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

Beam-Specific Spot Guidance and Optimization for PBS Proton Treatment of Bilateral Head and Neck Cancers.

PURPOSE: A multi-field optimization (MFO) technique that uses beam-specific spot placement volumes (SPVs) and spot avoidance volumes (SAVs) is introduced for bilateral head and neck (H&N) cancers. These beam-specific volumes are used to guide the optimizer to consistently achieve optimal organ-at-risk (OAR) sparing with target coverage and plan robustness. MATERIALS AND METHODS: Implementation of this technique using a 4-beam, 5-beam, and variant 5-beam arrangement is discussed. The generation of beam-specific SPVs and SAVs derived from target and OARs are shown. The SPVs for select fields are further partitioned into optimization volumes for uniform dose distributions that resemble those of single-field optimization (SFO). A conventional MFO plan that does not use beam-specific spot placement guidance (MFOcon) and an MFO plan that uses only beam-specific SPV (MFOspv) are compared with current technique (MFOspv/sav), using both simulated scenarios and forward-calculated plans on weekly verification computed tomography (VFCT) scans. RESULTS: Dose distribution characteristics of the 4-beam, 5-beam, and variant 5-beam technique are demonstrated with discussion on OAR sparing. When comparing the MFOcon, MFOspv, and MFOspv/sav, the MFOspv/sav is shown to have superior OAR sparing in 9 of the 14 OARs examined. It also shows clinical plan robustness when evaluated by using both simulated uncertainty scenarios and forward-calculated weekly VFCTs throughout the 7-week treatment course. CONCLUSION: The MFOspv/sav technique is a systematic approach using SPVs and SAVs to guide the optimizer to consistently reach desired OAR dose values and plan robustness

Utility of mosquito surveillance data for spatial prioritization of vector control against dengue viruses in three Brazilian cities

Background: Vector control remains the primary defense against dengue fever. Its success relies on the assumption that vector density is related to disease transmission. Two operational issues include the amount by which mosquito density should be reduced to minimize transmission and the spatio-temporal allotment of resources needed to reduce mosquito density in a cost-effective manner. Recently, a novel technology, MI-Dengue, was implemented city-wide in several Brazilian cities to provide real-time mosquito surveillance data for spatial prioritization of vector control resources. We sought to understand the role of city-wide mosquito density data in predicting disease incidence in order to provide guidance for prioritization of vector control work. Methods: We used hierarchical Bayesian regression modeling to examine the role of city-wide vector surveillance data in predicting human cases of dengue fever in space and time. We used four years of weekly surveillance data from Vitoria city, Brazil, to identify the best model structure. We tested effects of vector density, lagged case data and spatial connectivity. We investigated the generality of the best model using an additional year of data from Vitoria and two years of data from other Brazilian cities: Governador Valadares and Sete Lagoas. Results: We found that city-wide, neighborhood-level averages of household vector density were a poor predictor of dengue-fever cases in the absence of accounting for interactions with human cases. Effects of city-wide spatial patterns were stronger than within-neighborhood or nearest-neighborhood effects. Readily available proxies of spatial relationships between human cases, such as economic status, population density or between-neighborhood roadway distance, did not explain spatial patterns in cases better than unweighted global effects. Conclusions: For spatial prioritization of vector controls, city-wide spatial effects should be given more weight than within-neighborhood or nearest-neighborhood connections, in order to minimize city-wide cases of dengue fever. More research is needed to determine which data could best inform city-wide connectivity. Once these data become available, MI-dengue may be even more effective if vector control is spatially prioritized by considering city-wide connectivity between cases together with information on the location of mosquito density and infected mosquitos

Genetic Polymorphisms at TIMP3 Are Associated with Survival of Adenocarcinoma of the Gastroesophageal Junction

The poor survival of adenocarcinomas of the gastroesophageal junction (GEJ) makes them clinically important. Discovery of host genetic factors that affect outcome may guide more individualized treatment. This study tests whether constitutional genetic variants in matrix metalloproteinases (MMP) and tissue inhibitors of metalloproteinases (TIMP) genes are associated with outcome of GEJ adenocarcinoma. Single nucleotide polymorphisms (SNPs) at four TIMP (TIMP1-4) and three MMP genes (MMP2, MMP7 and MMP9) were genotyped in DNA samples from a prospective cohort of patients with primary adenocarcinoma of the GEJ admitted to the British Columbia Cancer Agency. Cox proportional hazards regression, with adjustment for patient, disease and treatment variables, was used to estimate the association of SNPs with survival. Genotypes for 85 samples and 48 SNPs were analyzed. Four SNPs across TIMP3, (rs130274, rs715572, rs1962223 and rs5754312) were associated with survival. Interaction analyses revealed that the survival associations with rs715572 and rs5754312 are specific and significant for 5FU+cisplatin treated patients. Sanger sequencing of the TIMP3 coding and promoter regions revealed an additional SNP, rs9862, also associated with survival. TIMP3 genetic variants are associated with survival and may be potentially useful in optimizing treatment strategies for individual patients

Structure of the <i>TIMP3</i> gene.

<p>Coding regions of exons are shown as dark bars; 5′ and 3′ untranslated regions are shown as lighter bars; introns and flanking sequence are illustrated by a line. The diagram is not to scale. Thick lines below the gene structure indicate the regions sequenced. SNPs associated with survival are indicated by vertical lines. Variants detected by sequencing are shown as circles. An LD plot based on study data is below the gene. Numbers in the plot are r² values; boxes with darker shading illustrate higher LD; lighter shading represents weaker LD. Circled SNPs show significant association with survival.</p

Gel shift assay for TIMP3 SNPs rs9862 and rs11547635.

<p>A) Probe names and sequences. rs9862 and rs11547635 are indicated with arrows. The 12 bp palindromic sequence is highlighted in bold and core ETS1 consensus sites are underlined. Probes are named according to alleles at sites rs9862 and rs11547635, respectively. Only one strand of the double-stranded probes is shown. B) Results. Probe and competitor names correspond to the sequences in A. Lane 15 is a control, with no nuclear extract. Potential protein complexes bound to the probes are indicated with letters on the left side of the image. Complex I appears to be specific to probes with the rs9862 C allele, whereas complexes II and IV are specific to probes with the rs9862 T allele. Complex III binds irrespective of rs9862 allele, and is competed off by unlabelled ETS1.</p

Survival of the study cohort by <i>TIMP3</i> variations.

<p>Kaplan-Meier survival curves and log-rank test p-values are shown. <b>A</b>) rs130274, <b>B</b>) rs1962223, <b>C</b>) rs5754312, <b>D</b>) rs715572.</p

Demographic and clinical features of the cohort by survival status.

<p>Demographic and clinical features of the cohort by survival status.</p

Hazard ratio (HR) and 95% Confidence intervals (CI) estimated for the association between <i>TIMP3</i> gene variations and survival of the study cohort.

*<p>Adjusted for patient age, disease stage, surgery, chemotherapy, radiation therapy, location of tumor.</p