (VTE) is a common and impactful complication of cancer. Several clinical prediction rules have been devised to estimate the risk of a thrombotic event in this patient population, however they are associated with limitations. We aimed to develop a predictive model of cancer-associated VTE using machine learning as a means to better integrate all available data, improve prediction accuracy and allow applicability regardless of timing for systemic therapy administration. A retrospective cohort was used to fit and validate the models, consisting of adult patients who had next generation sequencing performed on their solid tumor for the years 2014 to 2019. A deep learning survival model limited to demographic, cancer-specific, laboratory and pharmacological predictors was selected based on results from training data for 23,800 individuals and was evaluated on an internal validation set including 5,951 individuals, yielding a time-dependent concordance index of 0.72 (95% CI = 0.70-0.74) for the first 6 months of observation. Adapted models also performed well overall compared to the Khorana Score (KS) in two external cohorts of individuals starting systemic therapy; in an external validation set of 1,250 patients, the C-index was 0.71 (95% CI = 0.65-0.77) for the deep learning model vs 0.66 (95% CI = 0.59-0.72) for the KS and in a smaller external cohort of 358 patients the C-index was 0.59 (95% CI = 0.50-0.69) for the deep learning model vs 0.56 (95% CI = 0.48-0.64) for the KS. The proportions of patients accurately reclassified by the deep learning model were 25% and 26% respectively. In this large cohort of patients with a broad range of solid malignancies and at different phases of systemic therapy, the use of deep learning resulted in improved accuracy for VTE incidence predictions. Additional studies are needed to further assess the validity of this model.

Relations of Current and Past Cancer with Severe Outcomes among 104,590 Hospitalized COVID-19 Patients: The COVID EHR Cohort at the University of Wisconsin

BACKGROUND

There is mixed evidence about the relations of current versus past cancer with severe COVID-19 outcomes and how they vary by patient and cancer characteristics.

METHODS

Electronic health record data of 104,590 adult hospitalized patients with COVID-19 were obtained from 21 United States health systems from February 2020 through September 2021. In-hospital mortality and ICU admission were predicted from current and past cancer diagnoses. Moderation by patient characteristics, vaccination status, cancer type, and year of the pandemic was examined.

RESULTS

6.8% of the patients had current (n = 7,141) and 6.5% had past (n = 6,749) cancer diagnoses. Current cancer predicted both severe outcomes but past cancer did not; adjusted odds ratios (aOR) for mortality were 1.58 [95% confidence interval (CI), 1.46-1.70] and 1.04 (95% CI, 0.96-1.13), respectively. Mortality rates decreased over the pandemic but the incremental risk of current cancer persisted, with the increment being larger among younger vs. older patients. Prior COVID-19 vaccination reduced mortality generally and among those with current cancer (aOR, 0.69; 95% CI, 0.53-0.90).

CONCLUSIONS

Current cancer, especially among younger patients, posed a substantially increased risk for death and ICU admission among patients with COVID-19; prior COVID-19 vaccination mitigated the risk associated with current cancer. Past history of cancer was not associated with higher risks for severe COVID-19 outcomes for most cancer types.

IMPACT

This study clarifies the characteristics that modify the risk associated with cancer on severe COVID-19 outcomes across the first 20 months of the COVID-19 pandemic. See related commentary by Egan et al., p. 3.

Effectiveness of MRNA booster vaccine among healthcare workers in New York City during the Omicron surge, December 2021 to January 2022

OBJECTIVE

To describe effectiveness of mRNA vaccines by comparing 2-dose (2D) and 3-dose (3D) healthcare worker (HCW) recipients in the setting of Omicron variant dominance. Performance of 2D and 3D vaccine series against SARS-CoV-2 variants and the clinical outcomes of HCWs may inform return-to-work guidance.

METHODS

In a retrospective study from December 15, 2020 to January 15, 2022, SARS-CoV-2 infections among HCWs at a large tertiary cancer centre in New York City were examined to estimate infection rates (aggregated positive tests / person-days) and 95% CIs over the Omicron period in 3D and 2D mRNA vaccinated HCWs and were compared using rate ratios. We described the clinical features of post-vaccine infections and impact of prior (pre-Omicron) COVID infection on vaccine effectiveness.

RESULTS

Among the 20857 HCWs in our cohort, 20,660 completed the 2D series with an mRNA vaccine during our study period and 12461 had received a third dose by January 15, 2022. The infection rate ratio for 3D versus 2D vaccinated HCWs was 0.667 (95% CI 0.623, 0.713) for an estimated 3D vaccine effectiveness of 33.3% compared to two doses only during the Omicron dominant period from December 15, 2021 to January 15, 2022. Breakthrough Omicron infections after 3D + 14 days occurred in 1,315 HCWs. Omicron infections were mild, with 16% of 3D and 11% 2D HCWs being asymptomatic.

DISCUSSION

Study demonstrates improved vaccine-derived protection against COVID-19 infection in 3D versus 2D mRNA vaccinees during the Omicron surge. The advantage of 3D vaccination was maintained irrespective of prior COVID-19 infection status.

Implementing a Clinical Decision Tool to Improve Oncologic Venous Thromboembolism Management

Background:

Cancer patients with venous thromboembolic (VTE) disease are complex, and many factors must be considered when initiating anticoagulation management. Clinical decision support systems can aid in decision-making by utilizing guidelines at the point of care.

Objectives:

The purpose of our project was to develop, implement, and evaluate an electronic clinical decision tool (CDT) utilizing evidence-based guidelines to aid in decision-making for adult oncologic patients who present with new VTE to symptom care clinics.

Methods:

We compared a pre-intervention group of patients who were prescribed anticoagulation (n = 98) with two post-intervention groups: CDT applied (n = 96) and not applied (n = 46). Outcomes included whether the CDT anticoagulation recommendations were followed and if the tool was perceived to be helpful or improve confidence in initiating management for new VTE by the SCC advanced practitioners and physicians.

Results:

There was no significant difference between the pre- and post-intervention groups in how many of the CDT anticoagulation recommendations were followed (68.8% pre-intervention, 60.8% post-intervention tool applied, and 63.5% post-intervention tool not applied; χ² [2, N = 161] = .921, p = .631). However, the tool was found to be helpful and improved confidence of the providers in initiating management for new VTE (pre median = 3, interquartile range [IQR] = 2, 3.5; post median = 3, IQR 3, 4; p = .033).

Conclusion:

This CDT provided evidence-based anticoagulation recommendations for cancer-associated VTE and enhanced familiarity with the standard of care. Further development of the CDT will be required to account for situations that resulted in deviation from the recommendations.

Clinical and Genomic Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Infections in mRNA Vaccinated Health Care Personnel in New York City

BACKGROUND

Vaccine-induced clinical protection against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) variants is an evolving target. There are limited genomic level data on SARS CoV-2 breakthrough infections and vaccine effectiveness (VE) since the global spread of the B.1.617.2 (Delta) variant.

METHODS

In a retrospective study from 1 November 2020 to 31 August 2021, divided as pre-Delta and Delta-dominant periods, laboratory-confirmed SARS CoV-2 infections among healthcare personnel (HCP) at a large tertiary cancer center in New York City were examined to compare the weekly infection rate-ratio in vaccinated, partially vaccinated, and unvaccinated HCP. We describe the clinical and genomic epidemiologic features of post-vaccine infections to assess for selection of variants of concern (VOC)/variants of interest (VOI) in the early post-vaccine period and impact of B.1.617.2 (Delta) variant domination on VE.

RESULTS

Among 13658 HCP in our cohort, 12379 received at least 1 dose of a messenger RNA (mRNA) vaccine. In the pre-Delta period overall VE was 94.5%. Whole genome sequencing (WGS) of 369 isolates in the pre-Delta period did not reveal a clade bias for VOC/VOI specific to post-vaccine infections. VE in the Delta dominant phase was 75.6%. No hospitalizations occurred among vaccinated HCP in the entire study period, compared to 17 hospitalizations and 1 death among unvaccinated HCP.

CONCLUSIONS

Findings show high VE among HCP in New York City in the pre-Delta phase, with moderate decline in VE post-Delta emergence. SARS CoV-2 clades were similarly distributed among vaccinated and unvaccinated infected HCP without apparent clustering during the pre-Delta period of diverse clade circulation. Strong vaccine protection against hospitalization was maintained through the entire study period.

Poor predictive value of cytomegalovirus (CMV)-specific T cell assays for the development of CMV retinitis in patients with AIDS

BACKGROUND

We examined the potential clinical utility of using a cytomegalovirus (CMV)-specific T cell immunoassay to determine the risk of developing new-onset CMV retinitis (CMVR) in patients with acquired immunodeficiency syndrome (AIDS).

METHODS

CMV-specific T cell assays were performed by multiparameter flow cytometry using stored peripheral blood mononuclear cells that had been obtained in an observational study 2-6 months before new-onset CMVR was diagnosed in case patients (at a study visit during which a dilated ophthalmologic examination revealed no evidence of CMVR) and at the same study visit in control subjects (matched by absolute CD4(+) T cell count at entry) who did not subsequently develop retinitis during 1-6 years of study follow-up.

RESULTS

There were no significant differences in CMV-specific CD4(+) or CD8(+) T cell interferon-gamma or interleukin-2 expression in peripheral blood mononuclear cells from case patients and control subjects. Although there were trends toward lower percentages and absolute numbers of CMV-specific, cytokine-expressing CD8(+) T cells with a "late memory" phenotype (CD27(-)CD28(-)) as well as with an "early memory" phenotype (CD27(+)CD28(+)CD45RA(+)) in case patients than in control subjects, these differences were not statistically significant.

CONCLUSIONS

Many studies have reported that CMV-specific CD4(+) and CD8(+) T cell responses distinguish patients with active CMVR (i.e., who lack CMV-protective immunity) from those with inactive CMVR after immune restoration by antiretroviral treatment (i.e., who have CMV-protective immunity). However, the multiple CMV-specific immune responses we measured do not appear to have clinical utility for predicting the risk for patients with AIDS of developing new-onset CMVR with sufficient accuracy to be used in guiding therapeutic management.

Factors affecting knee cartilage volume in healthy men

OBJECTIVES

To understand the factors that influence joint cartilage in health and disease as they are important for the prevention and management of osteoarthritis.

METHODS

We conducted a cross-sectional study to determine factors influencing knee cartilage volume in 45 males aged (mean+/-S.D.) 52.5+/-13.2 yr.

RESULTS

Total and medial tibial volumes were inversely associated with age, body mass index (BMI) and amount of physical activity and positively associated with total bone content. BMI explained the largest amount of the variation in tibial cartilage volume (18.7%). There were similar findings at the lateral tibial cartilage, but for age and total bone content this did not reach statistical significance. There was a positive association with serum testosterone at all tibial cartilage sites, but this only reached statistical significance for medial tibial cartilage, where serum testosterone explained up to 8% of the variation in cartilage volume.

CONCLUSIONS

Modifiable risk factors of osteoarthritis also appear to be significant determinants of tibial cartilage volume. Serum testosterone may provide one possible explanation for gender differences in tibial cartilage volume and prevalence of tibiofemoral osteoarthritis. The proposed link between osteoarthritis and knee cartilage volume and the effect of testosterone will need to be confirmed in longitudinal studies.

Effects of calcitriol or calcium on bone mineral density, bone turnover, and fractures in men with primary osteoporosis: a two-year randomized, double blind, double placebo study

Osteoporosis in men is an emerging public health problem. As calcitriol reduces the rate of vertebral fractures in osteoporotic postmenopausal women, we conducted a prospective study of this treatment in men with primary osteoporosis. Our study was a 2-yr, randomized, double masked, double placebo-controlled trial of calcitriol (0.25 microg twice daily) or calcium (500 mg twice daily) in 41 men with primary osteoporosis and at least 1 baseline fragility fracture. Thirty-three men (85%) completed the study. There were no differences in baseline characteristics. Spinal and femoral neck bone mineral densities at 2 yr were unchanged in both groups. Serum osteocalcin decreased in both groups by 30% (P < 0.05), whereas urine N-telopeptide cross-links decreased only in the calcium group by 30% (P < 0.05). After 2 yr, fractional calcium absorption increased by 34% (P < 0.01) in the calcitriol group. Nineteen incident fragility fractures occurred (14 vertebral and 5 nonvertebral) in 7 men. Over 2 yr, the number of men with vertebral fractures (6 vs. 1; P = 0.097) was similar in both groups. In conclusion, the efficacy of calcitriol remains unproven as a single agent for the treatment of osteoporosis in men.

Overexpression of macrophage colony-stimulating factor receptor on microglial cells induces an inflammatory response

Microglia are important in the inflammatory response in Alzheimer's disease (AD). We showed previously that macrophage colony-stimulating factor receptor (M-CSFR), encoded by the c-fms protooncogene, is overexpressed on microglia surrounding amyloid beta (Abeta) deposits in the APP(V717F) mouse model for AD. The M-CSFR is also increased on microglia after experimental brain injury and in AD. To determine the relevance of these findings, we transiently expressed M-CSFR on murine BV-2 and human SV-A3 microglial cell lines using an SV40-promoted c-fms construct. M-CSFR overexpression resulted in microglial proliferation and increased expression of inducible nitric-oxide synthase, the proinflammatory cytokines interleukin-1alpha, macrophage inflammatory protein 1-alpha, and interleukin-6 and of macrophage colony-stimulating factor (M-CSF) itself. Antibody neutralization of M-CSF showed that the M-CSFR-induced proinflammatory response was dependent on M-CSF in the culture media. By using a co-culture of c-fms-transfected murine microglia and rat organotypic hippocampal slices and a species-specific real time reverse transcriptase-polymerase chain reaction assay and enzyme-linked immunosorbent assay, we showed that M-CSFR overexpression on exogenous microglia induced expression of interleukin-1alpha by the organotypic culture. These results show that increased M-CSFR expression induces microglial proliferation, cytokine expression, and a paracrine inflammatory response, suggesting that in APP(V717F) mice increased M-CSFR on microglia could be an important factor in Abeta-induced inflammatory response.

DNA hypomethylation perturbs the function and survival of CNS neurons in postnatal animals

DNA methyltransferase I (Dnmt1), the maintenance enzyme for DNA cytosine methylation, is expressed at high levels in the CNS during embryogenesis and after birth. Because embryos deficient for Dnmt1 die at gastrulation, the role of Dnmt1 in the development and function of the nervous system could not be studied by using this mutation. We therefore used the cre/loxP system to produce conditional mutants that lack Dnmt1 in neuroblasts of embryonic day 12 embryos or in postmitotic neurons of the postnatal animal. Conditional deletion of the Dnmt1 gene resulted in rapid depletion of Dnmt1 proteins, indicating that the enzyme in postmitotic neurons turns over quickly. Dnmt1 deficiency in postmitotic neurons neither affected levels of global DNA methylation nor influenced cell survival during postnatal life. In contrast, Dnmt1 deficiency in mitotic CNS precursor cells resulted in DNA hypomethylation in daughter cells. Whereas mutant embryos carrying 95% hypomethylated cells in the brain died immediately after birth because of respiratory distress, mosaic animals with 30% hypomethylated CNS cells were viable into adulthood. However, these mutant cells were eliminated quickly from the brain within 3 weeks of postnatal life. Thus, hypomethylated CNS neurons were impaired functionally and were selected against at postnatal stages.

A Porphyromonas gingivalis genetic locus encoding a heme transport system

Porphyromonas gingivalis has been implicated in the onset and progression of periodontitis and the availability of hemin for in vitro growth has been associated with virulence of the bacterium in animal models. We report here the cloning and sequence analysis of a P. gingivalis TonB-linked outer membrane receptor gene tlr. This gene was previously identified as a TonB-linked adhesin gene tla and shown to be essential for growth at low concentrations of hemin. The tlr gene is immediately downstream of four open reading frames (htrABCD) that encode a putative ATP binding cassette transport system with sequence similarlity to heme transport systems of other bacteria. Analysis of P. gingivalis W50 mRNA revealed that the htrABCD genes are cotranscribed similar to hemin transport genes of other bacteria.

Placebo-controlled trial assessing the use of oral midazolam as a premedication to conscious sedation for pediatric endoscopy

BACKGROUND

This study was performed to evaluate the effect of midazolam, as premedication before intravenous conscious sedation, on preprocedural, procedural, and post-procedural patient comfort and anxiety in children undergoing endoscopy.

METHODS

A placebo-controlled, double-blind, randomized study was conducted in 123 children (age 7.75 +/- 4.46 years, 56% male) using oral midazolam (0.5 mg/kg, maximum 20 mg) as a premedication before insertion of an intravenous access device (i.v.) and upper endoscopy. Patients were evaluated with regard to changes in vital signs, level of sedation during i.v. placement, level of pre- and post-procedure conscious sedation, ease of separation from parents, ease and duration of procedure, recovery time, and amnesia to objects shown before i.v. placement and immediately before the start of the procedure.

RESULTS

A significant difference was noted in the study group for the following parameters: level of sedation for i.v. placement (p < 0.0001), pre-procedural sedation (p < 0.001), ease of i.v. insertion (p < 0.003), ease of separation from parents (p = 0.022), and ease of the nursing personnel's ability to monitor the patient during the procedure (p = 0.0012). The patient's amnesia to an object shown immediately before beginning the endoscopy was increased (p < 0.001). Patients and parents were also more satisfied with the procedure process (p < 0.05). No significant difference was noted with regard to the length or performance of the procedure or recovery time or in the dose of i.v. medication required for successful completion of the endoscopy.

CONCLUSION

Oral midazolam is an effective and safe premedication for children undergoing upper endoscopy and should be used in all anxious children and in patients previously judged to be difficult to sedate.

The prognostic value of thyrotropin receptor antibody measurement in the early stages of treatment of Graves' disease with antithyroid drugs

In most trials, at least 50% of patients with Graves' disease treated with antithyroid drugs (ATD) relapse after achieving euthyroidism. At present, there are no definitive prognostic parameters available early in treatment to indicate those likely to achieve long-term remission. Because thyrotropin receptor antibodies (TRAb) are specific for Graves' disease, the possibility that their rate of change early in treatment (0 to 6 months) might be such an indicator was explored. TRAb were measured both as thyrotropin binding inhibitory immunoglobulins (TBII) and as thyroid-stimulating antibodies (TSAb) in 85 patients with untreated Graves' disease at 6-month intervals throughout their ATD treatment. The patients in the study were treated for a minimum period of 12 months and were categorized retrospectively into two groups depending on whether or not they remained in remission after ATD treatment. Remission was deemed as reached in patients who remained euthyroid for a minimum period of 15 months after cessation of ATD. The mean initial TBII and TSAb values in the nonremission group were significantly higher than in the remission group (p < 0.001 for both parameters). The rates of fall in mean TBII levels were similar for each group in the first 6 months of treatment, but while they continued to fall in the remission group over the next 6 to 12 months, mean values for the nonremission group plateaued and failed to fall to control levels within that period. These results indicate that changes in TRAb levels, measured either as TBII or TSAb, occur more rapidly in the second 6 months of treatment in patients who ultimately achieve remission than those who do not. If TBII fall to control levels by 12 months, the patient has at least a 70% chance of ultimately achieving remission with ATD treatment alone.

Studies of the surgical scrub

BACKGROUND

To evaluate the effectiveness of various scrub techniques in reducing bacterial skin flora, the present study was developed in three stages.

METHODS

Each stage involved fingertip bacterial colony counts measured before, immediately after and 30 min after a variety of handwashing techniques using 10% povidone iodine solution. The first compared 1, 2 or 3 non-timed washes from fingertips to elbows in 10 volunteers. The second compared two volunteers scrubbing for equal durations with or without friction rubbing, while the third involved 15 volunteers who each scrubbed for different time intervals.

RESULTS

The first stage showed that a single wash episode failed to provide lasting bacterial colony count reductions on fingertip cultures. The second showed that enduring colony count reductions occur whether friction rubbing of the hands was used or not, and the third showed that a 30 s wash was as effective as washing for longer periods in reducing fingertip flora.

CONCLUSIONS

These findings suggest that prolonged vigorous pre-operative scrubbing is unnecessary, although more than a cursory wash is required to produce lasting fingertip antisepsis.

A placebo-controlled trial using intravenous atropine as an adjunct to conscious sedation in pediatric esophagogastroduodenoscopy

BACKGROUND

The usefulness of intravenous atropine as an adjunct to conscious sedation in pediatric esophagogastroduodenoscopy remains an unresolved issue.

METHODS

This prospective, double-blind, randomized study examined 101 patients, who were randomized to receive either intravenous atropine 0.02 mg/kg (maximum 0.4 mg) or a placebo of normal saline solution prior to the procedure.

RESULTS

The mean maximum heart rate during the procedure and the percentage of time that the heart rate was more than 1 standard deviation above mean for age was significantly greater in the atropine group as compared to the placebo group (p < 0.0005). There was no significant difference between groups in the amount of secretions noted, gastric motility, retching or vomiting, facial flushing, or dysphoria. There were no causes of significant bradycardia or hypotension in either group. There was a significant number of patients greater than 5 years of age and receiving meperidine and atropine (as compared with meperidine and placebo) whose arterial oxygen saturation dropped below 90% during the procedure (p = 0.0485).

CONCLUSIONS

We found that the use of atropine when used as an adjunct to conscious sedation in children undergoing upper endoscopy did not increase the safety of the procedure or provide significant benefits. We do not recommend the routine use of atropine for upper endoscopy in pediatric patients.

Specific effects of radioiodine treatment on TSAb and TBAb levels in patients with Graves' disease

Radioactive iodine (RAI)-induced changes in the levels of antibodies to the thyroid-stimulating hormone (TSH) receptor (TRAb) in patients undergoing treatment for autoimmune thyroid disease have been well documented. Previous studies have reported effects on the overall level of the antibodies present, TSH-binding inhibitory immunoglobulins (TBII), without detailed studies of specific effects on the levels of thyroid-stimulating (TSAb) or thyroid-blocking antibodies (TBAb). More detailed studies have been reported only in individual cases. In this study, the values of TSAb, TBAb, and TBII were measured longitudinally in 33 patients (27 females and 6 males) who received RAI. The bioassays for TSAb and TBAb were performed in JPO9 cells. Following RAI, there were significant and immediate effects on the values of TBII in 70% of patients. TBII levels fell in 7 patients (20%) (Group 1), rose in 16 patients (48%) (Group 2) or remained unchanged but elevated in 10 patients (32%) (Group 3). In the Group 1 patients, only TSAb were detectable and none of these patients became hypothyroid after treatment. In the 16 patients in Group 2, increases in TBII were attributable to specific increases in TSAb in 7 (44%), in TBAb in 3 (19%), and in both TSAb and TBAb in 3 (19%). There were 3 patients (19%) in this group in whom there was no detectable TSAb or TBAb activity despite the increase in TBII. Six patients from this group became hypothyroid within 6 months of RAI treatment.(ABSTRACT TRUNCATED AT 250 WORDS)

Apparatus for studying fretting fatique in vacuum

Recent investigations on the mechanism of fretting fatigue have indicated that mechanical damage, not chemical corrosion, has the largest effect in decreasing structural component life. Since there is no general agreement on the mechanism of fretting fatigue, an experiment has been designed to evaluate statistically the relative role of the mechanical process and the chemical process in reducing fatigue life. An initial step was to develop an apparatus that allows fretting fatigue tests to be performed in both laboratory air and vacuum environments. A detailed discussion of the experimental apparatus and experimental procedure are presented in this paper. Also typical test results are presented. It is found that fretting fatigue in vacuum is about ten times slower than that in laboratory air. Fractographic analysis of the wear surface indicated that less severe fretting damage occurred in the vacuum environment.