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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 847 records · Page 47
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DOE OSTI2019

Laparoscopic Hyperthermic Intraperitoneal Chemotherapy is Safe for Patients with Peritoneal Metastases from Gastric Cancer and May Lead to Gastrectomy

Background: Laparoscopic hyperthermic intraperitoneal chemotherapy (LS-HIPEC) is a novel strategy for patients with gastric adenocarcinoma (GA) metastatic to the peritoneum. We evaluated the safety profile of LS-HIPEC for patients with positive peritoneal cytology (PPC) or carcinomatosis from GA. Methods: Outcomes were reviewed of patients with stage IV GA with peritoneal involvement who received LS-HIPEC from June 2014 to January 2017. LS-HIPEC included a 60-minute perfusion of mitomycin-C (30 mg) and cisplatin (200 mg) with inflow temperatures of 41–42 °C and outflow temperatures of 39–40 °C. Results: A total of 71 LS-HIPEC procedures were performed in 44 patients. At diagnosis, 68% (n = 30) had carcinomatosis and 32% (n = 14) had isolated PPC. Three patients (7%) underwent LS-HIPEC for intractable ascites. All patients initially received systemic chemotherapy, and 20 patients (45%) received pre-procedural chemoradiotherapy. The median number of LS-HIPEC procedures performed per patient was one (range 1–5 procedures). There were no conversions to laparotomy, two outflow catheter obstructions, and one major (Clavien-Dindo grade III) surgical complication within 30 days. A total of seven postoperative adverse hematologic events (> CTCAE 2) were observed in five patients (11%), without any major renal or gastrointestinal adverse events within 30 days. The median overall length of hospital stay after LS-HIPEC was 2 (range 2–11) days. Eleven patients (25%) underwent secondary gastrectomy following resolution of peritoneal cytology. Conclusions: Laparoscopic HIPEC is a safe procedure and may be repeated in patients with peritoneal metastases from gastric cancer. Future studies are required to determine the optimal HIPEC regimen and timing relative to systemic therapy to best minimize morbidity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Determining the Safety and Efficacy of Enhanced Recovery Protocols in Major Oncologic Surgery: An Institutional NSQIP Analysis

Background: Enhanced-recovery (ER) protocols are increasingly being utilized in surgical practice. Outside of colorectal surgery, however, their feasibility, safety, and efficacy in major oncologic surgery have not been proven. This study compared patient outcomes before and after multispecialty implementation of ER protocols at a large, comprehensive cancer center. Methods: Surgical cases performed from 2011 to 2016 and captured by an institutional NSQIP database were reviewed. Following exclusion of outpatient and emergent surgeries, 2747 cases were included in the analyses. Cases were stratified by presence or absence of ER compliance, defined by preoperative patient education and electronic medical record order set-driven opioid-sparing analgesia, goal-directed fluid therapy, and early postoperative diet advancement and ambulation. Results: Approximately half of patients were treated on ER protocols (46%) and the remaining on traditional postoperative (TP) protocols (54%). Treatment on an ER protocol was associated with decreased overall complication rates (20% vs. 33%, p < 0.0001), severe complication rates (7.4% vs. 10%, p = 0.010), and median hospital length of stay (4 vs. 5 days, p < 0.0001). There was no change in readmission rates (ER vs. TP, 8.6% vs. 9.0%, p = 0.701). Subanalyses of high magnitude cases and specialty-specific outcomes consistently demonstrated improved outcomes with ER protocol adherence, including decreased opioid use. Conclusions: This assessment of a large-scale ER implementation in multispecialty major oncologic surgery indicates its feasibility, safety, and efficacy. Future efforts should be directed toward defining the long-term oncologic benefits of these protocols.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Effect of Noninvasive Follicular Thyroid Neoplasm with Papillary-Like Nuclear Features (NIFTP) on Malignancy Rates in Thyroid Nodules: How to Counsel Patients on Extent of Surgery

Purpose: To investigate the impact of the nomenclature change to “noninvasive follicular thyroid neoplasm with papillary-like nuclear features” (NIFTP) on reported malignancy rates following thyroidectomy. Methods: Retrospective cohort study of patients with thyroid nodules sampled preoperatively with fine-needle aspiration (FNA) and subsequently removed at one tertiary-care hospital from 4/2016 to 2/2017. Surgical procedure, anatomic pathology, thyroid cytopathology classification, and demographic characteristics were recorded. Results: Thyroidectomy was performed in 353 patients. Twenty-six patients (7.3%) had NIFTP on anatomic pathology. Preoperative FNA demonstrated atypia of undetermined significance (AUS/Bethesda III) in 13 (50%), suspicious for malignancy (SUS/Bethesda V) in 6 (23%), suspicious for follicular neoplasm (SFN/Bethesda IV) in 4 (15%), benign/Bethesda I in 2 (8%), and malignant/Bethesda VI in 1 (4%). Invasive malignancy rates across cytologic categories changed as follows: benign (n = 74) from 4 to 1%, AUS (n = 85) from 33 to 18% (p < 0.05), SFN (n = 58) from 29 to 22%, SUS (n = 33) from 91 to 73% (p < 0.05), and malignant (n = 99) from 99 to 98%. Overall decrease in invasive malignancy was 7.3% for the entire population and 13.1% for indeterminate preoperative FNA cytology (Bethesda III–V). Among 26 NIFTP patients, 17 had thyroid lobectomy (TL) and 9 underwent total thyroidectomy (TT). Eight of the nine patients with TT could have been definitively treated with TL, an 89% decrease. Conclusions: The NIFTP nomenclature change led to an overall decrease in the malignancy rate at our institution, especially for Bethesda III–V categories. Patients may be counseled toward more conservative surgical options if NIFTP is in the differential.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Is Robotic-Assisted Surgery Safe in the Elderly Population? An Analysis of Gynecologic Procedures in Patients ≥ 65 Years Old

Background: The elderly population is expanding worldwide but is underrepresented in clinical trials. We sought to assess the safety of robotic gynecologic surgery in an elderly cohort and to identify factors associated with unfavorable outcomes. Methods: All patients ≥ 65 years who underwent a robotically assisted procedure at a single institution between May 2007 to December 2016 were divided into three age groups: 65–74 (Group 1); 75–84 (Group 2); ≥ 85 (Group 3). Perioperative outcomes were recorded in patients who did not require conversion to laparotomy. We compared clinical variables among groups and performed multivariate logistic regression to detect variables associated with major complications (≥ Grade 3) or 90-day mortality. Results: We retrospectively identified 982 cases: 685 in Group 1; 249 in Group 2; 48 in Group 3. Median age = 71 years. Median BMI = 28.9. Malignancy was documented in 72.8% of cases; the majority were endometrial cancer (61.8%). Thirty-four patients (3.5%) were readmitted within 30 days. Seventy-seven (7.8%) had a postoperative complication, and 23 (2.3%) had a major complication. Ninety-day mortality was 0.5%. There was significant difference between groups with respect to body mass index (P = 0.026), ECOG PS (P ≤ 0.001), > 5 comorbidities (P = 0.005), hospital stay (P < 0.001), major complications (P = 0.001), and 90-day mortality (P < 0.001). On multivariable logistic regression, age ≥ 85 years was associated with major complications. Body mass index, age ≥ 85 years, and major complications were significantly associated with 90-day mortality. Conclusions: Robotic-assisted surgery appears to be safe in an elderly cohort. The incidence of overall and major complications is consistent with those reported in the literature. Patients ≥ 85 years old appear to be at higher risk of unfavorable outcomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Femoral Fracture in Primary Soft-Tissue Sarcoma of the Thigh and Groin Treated with Intensity-Modulated Radiation Therapy: Observed versus Expected Risk

Purpose: This study was designed to compare the observed risk of femoral fracture in primary soft-tissue sarcoma (STS) of the thigh/groin treated with intensity-modulated radiation therapy (IMRT) to expected risk calculated using the Princess Margaret Hospital (PMH) nomogram. Methods: Expected femoral fracture risk was calculated by using the PMH nomogram. Cumulative risk of fracture was estimated by using Kaplan–Meier statistics. Prognostic factors were assessed with univariate and multivariate analysis using Cox’s stepwise regression. Results: Between February 2002 and December 2010, 92 consecutive eligible patients were assessed. Median follow-up was 73 months (106 months in surviving patients). IMRT was delivered preoperatively (50 Gy) in 13 (14%) patients and postoperatively in 79 (86%) patients (median dose, 63 Gy; range, 59.4–66.6 Gy). The observed crude risk of fractures was 6.5% compared with 25.6% expected risk from the nomogram; the cumulative risk of fracture using IMRT at 5 years was 6.7% (95% CI 2.8–16.0%). The median time to fracture was 23 months (range, 6.9–88.6). Significant predictors of fracture on univariate analysis were age ≥ 60 years (p = 0.03), tumor location in the anterior thigh (p = 0.008), and periosteal stripping to > 20 cm (p < 0.0001). On multivariate analysis, age ≥ 60 years and periosteal stripping > 20 cm retained significance (p = 0.04 and p = 0.009, respectively). Conclusions: In this study, the cumulative risk of femur fracture in patients treated with IMRT (6.7%) is less than the expected risk using the PMH nomogram (25.6%). Established predictors of femur fracture, such as gender, tumor size, and dose of RT, seem to have less impact on fracture risk when using IMRT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Neoadjuvant Chemotherapy with Gemcitabine Plus Nab-Paclitaxel for Borderline Resectable Pancreatic Cancer Potentially Improves Survival and Facilitates Surgery

Background: Accumulation of evidence suggests that neoadjuvant chemotherapy improves the outcomes of borderline resectable pancreatic cancer (BRPC). Gemcitabine plus nab-paclitaxel (GnP) has been widely accepted as systemic chemotherapy for unresectable pancreatic cancer and reportedly results in remarkable tumor shrinkage. This study was performed to evaluate the safety and efficacy of neoadjuvant chemotherapy using neoadjuvant GnP for BRPC. Methods: The medical records of 57 patients who underwent treatment of BRPC from 2010 to 2017 were retrospectively reviewed. The patient characteristics and short- and intermediate-term outcomes were compared between the GnP and upfront surgery (UFS) groups. Results: The GnP group comprised 31 patients and the UFS group comprised 26 patients. The patient characteristics were comparable with the exception of a higher prevalence of arterial involvement in the GnP group. Twenty-seven of the 31 patients (87%) in the GnP group and all 26 patients in the UFS group underwent resection. The GnP group showed a significantly shorter operation time (429 vs. 509.5 min, p = 0.0068), less blood loss (760 vs. 1324 ml, p = 0.0115), and a higher R0 resection rate (100% vs. 77%, p = 0.0100) than the UFS group. Postoperative complications and hospital stay were comparable between the two groups, and no treatment-related mortality occurred in either group. Both the disease-free survival and overall survival times were significantly longer in the GnP group (p = 0.0018 and p = 0.0024, respectively). Conclusions: Neoadjuvant GnP is a safe and effective treatment strategy for BRPC. It potentially improves patients’ prognosis and facilitates surgical procedures.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Oncologic Outcomes of Self-Expandable Metallic Stent as a Bridge to Surgery and Safety and Feasibility of Minimally Invasive Surgery for Acute Malignant Colonic Obstruction

Background: Although self-expandable metal stents (SEMS) are widely used as a bridge to surgery (BTS) in patients with malignant colorectal cancer obstruction, there has been some debate about their effect on long-term oncological outcomes. Furthermore, data on the safety and feasibility of minimally invasive surgery (MIS) combined with stent placement are scarce. We aimed to determine the long-term oncological outcomes of SEMS as a BTS, and the short-term outcomes of SEMS used with minimally invasive colorectal surgery. Methods: Data from patients who were admitted with malignant obstructing colon cancer between January 2006 and December 2015 were retrospectively reviewed; 71 patients underwent direct surgery and 182 patients underwent SEMS placement as a BTS. Long-term and short-term outcomes of the groups were compared. In a subgroup analysis of the BTS group, the short-term outcomes of conventional open surgery and MIS were compared. Results: There were no differences in long-term oncologic outcomes between groups. The primary anastomosis rate was higher in the stent group than in the direct surgery group. In the stent group, postoperative complication rates were lower in the minimally invasive group than in the open surgery group. Time to flatus and time to soft diet resumption were shorter in the minimally invasive group, as was length of hospital stay. Conclusions: Elective surgery after stent insertion does not adversely affect long-term oncologic outcomes. Furthermore, MIS combined with stent insertion for malignant colonic obstruction is safe and feasible.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Predicting Outcome in Mammary Phyllodes Tumors: Relevance of Clinicopathological Features

Background: Phyllodes tumors (PTs) of the breast are uncommon fibroepithelial neoplasms. Most behave in a benign fashion but they also have the potential to recur locally or to metastasize. Methods: In the current study involving 290 PTs (181 benign, 76 borderline, and 33 malignant) from three hospitals over an 11-year period, we assessed the relationship between histologic parameters (including histologic features affecting grade and surgical margin status), postoperative adjuvant treatment, and local recurrences and distant metastases. Results: An involved surgical margin was the only factor associated with increased risk of local recurrences (hazard ratio [HR] 4.673, p = 0.003), but not for distant metastases. For local recurrences, a wider margin did not confer additional benefits. None of the histologic factors were predictive for local recurrences. In contrast, distant metastases were correlated with histologic parameters, particularly an infiltrative border (HR 10.935, p = 0.012) and the presence of necrosis (HR 15.311, p = 0.007). In this series, all local recurrences were found in patients without radiotherapy, regardless of surgical margin status. Conclusion: A negative surgical margin is mandatory for the effective local control of PT recurrence, and a minimal margin clearance may be sufficient. For distant metastases, the inherent characteristics of PTs are important, thus it may be prudent to evaluate additional histologic features, including necrosis, for patients’ prognostication.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Risk of Distant Metastasis in Parathyroid Carcinoma and Its Effect on Survival: A Retrospective Review from a High-Volume Center

Background: Development of distant metastases (DM) is associated with markedly decreased survival in parathyroid carcinoma (PC). We sought to identify factors associated with development of DM and to quantify the effect that development of DM had on overall survival (OS). Methods: Patients with surgically resected local/regional PC treated or surveilled at a tertiary-referral cancer hospital from 1980 to 2017 were included. We assessed the association between biochemical and clinicopathologic factors (preoperative parathyroid hormone (PTH) levels, sex, race, age, preoperative serum calcium levels, serum calcium levels at 6 months postop, tumor size, and extent of resection) with the development of DM. We also assessed the effect of development of DM on OS. Results: Seventy-five patients with PC were assessed; 17 (22.7%) developed DM at a median follow-up of 77 months. The cumulative incidence of DM in the cohort was 20, 30, and 38% at 5, 10, and 20 years respectively. Tumor size > 3.2 cm based on recursive partitioning analysis was the only significant predictor for development of DM (hazard ratio (HR) = 3.51; 95% confidence interval [CI] 1.04–11.91; p = 0.04). Median OS for the entire cohort was 17 years compared with 40 months for the cohort who developed DM. The HR for death after distant metastasis was 9.6 (95% CI 4.2–22.3; p < 0.0001). Conclusions: Development of distant metastasis during surveillance is associated with decreased OS, including late recurrences. Primary tumor size should be considered in future interval surveillance and development of treatment algorithms.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Obstruction-Free Survival Following Operative Intervention for Malignant Bowel Obstruction in Appendiceal Cancer

Background: Patients with peritoneal metastases from appendiceal cancer are at high risk of malignant bowel obstruction (MBO), which is associated with significant morbidity and mortality. There are no definitive treatment guidelines regarding operative intervention for MBO. We sought to evaluate the efficacy and safety of operative intervention in this population. Methods: We identified patients with peritoneal metastases from appendiceal cancer who underwent surgery for MBO at our institution between 2011 and 2018. Baseline characteristics, postoperative complications, and follow-up data were collected. The primary endpoint was obstruction-free survival (OFS). Other endpoints were postoperative recovery of bowel function, 60-day Clavien–Dindo (CD) morbidity, and overall survival (OS). Results: Twenty-six patients underwent operative treatment for MBO, of whom 14 had high-grade (HG) histology and 12 had low-grade (LG) histology. Seven (25.9%) patients had severe (CD grade 3 or higher) 60-day complications, including one (3.8%) postoperative death. All remaining patients had return of bowel function and resumed oral intake during hospitalization. Six (23.1%) patients had repeat admissions for MBO after surgery. Median OFS was 17.0 months (95% confidence interval [CI] 2.3–31.8), and median OS was 18.5 months (95% CI 3.6–33.3) following surgery. Conclusion: In this carefully selected group of patients with peritoneal metastases from appendiceal cancer, surgery for MBO provided durable palliation with acceptable morbidity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Inpatient Opioid Use After Pancreatectomy: Opportunities for Reducing Initial Opioid Exposure in Cancer Surgery Patients

Background: Despite advances in enhanced surgical recovery programs, strategies limiting postoperative inpatient opioid exposure have not been optimized for pancreatic surgery. The primary aims of this study were to analyze the magnitude and variations in post-pancreatectomy opioid administration and to characterize predictors of low and high inpatient use. Methods: Clinical characteristics and inpatient oral morphine equivalents (OMEs) were downloaded from electronic records for consecutive pancreatectomy patients at a high-volume institution between March 2016 and August 2017. Regression analyses identified predictors of total OMEs as well as highest and lowest quartiles. Results: Pancreatectomy was performed for 158 patients (73% pancreaticoduodenectomy). Transversus abdominus plane (TAP) block was performed for 80% (n = 127) of these patients, almost always paired with intravenous patient-controlled analgesia (IV-PCA), whereas 15% received epidural alone. All the patients received scheduled non-opioid analgesics (median, 2). The median total OME administered was 423 mg (range 0–4362 mg). Higher total OME was associated with preoperative opioid prescriptions (p < 0.001), longer hospital length of stay (LOS; p < 0.001), and no epidural (p = 0.006). The lowest and best quartile cutoff was 180 mg of OME or less, whereas the highest and worst quartile cutoff began at 892.5 mg. After adjustment for inpatient team, only epidural use [odds ratio (OR) 0.3; p = 0.04] predicted lowest-quartile OME. Preoperative opioid prescriptions (OR 8.1; p < 0.001), longer operative time (OR 3.4; p = 0.05), and longer LOS (OR 1.1; p = 0.007) predicted highest-quartile OME. Conclusions: Preoperative opioid prescriptions and longer LOS were associated with increased inpatient OME, whereas epidural use reduced inpatient OME. Understanding the predictors of inpatient opioid use and the variables predicting the lowest and highest quartiles can inform decision-making regarding preoperative counseling, regional anesthetic block choice, and novel inpatient opioid weaning strategies to reduce initial postoperative opioid exposure.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Physician Perspectives on Fertility Preservation Discussions with Premenopausal Breast Cancer Patients: Results from a Multihospital Health Care System

Background: Ten percent of new breast cancer diagnoses occur in premenopausal women, and oncologic therapies may compromise fertility. Thus, fertility preservation discussions (FPDs) and referral to fertility specialists are imperative prior to initiation of therapy. A previous retrospective chart review showed 45% FPD rates at our institution. The aim of this study is to investigate physician perspectives and limitations regarding FPD. Methods: An electronic survey was distributed to 30 surgical, medical, and radiation oncologists across ten regional hospitals. Questions addressed provider demographics, and barriers to and facilitators of FPD. Results: The survey response rate was 63.3%. Only 31.6% of physicians reported “always” documenting FPD. Respondents opined that the physician prescribing systemic therapy was the most appropriate person to provide FPD. Patient age, treatment with chemotherapy, and patient desire for FPD were more likely to increase FPD (p < 0.0001, p < 0.05, and p < 0.0001, respectively). The majority of physicians (84.2%) expressed intent to increase FPD rates. Conclusions: Fertility preservation is an integral aspect of breast cancer care, requiring thorough discussion and clear documentation. This study identified that physicians believe the medical oncologist is the most appropriate person to have FPDs with patients and that empowering patients to bring up fertility concerns may improve rates of FPDs. Education of physicians and patients about fertility preservation techniques is likely to improve FPDs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Radiological Staging for Distant Metastases in Breast Cancer Patients with Confirmed Local and/or Locoregional Recurrence: How Useful are Current Guideline Recommendations?

Background: Breast cancer patients with local and/or locoregional recurrence (LR) are at higher risk of developing distant metastases (DM) at a later time. Once LR has been confirmed, some international interdisciplinary guidelines recommend performing radiological examinations for DM to determine the course of further therapy (curative or palliative approach). This study analyzed the metastatic patterns of patients with LR with particular regard to the frequency of concurrent diagnosis of LR and DM; in other words: are radiological staging procedures actually justified for DM at the time of diagnosis of LR? Methods: This study included all patients (n = 1368) who were diagnosed and treated for nonmetastatic breast cancer (Stage I–III) at the University Women’s Hospital Basel, Switzerland between 1990 and 2009. Results: In 137 patients, LR was diagnosed without a history of DM: in-breast/thoracic wall only, n = 90 (65.7%); involvement of axillary/supra-/infraclavicular lymph nodes, n = 47 (34.3%). DM was found at the time of diagnosis of LR in 44 patients (32.1%). Concurrent diagnosis of LR and DM occurred significantly more often in patients with lymph node recurrence compared with those with in-breast/chest wall recurrence (48.9% vs. 23.3%; p = 0.004). Conclusions: Approximately one-third of patients with a LR had synchronous DM at the time of their local/locoregional event. For this reason, routine systemic staging imaging at the time of LR should be an absolute requirement for planning further therapy. Confirmation of DM may spare the patients radical surgical interventions with questionable impact on survival in the face of an incurable disease.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Forecasting the 2013–2014 influenza season using Wikipedia

Infectious diseases are one of the leading causes of morbidity and mortality around the world; thus, forecasting their impact is crucial for planning an effective response strategy. According to the Centers for Disease Control and Prevention (CDC), seasonal influenza affects 5% to 20% of the U.S. population and causes major economic impacts resulting from hospitalization and absenteeism. Understanding influenza dynamics and forecasting its impact is fundamental for developing prevention and mitigation strategies. We combine modern data assimilation methods with Wikipedia access logs and CDC influenza-like illness (ILI) reports to create a weekly forecast for seasonal influenza. The methods are applied to the 2013-2014 influenza season but are sufficiently general to forecast any disease outbreak, given incidence or case count data. We adjust the initialization and parametrization of a disease model and show that this allows us to determine systematic model bias. In addition, we provide a way to determine where the model diverges from observation and evaluate forecast accuracy. Wikipedia article access logs are shown to be highly correlated with historical ILI records and allow for accurate prediction of ILI data several weeks before it becomes available. The results show that prior to the peak of the flu season, our forecasting method produced 50% and 95% credible intervals for the 2013-2014 ILI observations that contained the actual observations for most weeks in the forecast. However, since our model does not account for re-infection or multiple strains of influenza, the tail of the epidemic is not predicted well after the peak of flu season has passed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program

The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n = 35) or hospitalization (n = 42) due to severe COVID-19 using genome-wide association summary data from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (n rs495828 = 53 and n rs505922 = 59); strongest association with venous embolism, odds ratio (OR rs495828 1.33 (p = 1.32 x 10 –199 ), and thrombosis OR rs505922 1.33, p = 2.2 x10 -265 . Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p = 4.12 × 10 –191 ; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p = 2.26× 10 –12 . The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p = 6.48 x10 -23 , lupus OR 0.84, p = 3.97 x 10 –06 . PheWAS stratified by ancestry demonstrated differences in genotype-phenotype associations. LMNA (rs581342) associated with neutropenia OR 1.29 p = 4.1 x 10 –13 among Veterans of African and Hispanic ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)

Infants in Neonatal Intensive Care Units (NICUs) are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs) in the spread of infections. Here, we used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S) ribosomal RNA gene sequence using ‘universal’ barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation) bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium). In one NICU, we also detected fecal coliform bacteria (Enterobacteriales) in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities), as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗
DOE OSTI2021

Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States

Salmonella enterica subspecies enterica serotype Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. The primary clinical manifestation of Salmonella Dublin infection in cattle, especially calves, is respiratory disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S . Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S . Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S . Dublin isolates (n = 140) were selected from submissions to the NVSL for Salmonella serotyping (2014–2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S . Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to beta-lactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(6)-Id (97.9%), aph(3’’)-Ib, (97.1%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyr A. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S . Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S . Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S . Dublin isolates may provide valuable insight on increased virulence observed in humans.

60 APPLIED LIFE SCIENCES↗