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

Pre-testing international press advertising: the need for informed consensus on methodology

Focuses on the pre-testing of a global press advertising campaign for Seagram’s Chivas Regal whisky and contrasts the contributions of qualitative and quantitative applications. Examines how an informed decision could be made on the most appropriate research approach - in particular the value of the concept of validity; and the strengths and weaknesses of qualitative and quantitative pre-testing given the emotional nature of the product category, importance of branding and nature of advertising. These questions are addressed in this paper through focusing on the research needs for the “global campaign” as well as the need in Japan to evaluate the global campaign and an independently developed local campaign. In the case of Japan, Seagram’s management elected to examine two different research approaches - qualitative and quantitative - to address the question “how to effectively pre-test international press advertising”. This exercise demonstrated that the two approaches produced seemingly contradictory findings. Reasons for this are discussed

Molecular Characterization Of Myeloid Neoplasms Harboring Isochromosome 17q Abnormality

Abstract Isochromosome 17q [i(17q)], a poor prognostic cytogenetic abnormality is a product of the breakage or inappropriate division of the pericentromere leading to the duplication of the long and loss of the short arm of chromosome 17. The region of the breakpoints maps at 17p11, a region encompassing a key tumor suppressor gene: TP53. I(17q) are detected in myelodysplastic/ myeloproliferative neoplasms (MDS/ MPN), chronic myeloid leukemia (CML), and acute myeloid leukemia (AML). This abnormality can occur as a sole structural abnormality or in combination with other chromosomal defects. The presence of i(17q) is associated with poor therapeutic response, disease progression, and an unfavorable clinical outcome. Elucidation of the molecular architecture of patients (pts) carrying i(17q) may lead to better understanding of disease biology and development of novel compounds that can target this disease. We selected 11 pts with i(17q) to characterize their genomic differences. We applied whole exome sequencing (WES) in order to define latent molecular defects explaining the clinical phenotype of this disease. The index case was a male MDS/MPN pt with isolated i(17q), 27% RS, hypercellular bone marrow (BM), mild splenomegaly, and atypical megakaryocytes. The pt developed 7% BM blasts without clinical response to growth factors. Molecularly this pt was a wild type SF3B1, a gene frequently mutated in RARS-T and associated with lower transformation rate to leukemia, better survival, and good/intermediate risk cytogenetic abnormalities. WES was performed on 2 ug of total DNA extracted from BM cells. Non-clonal CD3+ cells were used as source of germ-line control. Twenty-millions reads were run on an Illumina HiSeq2000 sequencer. Using a stringent bio-informatic algorithm developed in house, all variants were filtered based on a variation score (>=30) and a coverage (30X) and the tumor nucleotide variation analysis was performed for each pair (tumor vs. germ-line), where only the variants unique to the tumor were retained. Variants were ultimately filtered in order to exclude SNPs by an in-house annotation and importing the hg19 SNP135. We detected 65 unique candidate genes. Four genes were confirmed to be somatic: 3 were novel: ZFP42 (4q35.2), P4HTM (3p21.31), and VPRBP (3p21.2) and 1 includes the newly discovered SETBP1 (18q12.3) gene. Three variants detected on the chromosome 17 had a wild type configuration. The subsequently genotyped all the pts (MDS/MPN/-U 3; AML 4; RCMD 1; CML 1; RAEB-1 2; mean age: 68 years; male/female: 8/3; i(17q)/other abnormalities:3/8) for the above genes and for a panel of genes known to be mutated in MDS/MPN and other diseases in order to find any genetic association explaining the disase phenotype. We applied Sanger sequencing to DNA derived from BM/peripheral blood cells (BM/PB:7/4) for the following genes and respective exons: TP53 (all exons), SF3B1 (13-16), SRSF2 (1-2), U2AF1 (2 and 6), TET2 (all exons), DNMT3A (18-23), IDH1/2 (4), CBL (8-9), N/KRAS (1-2), ASXL1 (12), JAK2 (12 and 14), EZH2 (16, 18 and 19), MPL (exon 10), BCAS3 (12, 15 and 16), FLT3 (11 and 17), and CSF3R (13,14, and 17). In total, we found 16 heterozygous missense mutations and 1 tandem duplication. We found somatic mutations in ZFP42, P4HTM, and VPRBP in 1 pt. The index case reported a mutation in SETBP1 and SRSF2. SF3B1 was detected as a sole abnormality in 1 patient. Of note, the patient with SF3B1 mutation (K700E) had 50% RS and achieved a complete hematologic remission after decitabine therapy. The most frequent mutations were found in SETBP1 and SRSF2. SETBP1 was found to be mutated in 4/11 (36.3%) pts (D868N, I871T, and G870S was common in 2 pts) while SRSF2 mutations (P95H/R) were found in 3/11 (27.2%) pts. Three pts showed concomitant SRSF2 and SETBP1 mutations. NRAS (G12D) was mutated in 1 pt and associated with SRSF2 and SETBP1 mutations. One pt showed mutations in TET2, JAK2, and TP53. Of note, this pt did not respond to treatment. One pt with MDS/MPN showed a mutation in CSF3R (Q741X), a novel gene discovered in chronic neutrophilic leukemia and atypical CML. The pt also has monosomy 7 and i(17q) abnormality. FLT3-ITD was found in 1 pt. As of last follow-up, only 2 pts remain alive. In sum, we found that poor risk molecular mutations in SRSF2 and SETBP1 are frequently found in i(17q) myeloid malignancies and may be the drivers of poor outcomes in this disease. Disclosures: No relevant conflicts of interest to declare

Delivery of acute ischaemic stroke treatments in the European region in 2019 and 2020.

INTRODUCTION We assessed best available data on access and delivery of acute stroke unit (SU) care, intravenous thrombolysis (IVT) and endovascular treatment (EVT) in the European region in 2019 and 2020. PATIENTS AND METHODS We compared national data per number of inhabitants and per 100 annual incident first-ever ischaemic strokes (AIIS) in 46 countries. Population estimates and ischaemic stroke incidence were based on United Nations data and the Global Burden of Disease Report 2019, respectively. RESULTS The estimated mean number of acute SUs in 2019 was 3.68 (95% CI: 2.90-4.45) per one million inhabitants (MIH) with 7/44 countries having less than one SU per one MIH. The estimated mean annual number of IVTs was 21.03 (95% CI: 15.63-26.43) per 100,000 and 17.14% (95% CI: 12.98-21.30) of the AIIS in 2019, with highest country rates at 79.19 and 52.66%, respectively, and 15 countries delivering less than 10 IVT per 100,000. The estimated mean annual number of EVTs in 2019 was 7.87 (95% CI: 5.96-9.77) per 100,000 and 6.91% (95% CI: 5.15-8.67) of AIIS, with 11 countries delivering less than 1.5 EVT per 100,000. Rates of SUs, IVT and EVT were stable in 2020. There was an increase in mean rates of SUs, IVT and EVT compared to similar data from 2016. CONCLUSION Although there was an increase in reperfusion treatment rates in many countries between 2016 and 2019, this was halted in 2020. There are persistent major inequalities in acute stroke treatment in the European region. Tailored strategies directed to the most vulnerable regions should be prioritised

The Solar Probe ANalyzers-Electrons on the Parker Solar Probe

International audienceElectrostatic analyzers of different designs have been used since the earliest days of the space age, beginning with the very earliest solar-wind measurements made by Mariner 2 en route to Venus in 1962. The Parker Solar Probe (PSP) mission, NASA's first dedicated mission to study the innermost reaches of the heliosphere, makes its thermal plasma measurements using a suite of instruments called the Solar Wind Electrons, Alphas, and Protons (SWEAP) investigation. SWEAP's electron PSP Analyzer (Solar Probe ANalyzer-Electron (SPAN-E)) instruments are a pair of top-hat electrostatic analyzers on PSP that are capable of measuring the electron distribution function in the solar wind from 2 eV to 30 keV. For the first time, in situ measurements of thermal electrons provided by SPAN-E will help reveal the heating and acceleration mechanisms driving the evolution of the solar wind at the points of acceleration and heating, closer than ever before to the Sun. This paper details the design of the SPAN-E sensors and their operation, data formats, and measurement caveats from PSP's first two close encounters with the Sun

The Solar Probe Cup on the Parker Solar Probe

Solar Probe Cup (SPC) is a Faraday cup instrument on board NASA's Parker Solar Probe (PSP) spacecraft designed to make rapid measurements of thermal coronal and solar wind plasma. The spacecraft is in a heliocentric orbit that takes it closer to the Sun than any previous spacecraft, allowing measurements to be made where the coronal and solar wind plasma is being heated and accelerated. The SPC instrument was designed to be pointed directly at the Sun at all times, allowing the solar wind (which is flowing primarily radially away from the Sun) to be measured throughout the orbit. The instrument is capable of measuring solar wind ions with an energy between 100 and 6000 V (protons with speeds from 139 to 1072 km s(-1)). It also measures electrons with an energy/charge between 100 and 1500 V. SPC has been designed to have a wide dynamic range that is capable of measuring protons and alpha particles at the closest perihelion (9.86 solar radii from the center of the Sun) and out to 0.25 au. Initial observations from the first orbit of PSP indicate that the instrument is functioning well.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Solar Wind Electrons Alphas and Protons (SWEAP) Investigation: Design of the Solar Wind and Coronal Plasma Instrument Suite for Solar Probe Plus

International audienceThe Solar Wind Electrons Alphas and Protons (SWEAP) Investigation on Solar Probe Plus is a four sensor instrument suite that provides complete measurements of the electrons and ionized helium and hydrogen that constitute the bulk of solar wind and coronal plasma. SWEAP consists of the Solar Probe Cup (SPC) and the Solar Probe Analyzers (SPAN). SPC is a Faraday Cup that looks directly at the Sun and measures ion and electron fluxes and flow angles as a function of energy. SPAN consists of an ion and electron electrostatic analyzer (ESA) on the ram side of SPP (SPAN-A) and an electron ESA on the anti-ram side (SPAN-B). The SPAN-A ion ESA has a time of flight section that enables it to sort particles by their mass/charge ratio, permitting differentiation of ion species. SPAN-A and -B are rotated relative to one another so their broad fields of view combine like the seams on a baseball to view the entire sky except for the region obscured by the heat shield and covered by SPC. Observations by SPC and SPAN produce the combined field of view and measurement capabilities required to fulfill the science objectives of SWEAP and Solar Probe Plus. SWEAP measurements, in concert with magnetic and electric fields, energetic particles, and white light contextual imaging will enable discovery and understanding of solar wind acceleration and formation, coronal and solar wind heating, and particle acceleration in the inner heliosphere of the solar system. SPC and SPAN are managed by the SWEAP Electronics Module (SWEM), which distributes power, formats onboard data products, and serves as a single electrical interface to the spacecraft. SWEAP data products include ion and electron velocity distribution functions with high energy and angular resolution. Full resolution data are stored within the SWEM, enabling high resolution observations of structures such as shocks, reconnection events, and other transient structures to be selected for download after the fact. This paper describes the implementation of the SWEAP Investigation, the driving requirements for the suite, expected performance of the instruments, and planned data products, as of mission preliminary design review