Distance Functions and Attribute Weighting in a K-Nearest Neighbors Classifier

To assess environmental health of a stream, field, or other ecological object, characteristics of that object should be compared to a set of reference objects known to be healthy. Using streams as objects, we propose a k-nearest neighbors algorithm (Bates Prins and Smith, 2006) to find the appropriate set of reference streams to use as a comparison set for any given test stream. Previously, investigations of the k-nearest neighbors algorithm have utilized a variety of distance functions, the best of which has been the Interpolated Value Difference Metric (IVDM), proposed by Wilson and Martinez (1997). We propose two alternatives to the IVDM: Wilson and Martinez\u27s Windowed Value Difference Metric (WVDM) and the Density-Based Value Difference Metric (DBVDM) developed by Wojna (2005). We extend the WVDM and DBVDM to handle continuous response variables and compare these distance measures to the IVDM within the ecological k-nearest neighbors context. Additionally, we compare two existing attribute weighting schemes (Wojna 2005) when applied to the IVDM, WVDM, and DBVDM, and we propose a new attribute weighting method for use with these distance functions as well. In assessing environmental impairment, the WVDM and DBVDM were slight improvements over the IVDM. Attribute weighting also increased the effectiveness of the k-nearest neighbors algorithm in this ecological setting. This research was supported by NSF grant NSF-DMS 0552577 and was conducted during an 8-week summer research experience for undergraduates (REU)

Distance Functions and Attribute Weighting in a K-Nearest Neighbors Classifier

To assess environmental health of a stream, field, or other ecological object, characteristics of that object should be compared to a set of reference objects known to be healthy. Using streams as objects, we propose a k-nearest neighbors algorithm (Bates Prins and Smith, 2006) to find the appropriate set of reference streams to use as a comparison set for any given test stream. Previously, investigations of the k-nearest neighbors algorithm have utilized a variety of distance functions, the best of which has been the Interpolated Value Difference Metric (IVDM), proposed by Wilson and Martinez (1997). We propose two alternatives to the IVDM: Wilson and Martinez\u27s Windowed Value Difference Metric (WVDM) and the Density-Based Value Difference Metric (DBVDM) developed by Wojna (2005). We extend the WVDM and DBVDM to handle continuous response variables and compare these distance measures to the IVDM within the ecological k-nearest neighbors context. Additionally, we compare two existing attribute weighting schemes (Wojna 2005) when applied to the IVDM, WVDM, and DBVDM, and we propose a new attribute weighting method for use with these distance functions as well. In assessing environmental impairment, the WVDM and DBVDM were slight improvements over the IVDM. Attribute weighting also increased the effectiveness of the k-nearest neighbors algorithm in this ecological setting. This research was supported by NSF grant NSF-DMS 0552577 and was conducted during an 8-week summer research experience for undergraduates (REU)

A Retrospective Review of Neonatal Sepsis among GBS-Colonized Women Undergoing Planned Cesarean Section after Labor Onset or Rupture of Membranes

Background. Sepsis is a leading cause of mortality and morbidity in neonates, with group B streptococcus (GBS) remaining the most frequent pathogen isolated from term infants. Surveillance data showed that the majority of cases of early-onset GBS disease were neonates born to women who either received no or suboptimal intrapartum antibiotic prophylaxis with a notable portion of those women having a missed opportunity to receive ≥4 hours of chemoprophylaxis. Women planning delivery by cesarean section who present in labor or rupture of membranes prior to their scheduled surgery are unlikely to receive optimal GBS chemoprophylaxis and thus their neonates are at risk of having sepsis. Materials and Methods. A retrospective cohort study of women-infant dyads was extracted from the Consortium on Safe Labor dataset. Women who had an unlabored cesarean section at ≥37+0 week gestation were selected and divided into four groups based on GBS status and timing of cesarean section with respect to onset of labor or rupture of membranes. The rate of neonatal sepsis and the patterns of intrapartum antibiotic chemoprophylaxis were determined. Results. The sepsis rate (4.5%) among neonates of GBS-colonized women having their unlabored cesarean section after onset of labor or rupture of membranes was significantly higher than that in any other group in this study. In this group, 9.4% of women received chemoprophylaxis for ≥4 hours, while 31% had a missed opportunity to receive ≥4 hours of chemoprophylaxis. Conclusion. This study suggests that neonates of GBS-colonized women having a planned cesarean section after onset of labor or rupture of membranes are at increased risk of having a sepsis diagnosis. This finding suggest the need for additional studies to assess the risk of sepsis among neonates of women in this group

Metabolic PET/CT analysis of aggressive Non-Hodgkin lymphoma prior to Axicabtagene Ciloleucel CAR-T infusion: predictors of progressive disease, survival, and toxicity

Abstract PET/CT is used to evaluate relapsed/refractory non-Hodgkin lymphoma (NHL) prior to chimeric antigen receptor T-cell (CAR-T) infusion at two time points: pre-leukapheresis (pre-leuk) and pre-lymphodepletion chemotherapy (pre-LD). We hypothesized that changes in PET/CT between these time points predict outcomes after CAR-T. Metabolic tumor volume (MTV), total lesion glycolysis (TLG), and other metrics were calculated from pre-leuk and pre-LD PET/CT scans in patients with NHL who received axicabtagene ciloleucel, and assessed for association with outcomes. Sixty-nine patients were analyzed. While single time point PET/CT characteristics were not associated with risk of PD or death, increases from pre-leuk to pre-LD in parenchymal MTV, nodal MTV, TLG of the largest lesion, and total number of lesions were associated with increased risk of death (p < 0.05 for all). LASSO analysis identified increasing extranodal MTV and increasing TLG of the largest lesion as strong predictors of death (AUC 0.74). Greater pre-LD total MTV was associated with higher risk of grade 3+ immune effector cell-associated neurotoxicity syndrome (ICANS) (p = 0.042). Increasing metabolic disease burden during CAR-T manufacturing is associated with increased risk of progression and death. A two variable risk score stratifies prognosis prior to CAR-T infusion and may inform risk-adapted strategies

Procalcitonin as a biomarker for predicting bacterial infection in chimeric antigen receptor T‐cell therapy recipients

Abstract Background It is unknown whether serum procalcitonin (PCT) concentration monitoring can differentiate between bacterial infection or cytokine release syndrome (CRS) when chimeric antigen receptor T‐cell (CAR‐T) recipients present with a constellation of signs and symptoms that may represent both complications. Objective The objective of the study was to assess the utility of serum PCT concentrations as a biomarker of bacterial infection in CAR‐T recipients. Study design This single‐center, retrospective, medical record review evaluated patients prescribed CAR‐T therapy until death or 30 days after infusion. Logistic regression modeling determined the association between elevated serum PCT concentrations within 48 h of fever onset and microbiologically confirmed infection. Secondary outcomes included clinically suspected infection, CAR‐T toxicity rates, and broad‐spectrum antibiotic usage. Predictive performance of PCT was assessed by area under the receiver operating characteristic curve (AUC). Results The 98 included patients were a median age of 63 (IQR: 55–69) years old, 47 (48%) were male, and 87 (89%) were Caucasian. Baseline demographics and clinical characteristics were similar between patients with and without a bacterial infection. Serum PCT >0.4 ng/mL within 48 h of fever was significantly associated with a microbiologically confirmed bacterial infection (OR: 2.75 [95% CI: 1.02–7.39], p = 0.045). Median PCT values in patients with and without confirmed infections were 0.40 ng/mL (IQR: 0.26, 0.74) and 0.26 ng/mL (IQR: 0.13, 0.47), respectively. The AUC for PCT to predict bacterial infection was 0.62 (95% CI 0.48–0.76). All patients experienced CRS of some grade, with no difference in CRS severity based on elevated PCT. Broad‐spectrum antibiotics were used for a median of 45% and 23% of days in those with and without confirmed infection, respectively (p = 0.075). Conclusion Elevated serum PCT concentrations above 0.4 ng/mL at time of first fever after CAR‐T infusion was significantly associated with confirmed bacterial infection. Furthermore, rigorous, prospective studies should validate our findings and evaluate serial PCT measurements to optimize antimicrobial use after CAR‐T therapy

Acceptability of Electronic Visits for Return of Research Results in the Mayo Clinic Biobank

Objective: To understand patient characteristics related to acceptability of returning individual research results via various modalities, focusing on electronic visits (e-visits). Patients and Methods: Twelve hundred participants from the Mayo Clinic Biobank were selected using a stratified random sampling approach based on sex, age, and education level. Mailed surveys ascertained return of results preferences for 2 disease vignettes (cystic fibrosis and hereditary breast cancer) and a pharmacogenomics vignette. The study was conducted from October 1, 2013, through March 31, 2014. Results: In all, 685 patients (57%) responded, and 60% reported liking e-visits, although the option of receiving results in an office visit was liked most frequently. Multivariable logistic models showed that the odds of liking the use of e-visits for returning results for cystic fibrosis and hereditary breast cancer were higher among those with higher education and better genetic knowledge and among those not living in proximity to the Mayo Clinic (Rochester, Minnesota). Level of genetic knowledge was not considerably associated with accepting e-visits, whereas education level remained important. For all vignettes, those who are divorced were less likely to accept e-visits. Conclusion: Researchers are faced with a difficult challenge of returning results with a method that is both acceptable to recipients and logistically feasible. This study implies that the use of e-visits may be a viable option for return of results to stratify the chasm between in-person genetic counseling and online portal receipt of results