Stepwise approach to SNP-set analysis illustrated with the Metabochip and colorectal cancer in Japanese Americans of the Multiethnic Cohort.

BACKGROUND: Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome scans. Because of low frequency (low statistical power), less-common variants are best analyzed using SNP-set methods such as gene-set or pathway-based analyses. However, there is as yet no clear consensus regarding how to focus in on potential risk variants following set-based analyses. We used a stepwise, telescoping approach to analyze common- and rare-variant data from the Illumina Metabochip array to assess genomic association with colorectal cancer (CRC) in the Japanese sub-population of the Multiethnic Cohort (676 cases, 7180 controls). We started with pathway analysis of SNPs that are in genes and pathways having known mechanistic roles in colorectal cancer, then focused on genes within the pathways that evidenced association with CRC, and finally assessed individual SNPs within the genes that evidenced association. Pathway SNPs downloaded from the dbSNP database were cross-matched with Metabochip SNPs and analyzed using the logistic kernel machine regression approach (logistic SNP-set kernel-machine association test, or sequence kernel association test; SKAT) and related methods. RESULTS: The TGF-ß and WNT pathways were associated with all CRC, and the WNT pathway was associated with colon cancer. Individual genes demonstrating the strongest associations were TGFBR2 in the TGF-ß pathway and SMAD7 (which is involved in both the TGF-ß and WNT pathways). As partial validation of our approach, a known CRC risk variant in SMAD7 (in both the TGF-ß and WNT pathways: rs11874392) was associated with CRC risk in our data. We also detected two novel candidate CRC risk variants (rs13075948 and rs17025857) in TGFBR2, a gene known to be associated with CRC risk. CONCLUSIONS: A stepwise, telescoping approach identified some potentially novel risk variants associated with colorectal cancer, so it may be a useful method for following up on results of set-based SNP analyses. Further work is required to assess the statistical characteristics of the approach, and additional applications should aid in better clarifying its utility.

Oral Care Associated With Less Microaspiration in Ventilated Cardiac Patients.

Aspiration is common in mechanically ventilated patients and may predispose patients to aspiration pneumonia, chemical pneumonitis, and chronic lung damage. Pepsin A is a specific marker of gastric fluid aspiration and is often detected in ventilated pediatric patients. We investigated the effect of oral care and throat suctioning in the detection of pepsin A in tracheal aspirates (TAs) up to 4 hours after these procedures. Methods: Twelve pediatric patients between age 2 weeks to 14 years who underwent intubation for cardiac surgery were enrolled in this study. Six of the 12 patients were consented before their surgery with initial specimen collected at the time of intubation and last one shortly before extubation (intubation duration < 24 hours). The remaining 6 patients were consented after cardiac surgery. All specimens were collected per routine care per respiratory therapy protocol and shortly before extubation (intubation duration > 24 hours). Tracheal fluid aspirates were collected every 4 to 12 hours in the ventilated patients. Enzymatic assay for gastric pepsin A and protein determination were performed. The time of oral care and throat suctioning within 4 hours prior was recorded prospectively. Results: A total of 342 TA specimens were obtained from the 12 intubated pediatric patients during their course of hospitalization; 287 (83.9%) showed detectable total pepsin (pepsin A and C) enzyme activity (> 6 ng/mL) and 176 (51.5%) samples had detectable pepsin A enzyme levels (>6 ng/mL of pepsin A). Only 29 samples of 76 samples (38.2%) had evidence of microaspiration after receiving oral care, while 147 of 266 (55.3%) samples were pepsin A positive when no oral care was provided. Odds ratio is 0.50 (Cl 0.30-0.84), and the number needed to treat is 5.8 (Confidence interval 3.4-22.3). Testing air filters for pepsin was not beneficial. Conclusion: Oral care is a highly effective measure to prevent microaspiration of gastric fluid in ventilated pediatric patients. The number needed to treat (5.8) suggests this is a very effective prevention strategy. Our study suggests that pepsin A is a useful and sensitive biomarker that allows identification of gastric aspiration.

Self-Determination Theory and Accountant Employees' Psychological Wellbeing: The Roles of Positive Affectivity and Psychological Safety.

This study investigates the influence of self-determination motivations on accountant employees' psychological wellbeing with the mediating role of positive affectivity and the moderating role of psychological safety. Multivariate analysis and structural equation modeling are used to analyze a three-way time-lagged sample data of 391 accountant employees. Results indicate that positive affectivity positively mediates the relationship between extrinsic motivation and psychological wellbeing and between intrinsic motivation and psychological wellbeing. Furthermore, psychological safety positively moderates the relationship between extrinsic motivation and positive affectivity and between intrinsic motivation and positive affectivity. In addition, psychological safety also positively moderates the relationship between positive affectivity and psychological wellbeing. The findings of this study provide implications for researchers and business managers in managing and enhancing accountant employees' psychological wellbeing.

Primary Palliative Care for Emergency Medicine (PRIM-ER): Applying form and function to a theory-based complex intervention.

BACKGROUND: Emergency departments are seeing an increase in acute exacerbations of chronic disease in the older-adult population. The delivery of palliative care in the emergency department can increase goal-concordant care at the end-of-life for this population. New interventions in palliative care for emergency medicine require large, pragmatic, complex health interventions due to the heterogeneous and dynamic environment of emergency departments. These complex interventions must balance fidelity with adaptability, while being rooted in theory, to produce an intervention that can be applied in a variety of contexts. METHODS: Primary Palliative Care for Emergency Medicine (PRIM-ER) is a large, pragmatic, complex health intervention. This paper outlines the conceptual theory-based design as well as the study form and functions of PRIM-ER to exemplify how this complex intervention has balanced fidelity with adaptability. RESULTS: A form and function matrix was created to highlight the key objectives and tailored intervention components of PRIM-ER. Each intervention component was also linked to one or more elements of the Theory of Planned Behavior to support provider behavior change and the delivery of palliative care services and referrals. CONCLUSION: The application of theory and delineation of forms and functions, as well prospective adaptation monitoring of large complex interventions can support the balance of fidelity with adaptability to encourage successful interventions among a variety of clinical environments.

STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.

Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.

Barriers to Repair in Maxillofacial Trauma.

IMPORTANCE: Multiple factors can be associated with the delayed repair of maxillofacial injuries that may be associated with increased morbidity. OBJECTIVE: To assess factors affecting timing of repair and barriers which may exist in the management of maxillofacial trauma. DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study at a tertiary care facility used the Current Procedural Terminology coding to identify adult patients undergoing operative repair of maxillofacial injuries between January 2010 and December 2013. Demographic information, presence and severity of concomitant injuries, as well as fracture-specific data including fracture type(s), mechanism of injury, and documented complications were recorded. Identifiable delays for medical, logistical, or other reasons were also documented. Multivariate regression modeling was used to determine factors associated with increased time to repair. A comparative analysis was used to identify association between complications and time to operative repair. MAIN OUTCOMES AND MEASURES: Time to operative repair from date of presentation; association of known operative delay and perioperative complications. RESULTS: Overall, 780 patients were included in the study. Of patients meeting inclusion criteria, mean (SD) age was 36.7 (14.2) years (range, 18-88 years), and 616 patients (79%) were male. Average time to repair was 6.5 days (range, 0-43 days), and 138 patients (17.7%) were observed to have a documented reason for delay for medical reasons (n = 62 [44.9%]), operating room logistical factors (n = 17 [12.3%]), or other reasons (n = 59 patients [42.8%]) either as a function of delayed patient presentation or failure of patients to make scheduled appointments or operations. Injury severity score (ρ = 0.45; P < .001), concurrent injuries (P < .001), decreased Glasgow Coma Scale (P < .001) and inpatient status at time of surgery (P < .001), were associated with increased time to repair. The observed complication rate was 13.6%. There was no statistically significant association between known operative delay and development of complications (χ21 = 2.92; P = .08). CONCLUSIONS AND RELEVANCE: Management of maxillofacial trauma appears to occur in a timely manner. Patient injury severity appears to have the greatest effect on timing of repair. While delays in operative repair may be unavoidable in certain circumstances, streamlining and managing causes of known delay may help improve and expedite patient care. LEVEL OF EVIDENCE: 3.

Prevalence of Giardia and Cryptosporidium species in dog park attending dogs compared to non-dog park attending dogs in one region of Colorado.

Dog parks are very popular in urban areas, but there are no current studies attempting to correlate visits to dog parks and risk of colonization by enteric parasites. The purpose of this study was to determine whether dog park visitation is associated with an increased prevalence of enteric parasites or an increase in prevalence of gastrointestinal signs in dogs in northern Colorado. Feces from dogs owned by veterinary students or Veterinary Teaching Hospital staff members were submitted with a completed survey form detailing dog park attendance rates, fecal character scores, and other clinical information. Feces were examined microscopically for parasites after sugar centrifugation, for Giardia spp. cysts and Cryptosporidium spp. oocysts by a commercially available immunofluorescence assay (FA) and the FA positive samples were genotyped after PCR amplification. The Giardia assemblages were determined using the glutamate dehydrogenase (GDH) ß-giardin and triose phosphate isomerase (TPI) genes and the Cryptosporidium species were determined using the heat shock protein-70 gene. A total of 129 fecal samples were assayed; 66 were from dog park attending dogs and 63 were from non-dog park-attending dogs. The overall parasite prevalence rate was 7.0% (9 of 129 samples). Dog park attending dogs were more likely to be positive for Giardia or Cryptosporidium than non-dog park-attending dogs (p=0.0279), but there was no association of gastrointestinal signs with dog park attendance or with fecal flotation or FA results. The five Giardia isolates were assemblage C and/or D and the one Cryptosporidium isolate was Ctenocephalides canis.

Ectopic expression of HCMV IE72 and IE86 proteins is sufficient to induce early gene expression but not production of infectious virus in undifferentiated promonocytic THP-1 cells.

Human cytomegalovirus (HCMV) reactivation from latency causes disease in individuals who are immunocompromised or immunosuppressed. Activation of the major immediate-early (MIE) promoter is thought to be an initial step for reactivation. We determined whether expression of the MIE gene products in trans was sufficient to circumvent an HCMV latent-like state in an undifferentiated transformed human promonocytic (THP)-1 cell model system. Expression of the functional MIE proteins was achieved with a replication-defective adenovirus vector, Ad-IE1/2, which contains the MIE gene locus. Expression of the MIE proteins by Ad-IE1/2 prior to HCMV infection induced viral early gene expression accompanied by an increase in active chromatin signals. Expression of the anti-apoptotic protein encoded by UL37x1 increased viral early gene expression. However, viral DNA replication and production of infectious virus was not detected. As expected, cellular differentiation with phorbol 12-myristate 13-acetate and hydrocortisone induced virus production. Cellular differentiation is required for efficient viral reactivation.