Assessment of fungal and bacterial bioaerosols in ambient air in Fairbanks, Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2011Bioaerosols are solid or liquid particles of biological origin that are suspended in the surrounding air or other gaseous environments. Bioaerosols can cause diseases, allergenic or toxicological reactions, respiratory distress, and can be potential bioterrorism threats. Studies concerning ambient bioaerosols have never focused upon central Alaska, and only one experiment has utilized the DRUM (Davis Rotating Unit for Monitoring) impactor as the collection apparatus. This study focuses on the assessment and identification of fungi and bacteria present in the ambient air collected by the DRUM impactor from March 2008 to January 2009. The samples were collected on MylarTM and aluminum substrates (with or without apiezon coating) and subjected to DNA extraction and nested PCR using universal primers for the 16S rRNA gene in bacteria and ITS (internal transcribed spacer) region in fungi. The PCR products were used to generate a clone library, and selected clones from each sample clone library were sequenced. Sequences were taxonomically classified using BLAST for fungal identification and RDP Pipeline for bacterial identification to the genus level. Numerous species of bacteria (i.e., Ralstonia sp., Bradyrhizobium sp., Sphingomonas sp.) and fungi (i.e. Fusarium sp., Cladosporium sp., Penicillium sp.) were identified from the clone libraries, thus indicating that the DRUM impactor has potential for monitoring biological content in the air. The resulting patterns in bacteria and fungi during the course of the year indicate that the DRUM sampler may also have the potential to detect fluctuations in populations that result from meteorological conditions, seasonal cycles, and climatic conditions.Army Research Laboratory Grants W911NF-07-1-0346, W911NF-08-1-0318, W911NF-09-01-05431. Introduction -- 2. Methods & materials -- 2.1. The DRUM impactor -- 2.2. Justification for using DRUM impactor to collect bioaerosols -- 2.3. Bioaerosol collection -- 2.4. Bioaerosol DNA extractions -- 2.5. Bioaerosol DNA amplification and purification -- 2.6. Bioaerosol clone library construction -- 2.7. Taxonomic identification of microbes in bioaerosols -- 2.8. Bioaerosol richness calculations, weather correlations, and PCA analyses -- 3. Results -- 3.1. Community structure of bioaerosols -- 3.2. Microbial diversity of bioaerosols -- 3.3. Microbial communities in relation to weather trends -- 3.4. Monthly microbial composition comparison -- 4. Discussion -- 5. Conclusion -- 6. Acknowledgements -- 7. References -- 8. Appendix

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Western Indian Rural Gut Microbial Diversity in Extreme Prakriti Endo-Phenotypes Reveals Signature Microbes

Heterogeneity amidst healthy individuals at genomic level is being widely acknowledged. This, in turn, is modulated by differential response to environmental cues and treatment regimens, necessitating the need for stratified/personalized therapy. We intend to understand the molecular determinants of Ayurvedic way (ancient Indian system of medicine) of endo-phenotyping individuals into distinct constitution types termed “Prakriti,” which forms the basis of personalized treatment. In this study, we explored and analyzed the healthy human gut microbiome structure within three predominant Prakriti groups from a genetically homogenous cohort to discover differentially abundant taxa, using 16S rRNA gene based microbial community profiling. We found Bacteroidetes and Firmicutes as major gut microbial components in varying composition, albeit with similar trend across Prakriti. Multiple species of the core microbiome showed differential abundance within Prakriti types, with gender specific signature taxons. Our study reveals that despite overall uniform composition of gut microbial community, healthy individuals belonging to different Prakriti groups have enrichment of specific bacteria. It highlights the importance of Prakriti based endo-phenotypes to explain the variability amongst healthy individuals in gut microbial flora that have important consequences for an individual's health, disease and treatment

Results of Phase III Randomized Trial for Use of Docetaxel as a Radiosensitizer in Patients With Head and Neck Cancer, Unsuitable for Cisplatin-Based Chemoradiation

PURPOSE There is a lack of published literature on systemic therapeutic options in cisplatin-ineligible patients with locally advanced head and neck squamous cell carcinoma (LAHNSCC) undergoing chemoradiation. Docetaxel was assessed as a radiosensitizer in this situation.METHODS This was a randomized phase II/III study. Adult patients (age a-18 years) with LAHNSCC planned for chemoradiation and an Eastern Cooperative Oncology Group performance status of 0-2 and who were cisplatin-ineligible were randomly assigned in 1:1 to either radiation alone or radiation with concurrent docetaxel 15 mg/m2 once weekly for a maximum of seven cycles. The primary end point was 2-year disease-free survival (DFS).RESULTS The study recruited 356 patients between July 2017 and May 2021. The 2-year DFS was 30.3% (95% CI, 23.6 to 37.4) versus 42% (95% CI, 34.6 to 49.2) in the RT and Docetaxel-RT arms, respectively (hazard ratio, 0.673; 95% CI, 0.521 to 0.868; P value =.002). The corresponding median overall survival (OS) was 15.3 months (95% CI, 13.1 to 22.0) and 25.5 months (95% CI, 17.6 to 32.5), respectively (log-rank P value =.035). The 2-year OS was 41.7% (95% CI, 34.1 to 49.1) versus 50.8% (95% CI, 43.1 to 58.1) in the RT and Docetaxel-RT arms, respectively (hazard ratio, 0.747; 95% CI, 0.569 to 0.980; P value =.035). There was a higher incidence of grade 3 or above mucositis (22.2% v 49.7%; P &lt;.001), odynophagia (33.5% v 52.5%; P &lt;.001), and dysphagia (33% v 49.7%; P =.002) with the addition of docetaxel.CONCLUSION The addition of docetaxel to radiation improved DFS and OS in cisplatin-ineligible patients with LAHNSCC.</p

Results of Phase III Randomized Trial for Use of Docetaxel as a Radiosensitizer in Patients With Head and Neck Cancer, Unsuitable for Cisplatin-Based Chemoradiation

PURPOSE There is a lack of published literature on systemic therapeutic options in cisplatin-ineligible patients with locally advanced head and neck squamous cell carcinoma (LAHNSCC) undergoing chemoradiation. Docetaxel was assessed as a radiosensitizer in this situation.METHODS This was a randomized phase II/III study. Adult patients (age a-18 years) with LAHNSCC planned for chemoradiation and an Eastern Cooperative Oncology Group performance status of 0-2 and who were cisplatin-ineligible were randomly assigned in 1:1 to either radiation alone or radiation with concurrent docetaxel 15 mg/m2 once weekly for a maximum of seven cycles. The primary end point was 2-year disease-free survival (DFS).RESULTS The study recruited 356 patients between July 2017 and May 2021. The 2-year DFS was 30.3% (95% CI, 23.6 to 37.4) versus 42% (95% CI, 34.6 to 49.2) in the RT and Docetaxel-RT arms, respectively (hazard ratio, 0.673; 95% CI, 0.521 to 0.868; P value =.002). The corresponding median overall survival (OS) was 15.3 months (95% CI, 13.1 to 22.0) and 25.5 months (95% CI, 17.6 to 32.5), respectively (log-rank P value =.035). The 2-year OS was 41.7% (95% CI, 34.1 to 49.1) versus 50.8% (95% CI, 43.1 to 58.1) in the RT and Docetaxel-RT arms, respectively (hazard ratio, 0.747; 95% CI, 0.569 to 0.980; P value =.035). There was a higher incidence of grade 3 or above mucositis (22.2% v 49.7%; P &lt;.001), odynophagia (33.5% v 52.5%; P &lt;.001), and dysphagia (33% v 49.7%; P =.002) with the addition of docetaxel.CONCLUSION The addition of docetaxel to radiation improved DFS and OS in cisplatin-ineligible patients with LAHNSCC.</p