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At least 1,441 records · Page 80

Perceptions of Barriers Towards Active Surveillance for Low-Risk Prostate Cancer: Results From a National Survey of Radiation Oncologists and Urologists

Purpose: The reasons for low clinical adoption of active surveillance (AS) for low-risk prostate cancer (PCa) remain poorly understood. Thus, we conducted a national survey of radiation oncologists (ROs) and urologists (UROs) to elucidate perceived barriers to AS for low-risk PCa. Methods: In 2017, we undertook a four-wave mail survey of 1855 ROs and UROs. The survey instrument assessed attitudes about possible barriers towards AS for low-risk PCa. We used Pearson Chi square and multivariable logistic regression analyses to identify physician characteristics associated with attitudes about AS. Results: We received 691 completed surveys for an overall response rate of 37.3%. A majority of respondents indicated that they felt comfortable recommending AS (90.0%), agreed that high-level evidence supports it (82.3%), and considered AS equally effective for survival compared with surgery and radiation therapy (84.4%). UROs were less likely to agree that patients were not interested in AS for low-risk PCa compared with ROs (16.5 vs. 48.9%; adjusted odds ratio [OR] 0.18, p < 0.001). Similarly, UROs were less likely to concur patients avoid AS because of repeat prostate biopsies than ROs (36.3 vs. 55.4%; adjusted OR 0.41, p < 0.001). ROs and UROs were more likely to agree that patients preferred treatments delivered by the respondent’s specialty. Conclusions: Physician perceptions of patient lack of interest in AS, need for repeat prostate biopsies, and biases of patient treatment preferences in favor of their own specialty treatments represent key barriers to AS. Shared decision making may be a meaningful approach to engaging patients in conversations about treatment decisions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Intrahepatic Cholangiocarcinoma: Socioeconomic Discrepancies, Contemporary Treatment Approaches and Survival Trends from the National Cancer Database

Objective: The aim of this study was to evaluate socioeconomic discrepancies in current treatment approaches and survival trends among patients with intrahepatic cholangiocarcinoma (ICC). Methods: The 2004–2015 National Cancer Database was retrospectively analyzed for histopathologically proven ICC. Treatment predictors were evaluated using multinomial logistic regression and overall survival via multivariable Cox models. Results: Overall, 12,837 ICC patients were included. Multiple factors influenced treatment allocation, including age, education, comorbidities, cancer stage, grade, treatment center, and US state region (multivariable p < 0.05). The highest surgery rates were observed in the Middle Atlantic (28.7%) and lowest rates were observed in the Mountain States (18.4%). Decreased ICC treatment likelihood was observed for male African Americans with Medicaid insurance and those with low income (multivariable p < 0.05). Socioeconomic treatment discrepancies translated into decreased overall survival for patients of male sex (vs. female; hazard ratio [HR] 1.21, 95% confidence interval [CI] 1.16–1.26, p < 0.001), with low income (< $37,999 vs. ≥ $63,000 annually; HR 1.07, 95% CI 1.01–1.14, p = 0.032), and with Medicaid insurance (vs. private insurance; HR 1.13, 95% CI 1.04–1.23, p = 0.006). Both surgical and non-surgical ICC management showed increased survival compared with no treatment, with the longest survival for surgery (5-year overall survival for surgery, 33.5%; interventional oncology, 11.8%; radiation oncology/chemotherapy, 4.4%; no treatment, 3.3%). Among non-surgically treated patients, interventional oncology yielded the longest survival versus radiation oncology/chemotherapy (HR 0.73, 95% CI 0.65–0.82, p < 0.001). Conclusions: ICC treatment allocation and outcome demonstrated a marked variation depending on socioeconomic status, demography, cancer factors, and US geography. Healthcare providers should address these discrepancies by providing surgery and interventional oncology as first-line treatment to all eligible patients, with special attention to the vulnerable populations identified in this study.

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DCIS with Microinvasion: Is It In Situ or Invasive Disease?

Background: Ductal carcinoma in situ (DCIS) with microinvasion (DCISM) can be challenging in balancing the risks of overtreatment versus undertreatment. We compared DCISM, pure DCIS, and small volume (T1a) invasive ductal carcinoma (IDC) as related to histopathology, treatment patterns, and survival outcomes. Methods: Women ages 18–90 years who underwent breast surgery for DCIS, DCISM, or T1a IDC were selected from the SEER Database (2004–2015). Multivariate logistic regression and Cox proportional hazards models were used to estimate the association of diagnosis with treatment and survival, respectively. Results: A total of 134,569 women were identified: 3.2% DCISM, 70.9% DCIS, and 25.9% with T1a IDC. Compared with invasive disease, DCISM was less likely to be ER+ or PR+ and more likely to be HER2+. After adjustment, DCIS and invasive patients were less likely to undergo mastectomy than DCISM patients (DCIS: OR 0.53, 95% CI 0.49–0.56; invasive: OR 0.86, CI 0.81–0.92). For those undergoing lumpectomy, the likelihood of receiving radiation was similar for DCISM and invasive patients but lower for DCIS patients (OR 0.57, CI 0.52–0.63). After adjustment, breast-cancer-specific survival was significantly different between DCISM and the other two groups (DCIS: HR 0.59, CI 0.43–0.8; invasive: HR 1.43, CI 1.04–1.96). However, overall survival was not significantly different between DCISM and invasive disease, whereas patients with DCIS had improved OS (HR 0.83, CI 0.75–0.93). Conclusions: Although DCISM is a distinct entity, current treatment patterns and prognosis are comparable to those with small volume IDC. These findings may help providers counsel patients and determine appropriate treatment plans.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Outcomes of > 1300 Nipple-Sparing Mastectomies with Immediate Reconstruction: The Impact of Expanding Indications on Complications

Background: The enhanced esthetics and demonstrated oncologic safety of nipple-sparing mastectomy (NSM) in selected patients have resulted in increased rates among patients with locally advanced breast cancer and/or additional risk factors (obesity, prior radiation, surgery). Limited data exist on complication and reconstruction success rates in a contemporary patient cohort with expanded indications for NSM. Methods: With institutional review board (IRB) approval, patients treated from 2009 to 2017 with NSM were identified from our prospective breast surgery registry. Main outcomes were 30-day complications requiring treatment and 1-year reconstruction failure rates. Risk factors were assessed using logistic regression. Results: We evaluated 1301 breasts in 769 women undergoing NSM for cancer (n = 555) or risk reduction (n = 746) with median age of 48 (range 21–77) years. The overall 30-day complication rate was 7.5% (97/1301 breasts) and declined from 14.8% in 2009 to 6.3% in 2017 (p < 0.001), while the proportion of patients with obesity (p = 0.007) and treated with neoadjuvant chemotherapy (p < 0.001) increased. Prior radiation [odds ratio (OR) 2.35, p = 0.04], recent/current smoking (OR 3.37, p < 0.001), and body mass index (BMI) (OR 1.28 per 5-kg/m{sup 2} increase, p = 0.03) significantly increased 30-day complication rates. Reconstruction success at 1 year was 96.7%. Prior radiation (OR 5.65, p < 0.001), axillary surgery (OR 2.55, p = 0.006), and postoperative adjuvant radiation (OR 3.22, p = 0.007) significantly affected 1-year reconstruction failure. Conclusion: The 30-day complication rates of NSM decreased, despite broadened indications among higher-risk patients over time. These data confirm a team learning curve with NSM and also demonstrate that the nipple-sparing approach is suitable for appropriately selected higher-risk patients for both risk reduction and cancer treatment.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

Towards Estimation of HIV-1 Date of Infection: A Time-Continuous IgG-Model Shows That Seroconversion Does Not Occur at the Midpoint between Negative and Positive Tests

Estimating date of infection for HIV-1-infected patients is vital for disease tracking and informed public health decisions, but is difficult to obtain because most patients have an established infection of unknown duration at diagnosis. Previous studies have used HIV-1-specific immunoglobulin G (IgG) levels as measured by the IgG capture BED enzyme immunoassay (BED assay) to indicate if a patient was infected recently, but a time-continuous model has not been available. Therefore, we developed a logistic model of IgG production over time. We used previously published metadata from 792 patients for whom the HIV-1-specific IgG levels had been longitudinally measured using the BED assay. To account for patient variability, we used mixed effects modeling to estimate general population parameters. The typical patient IgG production rate was estimated at r = 6.72[approximate 95% CI 6.17,7.33]x10 -3 OD-n units day -1 , and the carrying capacity at K = 1.84[1.75,1.95] OD-n units, predicting how recently patients seroconverted in the interval Λ t = (31,711) days. Final model selection and validation was performed on new BED data from a population of 819 Swedish HIV-1 patients diagnosed in 2002–2010. On an appropriate subset of 350 patients, the best model parameterization had an accuracy of 94% finding a realistic seroconversion date. We found that seroconversion on average is at the midpoint between last negative and first positive HIV-1 test for patients diagnosed in prospective/cohort studies such as those included in the training dataset. In contrast, seroconversion is strongly skewed towards the first positive sample for patients identified by regular public health diagnostic testing as illustrated in the validation dataset. Our model opens the door to more accurate estimates of date of infection for HIV-1 patients, which may facilitate a better understanding of HIV-1 epidemiology on a population level and individualized prevention, such as guidance during contact tracing.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

We present an enzyme protein function identification algorithm, Catalytic Site Identification (CatSId), based on identification of catalytic residues. The method is optimized for highly accurate template identification across a diverse template library and is also very efficient in regards to time and scalability of comparisons. The algorithm matches three-dimensional residue arrangements in a query protein to a library of manually annotated, catalytic residues – The Catalytic Site Atlas (CSA). Two main processes are involved. The first process is a rapid protein-to-template matching algorithm that scales quadratically with target protein size and linearly with template size. The second process incorporates a number of physical descriptors, including binding site predictions, in a logistic scoring procedure to re-score matches found in Process 1. This approach shows very good performance overall, with a Receiver-Operator-Characteristic Area Under Curve (AUC) of 0.971 for the training set evaluated. The procedure is able to process cofactors, ions, nonstandard residues, and point substitutions for residues and ions in a robust and integrated fashion. Sites with only two critical (catalytic) residues are challenging cases, resulting in AUCs of 0.9411 and 0.5413 for the training and test sets, respectively. The remaining sites show excellent performance with AUCs greater than 0.90 for both the training and test data on templates of size greater than two critical (catalytic) residues. The procedure has considerable promise for larger scale searches.

59 BASIC BIOLOGICAL SCIENCES↗

Diverging Responses of Tropical Andean Biomes under Future Climate Conditions

Observations and projections for mountain regions show a strong tendency towards upslope displacement of their biomes under future climate conditions. Because of their climatic and topographic heterogeneity, a more complex response is expected for biodiversity hotspots such as tropical mountain regions. This study analyzes potential changes in the distribution of biomes in the Tropical Andes and identifies target areas for conservation. Biome distribution models were developed using logistic regressions. These models were then coupled to an ensemble of 8 global climate models to project future distribution of the Andean biomes and their uncertainties. We analysed projected changes in extent and elevational range and identified regions most prone to change. Our results show a heterogeneous response to climate change. Although the wetter biomes exhibit an upslope displacement of both the upper and the lower boundaries as expected, most dry biomes tend to show downslope expansion. Despite important losses being projected for several biomes, projections suggest that between 74.8% and 83.1% of the current total Tropical Andes will remain stable, depending on the emission scenario and time horizon. Between 3.3% and 7.6% of the study area is projected to change, mostly towards an increase in vertical structure. For the remaining area (13.1%–17.4%), there is no agreement between model projections. These results challenge the common believe that climate change will lead to an upslope displacement of biome boundaries in mountain regions. Instead, our models project diverging responses, including downslope expansion and large areas projected to remain stable. Lastly, a significant part of the area expected to change is already affected by land use changes, which has important implications for management. This, and the inclusion of a comprehensive uncertainty analysis, will help to inform conservation strategies in the Tropical Andes, and to guide similar assessments for other tropical mountains.

54 ENVIRONMENTAL SCIENCES↗