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At least 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Tumor-Infiltrating Lymphocytes in a Contemporary Cohort of Women with Ductal Carcinoma In Situ (DCIS)

Background: Growing evidence suggests that the tumor immune microenvironment influences breast cancer development and prognosis. Density of tumor-infiltrating lymphocytes (TILs) within invasive breast cancer is correlated with response to therapy, especially in triple-negative disease. The clinical relevance and outcomes of TILs within ductal carcinoma in situ (DCIS) are less understood. Methods: Our institutional database of 668 patients with pure DCIS from 2010 to 2018 was queried. TILs were evaluated by International TILs Working Group guidelines. Percentage of TILs was assessed from the densest focus (hotspot) in one high-power field of stroma touching the basement membrane. Statistical methods included cluster analyses (to define sparse versus dense TILs), logistic, and Cox regression models. Results: Sixty-nine patients with DCIS and TILs were evaluated, of whom 54 (78%) were treated by breast-conserving surgery. Thirteen (19%) patients had ipsilateral recurrence. Each recurrence (n = 13) was matched to four controls (n = 56) based on date of surgery. Median follow-up was 6.7 years. TILs were defined as sparse (< 45%) or dense (≥ 45%). Dense TILs were associated with younger age (p = 0.045), larger tumor size (p < 0.001), high nuclear grade (p = 0.010), comedo histology (p = 0.033), necrosis (p = 0.027), estrogen receptor (ER) negativity (p = 0.037), and ipsilateral recurrence (p = 0.001). Nine patients with dense TILs had mean time to recurrence of 73.5 months compared with four patients with sparse TILs with mean time to recurrence of 97.9 months (p = 0.003). Conclusions: Dense TILs were significantly associated with age, tumor size, nuclear grade, comedo histology, necrosis, and ER status and was a significant predictor of recurrence in patients with pure DCIS.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Surgical Management of the Axilla in Clinically Node-Positive Patients Receiving Neoadjuvant Chemotherapy: A National Cancer Database Analysis

Background: The feasibility of sentinel lymph node biopsy (SLNB) in patients with clinically node-positive (cN+) disease who convert to clinically node-negative (cN0) disease following neoadjuvant chemotherapy (NAC) has been evaluated in several large clinical trials, but it remains unclear whether the approach has been broadly adopted in the United States. Methods: The National Cancer Database was used to identify women diagnosed with cN+ breast cancer who received NAC followed by surgery between 2012 and 2015. Trends in axillary surgery were evaluated and multivariable logistic regression analyses performed to determine factors associated with receipt of SLNB. Results: Of 12,965 women cN+ at baseline, the use of SLNB increased from 31.8% in 2012 to 49% in 2015 (p < 0.001). Using axillary pCR as a surrogate for patients who convert to cN0 following NAC, among 5127 (39.5%) ypN0 patients, SLNB increased from 38.2 to 58.4% over the study period (p < 0.001), resulting in avoidance of axillary dissection in 42.2% of ypN0 patients by 2015. In adjusted analyses, factors significantly associated with SLNB attempt included cN1 disease, age < 45 years, treatment facility type, triple-negative and HER2-positive subtypes, and year of diagnosis. In women with residual isolated tumor cells (ITCs), micrometastases, and ypN1 disease, SLNB was the only axillary procedure performed in 36.9%, 23.6%, and 13.0% of cases. Conclusions: The use of SLNB in cN+ patients receiving NAC increased significantly between 2012 and 2015. SLNB alone was performed in more than 10% of patients with ypN1 disease, 20% with micrometastases, and 35% with ITCs; the oncologic safety of omitting axillary dissection in these patients requires further evaluation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Better Defining the Role of Total Neoadjuvant Radiation: Changing Paradigms in Locally Advanced Pancreatic Cancer

Background: This study was designed to better define the role of radiation (Neo-Rad) in addition to neoadjuvant multiagent chemotherapy (NAT) for the treatment of locally advanced pancreatic cancer. Methods: Retrospective cohort study using the NCDB. Individuals with AJCC clinical T3/T4 pancreatic carcinoma who underwent resection and multiagent chemotherapy were included. Kaplan–Meier, logistic-regression, and Cox proportional-hazard models were used for analysis. Results: A total of 2703 patients were included; 2039 had T3 and 664 had T4 tumors, and 1092 (40.4%) received Neo-Rad. Median follow-up was 22.5 months. During the study period, there was increased use of NAT and a decline in the use of Neo-Rad. Addition of Neo-Rad did not affect 30-day (2.51% vs. 3.24%, p = 0.272) or 90-day mortality (5.23% vs. 6.38%, p = 0.216). Neo-Rad was not associated with improved overall survival on univariable (25.95 vs. 24.7 months, p = 0.202), or multivariable analyses (hazard ratio [HR] 0.94; 95% confidence interval [CI] 0.85–1.05). Time from diagnosis to definitive surgery was increased by Neo-Rad (204 vs. 115 days, p < 0.001). Neo-Rad was associated with increased pathologic downstaging in T3 (32.8% vs. 14.4%) (odds ratio [OR] 2.90; 95% CI 2.30–3.66) and T4 tumors (88.9% vs. 77.8%) (OR 2.29; 95% CI 1.44–3.67); complete pathologic response (5.3% vs. 1.6%) (OR 2.89; 95% CI 1.73–4.83), and increased R0 resection rates (85.7% vs. 76.8%) (OR 1.79; 95% CI 1.44–2.23). Conclusions: The use of neoadjuvant therapy is increasing for the treatment of locally advanced pancreatic cancer. The addition of radiation to neoadjuvant chemotherapy is associated with improved antineoplastic effectiveness (downstaging, complete pathologic response), surgical resection (R0 rates), but has no effect on overall survival.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Ductal Carcinoma In Situ with Microinvasion on Core Biopsy: Evaluating Tumor Upstaging Rate, Lymph Node Metastasis Rate, and Associated Predictive Variables

Introduction: The role of sentinel lymph node biopsy (SLNB) when ductal carcinoma in situ with microinvasion (DCISM) is identified on core biopsy is unclear. Objective: Our aim was to assess the upstage rate to invasive cancer and axillary lymph node metastasis in patients diagnosed with DCISM, and whether predictive variables could be identified that may help inform who would most likely benefit from a surgical axillary evaluation. Methods: We performed a retrospective review of 70 patients diagnosed with DCISM on core biopsy. Patients with concomitant or prior invasive cancer were excluded. Demographic, clinical, radiographic, histologic, and treatment data were collected. Fisher’s exact test and univariable and multivariable logistic regression were performed to identify variables that may be associated with tumor upstaging and nodal metastasis. Time-to-event distributions were summarized using the Kaplan–Meier method. Results: On final surgical pathology, 49 patients (70%) had a final diagnosis of DCISM or T1mi cancer, whereas 21 patients (30%) were upstaged to measurable invasive cancer (> 1 mm). One of 49 patients (2%) with DCISM on final pathology and 4 of 21 patients (19%) with measurable invasive cancer showed sentinel lymph node metastases. Conclusion: Although the upstage rate to measurable invasive cancer in our cohort of patients with DCISM on core biopsy was 30%, findings of a positive SLNB remain low at 7%. No predictive variables were identified to inform whether the routine practice of SLNB may be omitted in some patients with DCISM.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Risk of Positive Sentinel Lymph Node After Neoadjuvant Systemic Therapy in Clinically Node-Negative Breast Cancer: Implications for Postmastectomy Radiation Therapy and Immediate Breast Reconstruction

Background: Residual axillary lymph node involvement after neoadjuvant systemic therapy (NST) is the determining factor for postmastectomy radiation therapy (PMRT). Preoperative identification of patients needing PMRT is essential to enable shared decision-making when choosing the optimal timing of breast reconstruction. We determined the risk of positive sentinel lymph node (SLN) after NST in clinically node-negative (cN0) breast cancer. Methods: All cT1-3N0 patients treated with NST followed by mastectomy and SLNB between 2010 and 2016 were identified from the Netherlands Cancer Registry. Rate of positive SLN for different breast cancer subtypes was determined. Logistic regression analysis was performed to determine correlated clinicopathological variables with positive SLN. Results: In total 788 patients were included, of whom 25.0% (197/788) had positive SLN. cT1-3N0 ER+HER2+, cT1-3N0 ER−HER2+ , and cT1-2N0 triple-negative patients had the lowest rate of positive SLN: 7.2–11.5%, 0–6.3%, and 2.9–6.2%, respectively. cT1-3N0 ER+HER2− and cT3N0 triple-negative patients had the highest rate of positive SLN: 23.8–41.7% and 30.4%, respectively. Multivariable regression analysis showed that cT2 (odds ratio [OR] 1.93; 95% confidence interval [CI] 1.01–3.96), cT3 (OR 2.56; 95% CI 1.30–5.38), grade 3 (OR 0.44; 95% CI 0.21–0.91), and ER+HER2− subtype (OR 3.94; 95% CI 1.77–8.74) were correlated with positive SLN. Conclusions: In cT1-3N0 ER+HER2+, cT1-3N0 ER−HER2+, and cT1-2N0 triple-negative patients treated with NST, immediate reconstruction can be considered an acceptable option due to low risk of positive SLN. In cT1-3N0 ER+HER2− and cT3N0 triple-negative patients treated with NST, risks and benefits of immediate reconstruction should be discussed with patients due to the relatively high risk of positive SLN.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Does Breast Density Increase the Risk of Re-excision for Women with Breast Cancer Having Breast-Conservation Therapy?

Background: Women with dense breasts may have less-accurate preoperative evaluation of extent of disease, potentially affecting the achievement of negative margins. The goal of this study is to examine the association between breast density and re-excision rates in women having breast-conserving surgery for invasive breast cancer. Patients and Methods: Women with stage I/II invasive breast cancer treated with breast-conserving surgery between 1/1/2014 and 10/31/2014 were included. Breast density was assessed by two radiologists. The association between breast density and re-excision was examined using logistic regression. Results: Seven hundred and one women were included. Overall, 106 (15.1%) women had at least one re-excision. Younger age at diagnosis was associated with increased breast density (p < 0.001). On univariable analysis, increased breast density was associated with significantly increased odds of re-excision (odds ratio [OR] 1.38, 95% confidence interval [CI] 1.04–1.83), as was multifocal disease, human epidermal growth factor receptor 2 (HER2) positive status, and extensive intraductal component (EIC) (all p < 0.05). On multivariable analysis, breast density remained significantly associated with increased odds of re-excision (OR 1.37, 95% CI 1.00–1.86), as did multifocality and EIC. HER2 positive status was not significantly associated with re-excision on multivariable analysis. Conclusions: Women with dense breasts are more likely to need additional surgery (re-excision after breast-conserving surgery), but increased breast density did not adversely affect disease-free survival in our study. Our findings support the need for further study in developing techniques that can help decrease re-excisions for women with dense breasts who undergo breast-conserving surgery.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Squamous Cell Carcinoma with Regional Metastasis to Axilla or Groin Lymph Nodes: a Multicenter Outcome Analysis

Background: Cutaneous squamous cell carcinoma (cSCC) of the trunk/extremities with nodal metastasis represents a rare but significant clinical challenge. Treatment patterns and outcomes are poorly described. Patients and Methods: Patients with cSCC who developed axilla/groin lymph node metastasis and underwent curative-intent surgery between 2005 and 2015 were identified at four Canadian academic centers. Demographics, tumor characteristics, treatment patterns, recurrence rates, and mortality were described. Overall survival (OS) and disease-free survival (DFS) were calculated using Kaplan–Meier analysis. Predictors of survival and any recurrence were explored using Cox regression and logistic regression models, respectively. Results: Of 43 patients, 70% were male (median age 74 years). Median follow-up was 38 months. Median time to nodal metastasis was 11.3 months. Thirty-one and 12 patients had nodal metastasis to the axilla and groin, respectively. A total of 72% and 7% received adjuvant and neoadjuvant radiation, respectively, while 5% received adjuvant chemotherapy. Following surgery, 26% patients developed nodal and/or distant disease recurrence. Crude mortality rate was 39.5%. Mean OS was 5.3 years [95% confidence interval (CI) 3.9–6.8 years], and 5-year OS was 55.1%. Mean DFS was 4.8 years (95% CI 3.3–6.2 years), and five-year DFS was 49.3%. Any recurrence was the only independent predictor of death [p = 0.036, odds ratio (OR) = 29.5], and extracapsular extension (p = 0.028, OR = 189) and age (p = 0.017, OR = 0.823) were independent predictors of recurrence. Conclusions: This represents the largest contemporary series to date of outcomes for patients with axilla/groin nodal metastases from cSCC. Despite aggressive treatment, outcomes remain modest, indicating the need for a continued multidisciplinary approach and integration of new systemic agents.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Trends in Regional Nodal Management of Breast Cancer Patients with Low Nodal Burden

Background: American College of Surgeons Oncology Group Z0011 confirms the safety of omitting axillary lymph node dissection (ALND) and regional nodal irradiation (RNI) in breast cancer patients with one to two positive sentinel lymph nodes (SLNs), without compromising disease-free survival (DFS) and overall survival (OS). In contrast, the NCIC MA20 trial showed improved DFS in node-positive patients undergoing ALND and RNI. We sought to examine how these data have influenced the management of patients with limited nodal burden. Methods: Using the National Cancer Database, patients diagnosed between 2010 and 2015 and who met the criteria for Z0011 were identified. Logistic regression was used to analyze factors associated with practice patterns. The Cox proportional hazards model was used to assess the association of ALND and RNI with OS. Results: Omission of ALND in Z0011-eligible patients reached 89.2% in 2015. This Z0011-compliant group was more likely to undergo RNI compared with the non-compliant group (36.4% vs. 31.3%; p < 0.05), with RNI increasing to 43.8% by 2015. Factors associated with the use of RNI included later year of diagnosis [odds ratio (OR) 1.8, 95% confidence interval (CI) 1.6–2.1], hormone receptor-negative tumor (OR 1.2, 95% CI 1.1–1.4), grade 3 tumor (OR 1.2, 95% CI 1.1–1.3), treatment at a non-academic site (OR 1.2, 95% CI 1.1–1.3) and two versus one positive SLN (OR 2.0, 95% CI 1.8–2.2). With 43 months median follow-up, RNI was not associated with improved OS. Conclusion: Since the publication of Z0011, the omission of ALND has become widespread; however nearly half of these women now receive RNI. The optimal radiation therapy approach for this low nodal burden population warrants further study.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Public Acceptance of Pre-Commercial Thinning and Energy and Soil Amendment Products from Post-Harvest Residues in Western Forests of the United States

Abstract . The goals of the Waste-to-Wisdom project is to produce bioenergy products and biochar from post-harvest forest residues and thus understanding public acceptance of the forest management and utilizing forest residues for biomass-based products is critical. This research explores the public perceptions of producing bioenergy products and biochar from forest thinning activities in the western Pacific Northwest region. A web-based survey was conducted in Washington, Oregon, and Northern California generating 1,202 responses. Multinomial regression techniques and simulation-based approach were applied to analyze how demographic and socio-economic factors influence public perceptions. People living in less populated areas are more likely to support forest thinning. Higher levels of education and household income also lead to higher levels of support for forest thinning. On the other hand, supports for forest thinning results in supports for using forest residuals to produce bioenergy products. These results suggest that different strategies are necessary to effectively communicate the environmental and ecological benefits of using forest residuals derived from forest thinning activities to produce biomass-based products. Keywords: Environmental Perceptions, Multinomial Logistic Regression, Natural Resource Management, Rural vs. Urban, Simulation-Based Approach.

Agriculture↗
DOE OSTI2018

Strategies for Reducing Moisture Content in Forest Residues at the Harvest Site

Abstract. The moisture content (MC) of biomass derived from forest residues can pose a challenge to biomass utilization. It plays a significant role in determining the cost of transportation and subsequent market price. Additionally, emerging biomass conversion technologies, such as gasification, torrefaction, and briquetting, have very narrow specifications for the MC (e.g., <15%) in their feedstocks. The goal of this study was to develop strategies for reducing moisture content by evaluating different arrangement patterns of forest residues and its effect on MC reduction at the harvest site. The study compared four different arrangement patterns including criss-cross, teepees, traditional piling (processor piled), and scattered residues in three different timber harvest units in northern California. Two of the arrangement patterns (criss-cross and processor piled) were also covered with a plastic cover. Samples were collected from each treatment using a transect method and were recorded for 12 months. There was an overall drop of MC from 52% (freshly cut) to 12% between all arrangements over the study period. The cost of construction per pile, averaged $37, $41, and $48 for teepees, criss-cross, and processor piles, respectively. Even though, there was no significant difference in MC reduction between piles (except scattered), each pile arrangement of forest residues directly affected biomass feedstock operations, logistics, and costs. Keywords: Feedstock quality, Logging slash, Transect sampling method, Woody biomass energy.

Agriculture↗
DOE OSTI2020

Early prediction of antigenic transitions for influenza A/H3N2

Influenza A/H3N2 is a rapidly evolving virus which experiences major antigenic transitions every two to eight years. Anticipating the timing and outcome of transitions is critical to developing effective seasonal influenza vaccines. Using a published phylodynamic model of influenza transmission, we identified indicators of future evolutionary success for an emerging antigenic cluster and quantified fundamental trade-offs in our ability to make such predictions. The eventual fate of a new cluster depends on its initial epidemiological growth rate––which is a function of mutational load and population susceptibility to the cluster––along with the variance in growth rate across co-circulating viruses. Logistic regression can predict whether a cluster at 5% relative frequency will eventually succeed with ~80% sensitivity, providing up to eight months advance warning. As a cluster expands, the predictions improve while the lead-time for vaccine development and other interventions decreases. However, attempts to make comparable predictions from 12 years of empirical influenza surveillance data, which are far sparser and more coarse-grained, achieve only 56% sensitivity. By expanding influenza surveillance to obtain more granular estimates of the frequencies of and population-wide susceptibility to emerging viruses, we can better anticipate major antigenic transitions. This provides added incentives for accelerating the vaccine production cycle to reduce the lead time required for strain selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Geographic Mosaic of Climate Change Impacts on Terrestrial Vegetation: Which Areas Are Most at Risk?

Changes in climate projected for the 21st century are expected to trigger widespread and pervasive biotic impacts. Forecasting these changes and their implications for ecosystem services is a major research goal. Much of the research on biotic responses to climate change has focused on either projected shifts in individual species distributions or broad-scale changes in biome distributions. Here, we introduce a novel application of multinomial logistic regression as a powerful approach to model vegetation distributions and potential responses to 21st century climate change. We modeled the distribution of 22 major vegetation types, most defined by a single dominant woody species, across the San Francisco Bay Area. Predictor variables included climate and topographic variables. The novel aspect of our model is the output: a vector of relative probabilities for each vegetation type in each location within the study domain. The model was then projected for 54 future climate scenarios, spanning a representative range of temperature and precipitation projections from the CMIP3 and CMIP5 ensembles. We found that sensitivity of vegetation to climate change is highly heterogeneous across the region. Surprisingly, sensitivity to climate change is higher closer to the coast, on lower insolation, north-facing slopes and in areas of higher precipitation. While such sites may provide refugia for mesic and cool-adapted vegetation in the face of a warming climate, the model suggests they will still be highly dynamic and relatively sensitive to climate-driven vegetation transitions. The greater sensitivity of moist and low insolation sites is an unexpected outcome that challenges views on the location and stability of climate refugia. Projections provide a foundation for conservation planning and land management, and highlight the need for a greater understanding of the mechanisms and time scales of potential climate-driven vegetation transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Virologic outcome among patients receiving antiretroviral therapy at five hospitals in Haiti

Introduction Viral load (VL) assessment is the preferred method for diagnosing and confirming virologic failure for patients on antiretroviral therapy (ART). We conducted a retrospective cross-sectional study to evaluate the virologic suppression rate among patients on ART for 6 months in five hospitals around Port-au-Prince, Haiti. Methods Plasma VL was measured and patients with VL <1,000 copies/mL were defined as virologically suppressed. A second VL test was performed within at least six months of the first test. Factors associated with virologic suppression were analyzed using logistic regression models accounting for site-level clustering using complex survey procedures. Results Data were analyzed for 2,313 patients on ART for six months or longer between July 2013 and February 2015. Among them, 1,563 (67.6%) achieved virologic suppression at the first VL test. A second VL test was performed within at least six months for 718 (31.0%) of the patients. Of the 459 patients with an initial HIV-1 RNA <1,000 copies/mL who had a second VL performed, 394 (85.8%) maintained virologic suppression. Virologic suppression was negatively associated with male gender (adjusted odds ratio [aOR]: 0.80, 95% CI: 0.74– 0.0.86), 23 to 35 months on ART (aOR:0.72[0.54–0.96]), baseline CD4 counts of 201–500 cells/mm 3 and 200 cells/mm 3 or lower (aORs: 0.77 [0.62–0.95] and 0.80 [0.66–0.98], respectively), poor adherence (aOR: 0.69 [0.59–0.81]), and TB co-infection (aOR: 0.73 [0.55–0.97]). Conclusions This study showed that over two-thirds of the patients in this evaluation achieved virologic suppression after six months on ART and the majority of them remained suppressed. These results reinforce the importance of expanding access to HIV-1 viral load testing in Haiti for monitoring ART outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Development and validation of a 30-day mortality index based on pre-existing medical administrative data from 13,323 COVID-19 patients: The Veterans Health Administration COVID-19 (VACO) Index

Background Available COVID-19 mortality indices are limited to acute inpatient data. Using nationwide medical administrative data available prior to SARS-CoV-2 infection from the US Veterans Health Administration (VA), we developed the VA COVID-19 (VACO) 30-day mortality index and validated the index in two independent, prospective samples. Methods and findings We reviewed SARS-CoV-2 testing results within the VA between February 8 and August 18, 2020. The sample was split into a development cohort (test positive between March 2 and April 15, 2020), an early validation cohort (test positive between April 16 and May 18, 2020), and a late validation cohort (test positive between May 19 and July 19, 2020). Our logistic regression model in the development cohort considered demographics (age, sex, race/ethnicity), and pre-existing medical conditions and the Charlson Comorbidity Index (CCI) derived from ICD-10 diagnosis codes. Weights were fixed to create the VACO Index that was then validated by comparing area under receiver operating characteristic curves (AUC) in the early and late validation cohorts and among important validation cohort subgroups defined by sex, race/ethnicity, and geographic region. We also evaluated calibration curves and the range of predictions generated within age categories. 13,323 individuals tested positive for SARS-CoV-2 (median age: 63 years; 91% male; 42% non-Hispanic Black). We observed 480/3,681 (13%) deaths in development, 253/2,151 (12%) deaths in the early validation cohort, and 403/7,491 (5%) deaths in the late validation cohort. Age, multimorbidity described with CCI, and a history of myocardial infarction or peripheral vascular disease were independently associated with mortality–no other individual comorbid diagnosis provided additional information. The VACO Index discriminated mortality in development (AUC = 0.79, 95% CI: 0.77–0.81), and in early (AUC = 0.81 95% CI: 0.78–0.83) and late (AUC = 0.84, 95% CI: 0.78–0.86) validation. The VACO Index allows personalized estimates of 30-day mortality after COVID-19 infection. For example, among those aged 60–64 years, overall mortality was estimated at 9% (95% CI: 6–11%). The Index further discriminated risk in this age stratum from 4% (95% CI: 3–7%) to 21% (95% CI: 12–31%), depending on sex and comorbid disease. Conclusion Prior to infection, demographics and comorbid conditions can discriminate COVID-19 mortality risk overall and within age strata. The VACO Index reproducibly identified individuals at substantial risk of COVID-19 mortality who might consider continuing social distancing, despite relaxed state and local guidelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Development and validation of a diabetes risk score among two populations

The purpose of this study was to assess the validity of a practical diabetes risk score amongst two heterogenous populations, a working population and a non-working population. Study population 1 (n = 2,089) participated in a large-scale screening program offered to retired workers to discover previously undetected/incipient chronic illness. Study population 2 (n = 3,293) was part of a Colorado worksite wellness program health risk assessment. We assessed the relationship between a continuous diabetes risk score at baseline and development of diabetes in the future using logistic regression. Receiver operating curves and sensitivity/specificity of the models were calculated. Across both study populations, we observed that participants with diabetes at follow-up had higher diabetes risk scores at baseline than participants who did not have diabetes at follow-up. On average, the odds ratio of developing diabetes in the future was 1.38 (95% CI: 1.26–1.50, p < 0.0001) for study population 1 and 1.68 (95% CI: 1.45–1.95, p-value < 0.0001) for study population 2. These findings indicate that the diabetes risk score may be generalizable to diverse individuals, and thus potentially a population level diabetes screening tool. Minimally-invasive diabetes risk scores can aid in the identification of sub-populations of individuals at risk for diabetes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Gamma radiation sterilization of N95 respirators leads to decreased respirator performance

In response to personal protective equipment (PPE) shortages in the United States due to the Coronavirus Disease 2019, two models of N95 respirators were evaluated for reuse after gamma radiation sterilization. Gamma sterilization is attractive for PPE reuse because it can sterilize large quantities of material through hermetically sealed packaging, providing safety and logistic benefits. The Gamma Irradiation Facility at Sandia National Laboratories was used to irradiate N95 filtering facepiece respirators to a sterilization dose of 25 kGy(tissue). Aerosol particle filtration performance testing and electrostatic field measurements were used to determine the efficacy of the respirators after irradiation. Both respirator models exhibited statistically significant decreases in particle filtering efficiencies and electrostatic potential after irradiation. The largest decrease in capture efficiency was 40–50% and peaked near the 200 nm particle size. The key contribution of this effort is correlating the electrostatic potential change of individual filtration layer of the respirator with the decrease filtration efficiency after irradiation. This observation occurred in both variations of N95 respirator that we tested. Electrostatic potential measurement of the filtration layer is a key indicator for predicting filtration efficiency loss.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗