Machine learning based DNA melt curve profiling enables automated novel genotype detection

Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.

Plasma Biomarker for Post-concussive Syndrome: A Pilot Study Using an Alternating Current Electro-Kinetic Platform

Background: Technology platforms that afford biomarker discovery in patients suffering from traumatic brain injury (TBI) remain an unmet medical need. Here, we describe an observational pilot study to explore the utility of an alternating current electrokinetic (ACE) microchip device in this context.

Methods: Blood samples were collected from participating subjects with and without minor TBI. Plasma levels of glial fibrillary acidic protein (GFAP), Tau, ubiquitin C-terminal hydrolase L1 (UCH-L1), and cell-free DNA (cfDNA) were determined in subjects with and without minor TBI using ACE microchip device followed by on-chip immunofluorescent analysis. Post-concussive symptoms were assessed using the Rivermead Post Concussion Symptoms Questionnaire (RPCSQ) at one-month follow-up.

Results: Highest levels of GFAP, UCH-L1, and Tau were seen in two minor TBI subjects with abnormality on head computed tomography (CT). In patients without abnormal head CT, Tau and GFAP levels discriminated between plasma from minor-TBI and non-TBI patients, with sensitivity and specificity of 64–72 and 50%, respectively. Plasma GFAP, UCH-L1, and Tau strongly correlated with the cumulative RPCSQ score. Plasma UCH-L1 and GFAP exhibited highest correlation to sensitivity to noise and light (r = 0.96 and 0.91, respectively, p < 0.001). Plasma UCH-L1 and Tau showed highest correlation with headache (r = 0.74 and 0.78, respectively, p < 0.001), sleep disturbance (r = 0.69 and 0.84, respectively, p < 0.001), and cognitive symptoms, including forgetfulness (r = 0.76 and 0.74, respectively, p < 0.001), poor concentration (r = 0.68 and 0.76, respectively, p < 0.001), and time required for information processing (r = 0.77 and 0.81, respectively, p < 0.001). cfDNA exhibited a strong correlation with depression (r = 0.79, p < 0.01) and dizziness (r = 0.69, p < 0.01). While cfDNA demonstrated positive correlation with dizziness and depression (r = 0.69 and 0.79, respectively, p < 0.001), no significant correlation was observed between cumulative RPCSQ and cfDNA (r = 0.07, p = 0.81).

Conclusion: We provide proof-of-principle results supporting the utility of ACE microchip for plasma biomarker analysis in patients with minor TBI.

Epidemiology of 577 Pediatric Firearm Fatalities: A 2-year Review of the National Trauma Data Bank

The purpose of this study was to delineate the epidemiology of pediatric firearm injuries, including ethno-demographic patterns with impact on years of potential life lost (YPLL). A 2-year review of the National Trauma Data Bank (2007 to 2008) was conducted. Firearm fatalities in records of patients younger than 18 years were identified. Data were analyzed by demographic and injury characteristics and YPLL was calculated by ethnicity. A total of 577 deaths were identified in the pediatric group. Blacks accounted for 49.7 per cent of the fatalities; Hispanics, 19.2 per cent; whites, 17.7 per cent, and other ethnicity, 13.4 per cent. Median Injury Severity Score was 25 with a median Glasgow Coma Scale score of 3. Traumatic brain injury was present in 84.2 per cent of the records. Assault accounted for 72.8 per cent, self-inflicted injury 12.7 per cent, and unintentional injuries were 8.2 per cent. Most firearm fatalities occurred at home (33.6%). By emergency department (ED) disposition, 29.3 per cent died in the ED, 32.9 per cent were admitted to the intensive care unit, and 30.0 per cent taken to the operating room. Blacks had a total of 17,446 YPLL, Hispanics 6,776 YPLL, and whites 6,718 YPLL. Pediatric firearm fatalities still remain an important public health concern. Inclusive gun control policies focused on primary prevention of accidental injuries may be more effective in mitigating its impact.

Associated Injuries in Traumatic Sternal Fractures: A Review of the National Trauma Data Bank

Sternal fractures occur infrequently with blunt force trauma. The demographics and epidemiology of associated injuries have not been well characterized from a national trauma database. The National Trauma Data Bank was queried for patients with closed sternal fractures. The demographics were analyzed by age, gender, mechanism and indicators of anatomic and physiologic injuries. Types of commonly associated injuries were also determined. A total of 23,985 records were analyzed. Males accounted for 68.3 per cent and whites 70.9 per cent. Motor vehicle crash was the leading mechanism. More than 56 per cent had severe injuries based on Injury Severity Score (greater than 15) and 17 per cent with Glasgow Coma Score 8 or less. Crude mortality was 7.9 per cent. The majority (57.8%) and approximately one-third (33.7%) of the patients had rib fractures and lung contusions, respectively, 22.0 per cent with closed pneumothorax, 21.6 per cent had a closed thoracic vertebra fracture, 16.9 per cent with lumbar spine fracture, 3.9 per cent with concussion, and blunt cardiac injury in 3.6 per cent. Sternal fractures are usually associated with severe blunt trauma. Lung contusion remains the leading associated injury followed by vertebral spine fractures. Cardiac injuries are less frequent and vascular injuries less so. Mechanism of injury and presence of sternal fractures should alert providers to these potential associated injuries.

An Age-Based Analysis of Pediatric Melanoma: Staging, Surgery, and Mortality in the Surveillance, Epidemiology, and End Results Database

The pediatric melanoma population is not well described, and current guidelines for their management are not well defined. Our study aims to identify this population, treatment modalities, and outcomes using a national population-based database. We reviewed the Surveillance, Epidemiology, and End Results database (2004-2008). Patients ≤21 years old with melanoma were included and grouped into ≤12 years of age, 13 to 18 years, and 19 to 21 years. Clinical characteristics were analyzed across the groups. A total of 1255 patients were included: 52.7 per cent were 19 to 21 years of age, 36.3 per cent were 13 to 18 years of age, and 11.0 per cent were ≤12 years of age. The 19- to 21-year-olds had the highest proportion of stage I (50.5%) versus ≤12 years of age (31.9%); the ≤12-year-olds had the highest proportion of stage IV (3.6%) versus 19 to 21 years of age (0.9%), P < 0.001. The 19- to 21-year-olds had the highest proportion receiving wide local excisions only (34.8%) versus ≤12 years of age (26.4%); the ≤12-year-olds had the highest proportion of patients without any surgeries (16.0%) versus 13 to 18 years of age (9.4%), P = 0.169. On adjusted analysis, the 19- to 21-year-olds had worse survival compared with ≤12 years of age (hazard ratio: 5.26, P = 0.017, 95% confidence interval 1.34-20.65). Disparities were found in the ≤12-year-old melanoma population, as they had later stage melanomas, less invasive surgery, and lower survival. Clearer prognostic factors are needed to better elucidate their management.

An Age-Based Analysis of Pediatric Melanoma: Staging, Surgery, and Mortality in the Surveillance, Epidemiology, and End Results Database

The pediatric melanoma population is not well described, and current guidelines for their management are not well defined. Our study aims to identify this population, treatment modalities, and outcomes using a national population-based database. We reviewed the Surveillance, Epidemiology, and End Results database (2004–2008). Patients ≤21 years old with melanoma were included and grouped into ≤12 years of age, 13 to 18 years, and 19 to 21 years. Clinical characteristics were analyzed across the groups. A total of 1255 patients were included: 52.7 per cent were 19 to 21 years of age, 36.3 per cent were 13 to 18 years of age, and 11.0 per cent were ≤12 years of age. The 19- to 21-year-olds had the highest proportion of stage I (50.5%) versus ≤12 years of age (31.9%); the ≤12-year-olds had the highest proportion of stage IV (3.6%) versus 19 to 21 years of age (0.9%), P < 0.001. The 19- to 21-year-olds had the highest proportion receiving wide local excisions only (34.8%) versus ≤12 years of age (26.4%); the ≤12-year-olds had the highest proportion of patients without any surgeries (16.0%) versus 13 to 18 years of age (9.4%), P = 0.169. On adjusted analysis, the 19- to 21-year-olds had worse survival compared with ≤12 years of age (hazard ratio: 5.26, P = 0.017, 95% confidence interval 1.34–20.65). Disparities were found in the ≤12-year-old melanoma population, as they had later stage melanomas, less invasive surgery, and lower survival. Clearer prognostic factors are needed to better elucidate their management.

Epidemiology of 577 pediatric firearm fatalities: a 2-year review of the National Trauma Data Bank

The purpose of this study was to delineate the epidemiology of pediatric firearm injuries, including ethno-demographic patterns with impact on years of potential life lost (YPLL). A 2-year review of the National Trauma Data Bank (2007 to 2008) was conducted. Firearm fatalities in records of patients younger than 18 years were identified. Data were analyzed by demographic and injury characteristics and YPLL was calculated by ethnicity. A total of 577 deaths were identified in the pediatric group. Blacks accounted for 49.7 per cent of the fatalities; Hispanics, 19.2 per cent; whites, 17.7 per cent, and other ethnicity, 13.4 per cent. Median Injury Severity Score was 25 with a median Glasgow Coma Scale score of 3. Traumatic brain injury was present in 84.2 per cent of the records. Assault accounted for 72.8 per cent, self-inflicted injury 12.7 per cent, and unintentional injuries were 8.2 per cent. Most firearm fatalities occurred at home (33.6%). By emergency department (ED) disposition, 29.3 per cent died in the ED, 32.9 per cent were admitted to the intensive care unit, and 30.0 per cent taken to the operating room. Blacks had a total of 17,446 YPLL, Hispanics 6,776 YPLL, and whites 6,718 YPLL. Pediatric firearm fatalities still remain an important public health concern. Inclusive gun control policies focused on primary prevention of accidental injuries may be more effective in mitigating its impact.

Estimating the influence of maternal height on under-five mortality in Nigeria

This study uses a nationally representative data sample to assess the effect of maternal height as an intergenerational influence on under-five mortality. Data from the 2003 and 2008 Nigerian Demographic Health Survey (NDHS) (n = 41,005) selecting women aged 15 to 49 yrs whose most recent births were within 5 years (n = 23,568), were analyzed. The outcome measure was under-five mortality. Independent variables included maternal height categorized as > or = 63 inch, 61-62.9 inch, 59.1-60.9 inch, < 59.1 inch. Confounding factors were controlled for. A multivariable logistic regression was used to obtain odds ratio estimates along with their respective confidence interval. After adjusting for confounding factors, we found that each 1 inch increase in maternal height, was associated with a decreased odds of mortality OR 0.98 (95% CI 0.97-0.99). The OR of under-five mortality when comparing women > or = 63 inch versus women < 59.1 inch was 1.13 (95% CI 0.98-1.31). The population attributable fraction of child death due to maternal short stature was 0.36.

Associated injuries in traumatic sternal fractures: a review of the National Trauma Data Bank

Sternal fractures occur infrequently with blunt force trauma. The demographics and epidemiology of associated injuries have not been well characterized from a national trauma database. The National Trauma Data Bank was queried for patients with closed sternal fractures. The demographics were analyzed by age, gender, mechanism and indicators of anatomic and physiologic injuries. Types of commonly associated injuries were also determined. A total of 23,985 records were analyzed. Males accounted for 68.3 per cent and whites 70.9 per cent. Motor vehicle crash was the leading mechanism. More than 56 per cent had severe injuries based on Injury Severity Score (greater than 15) and 17 per cent with Glasgow Coma Score 8 or less. Crude mortality was 7.9 per cent. The majority (57.8%) and approximately one-third (33.7%) of the patients had rib fractures and lung contusions, respectively, 22.0 per cent with closed pneumothorax, 21.6 per cent had a closed thoracic vertebra fracture, 16.9 per cent with lumbar spine fracture, 3.9 per cent with concussion, and blunt cardiac injury in 3.6 per cent. Sternal fractures are usually associated with severe blunt trauma. Lung contusion remains the leading associated injury followed by vertebral spine fractures. Cardiac injuries are less frequent and vascular injuries less so. Mechanism of injury and presence of sternal fractures should alert providers to these potential associated injuries.

Surgical management of complicated diverticulitis: a comparison of the laparoscopic and open approaches

BACKGROUND

Laparoscopy has become a commonly used method of performing colectomies, but the outcomes associated with laparoscopy in the emergency setting have not been well studied.

STUDY DESIGN

The American College of Surgeons-National Surgical Quality Improvement Program (ACS-NSQIP) database was queried for patients with diverticulitis without hemorrhage who underwent a colectomy. Patient data retrieved included demographics and preoperative comorbidities. Each member of the cohort received either a primary anastomosis (PA) or a colostomy. Open and laparoscopic procedures were compared within these subgroups. Multivariate logistic regression analyses were performed to compare the risk-adjusted odds of postoperative morbidity and mortality for laparoscopic and open procedures. The risk-adjusted impact of preoperative comorbidities was also assessed.

RESULTS

A total of 11,981 patients in the database met the study criteria. The majority were female (53%) and Caucasian (82%), and the mean age was 58 (±13) years. Comorbidities of the cardiovascular, pulmonary, or renal systems were present in 47%, 5%, and 1% of the cohort, respectively. On bivariate analysis, patients undergoing laparoscopy experienced lower rates of complications with both PA (14% vs 26%, p < 0.001) and colostomy (30% vs 37%, p = 0.02). The laparoscopic approach was associated with decreased mortality rates for patients undergoing PA (0.24% vs 0.79%, p < 0.001). Multivariate analysis revealed that preoperative cardiovascular and pulmonary comorbidities were each associated with increased postoperative morbidity, and that the laparoscopic approach was associated with lower postoperative morbidity for patients undergoing PA. The reduced risk of death for patients undergoing laparoscopic PA (vs open approach) did not achieve statistical significance (odds ratio 0.68, p = 0.3). A small number of patients underwent laparoscopic colostomy (n = 237, 2.4%), and they did not have a significantly different risk of death.

CONCLUSIONS

The laparoscopic approach is associated with lower complication rates compared with the open approach for the surgical treatment of diverticulitis with a primary anastomosis.