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"Ross, David"
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Automated analysis of bacterial flow cytometry data with FlowGateNIST
Flow cytometry is commonly used to evaluate the performance of engineered bacteria. With increasing use of high-throughput experimental methods, there is a need for automated analysis methods for flow cytometry data. Here, we describe FlowGateNIST, a Python package for automated analysis of bacterial flow cytometry data. The main components of FlowGateNIST perform automatic gating to differentiate between cells and background events and then between singlet and multiplet events. FlowGateNIST also includes a method for automatic calibration of fluorescence signals using fluorescence calibration beads. FlowGateNIST is open source and freely available with tutorials and example data to facilitate adoption by users with minimal programming experience.
Journal Article
Differences in words used to describe racial and gender groups in Medical Student Performance Evaluations
The transition from medical school to residency is a critical step in the careers of physicians. Because of the standardized application process-wherein schools submit summative Medical Student Performance Evaluations (MSPE's)-it also represents a unique opportunity to assess the possible prevalence of racial and gender disparities, as shown elsewhere in medicine.
The authors conducted textual analysis of MSPE's from 6,000 US students applying to 16 residency programs at a single institution in 2014-15. They used custom software to extract demographic data and keyword frequency from each MSPE. The main outcome measure was the proportion of applicants described using 24 pre-determined words from four thematic categories (\"standout traits\", \"ability\", \"grindstone habits\", and \"compassion\").
The data showed significant differences based on race and gender. White applicants were more likely to be described using \"standout\" or \"ability\" keywords (including \"exceptional\", \"best\", and \"outstanding\") while Black applicants were more likely to be described as \"competent\". These differences remained significant after controlling for United States Medical Licensing Examination Step 1 scores. Female applicants were more frequently described as \"caring\", \"compassionate\", and \"empathic\" or \"empathetic\". Women were also more frequently described as \"bright\" and \"organized\".
While the MSPE is intended to reflect an objective, summative assessment of students' qualifications, these data demonstrate for the first time systematic differences in how candidates are described based on racial/ethnic and gender group membership. Recognizing possible implicit biases and their potential impact is important for faculty who strive to create a more egalitarian medical community.
Journal Article
Billionaire boy
Joe has a lot of reasons to be happy. About a billion of them, in fact. You see, Joe's rich. Really, really rich. Joe's got his own bowling alley, his own cinema, even his own butler who is also an orangutan. He's the wealthiest twelve-year-old in the land. Yes, Joe has absolutely everything he could possibly want. But there's just one thing he really needs: a friend!
Book
Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H2O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers.
Journal Article
Awful Auntie
From number one bestselling author David Walliams comes another heartfelt but hilarious hoot of an adventure Stella Saxby is the sole heir to Saxby Hall. But awful Aunt Alberta and her giant owl will stop at nothing to get it from her. Luckily Stella has a secret - and slightly spooky - weapon up her sleeve.
Book
Policy Forum: Sailing Beyond the Sunset? Are De Jure Control and Other Bright-Line Tests Relevant After Deans Knight and the New GAAR?
This article takes readers on a voyage through the Supreme Court of Canada's decision in Deans Knight Income Corp. v. Canada and subsequent cases that apply its interpretation of the general anti-avoidance rule (GAAR). The author draws on metaphors from Greek philosophy and sailing to aid—and lighten—the discussion of the immortality of corporations, bright lines, and the Income Tax Act. The author argues that the majority of the Supreme Court in Deans Knight committed a \"purpose error\": in applying GAAR, the majority overemphasized subsection 111(5)'s primary purpose of stopping corporate loss trading at the expense of the legislation's other purposes, including providing certainty to public companies with high shareholder turnover. Future cases decided under the amended GAAR may be even more vulnerable to a purpose error. The author then considers whether other bright-line tests in the Act are vulnerable to the same sort of purpose error if GAAR is applied. For example, he examines whether the 30-day time limit in the Act's stop-loss rules could be abused by waiting an extra day to comply with the rule, whether waiting one more day to sell a house could abuse the \"flipped property\" rules in subsections 12(12) to (14), and whether buying one more share to meet an ownership threshold could abuse part IV or section 113. While each of those strategies could arguably be abusive under the approach taken in Deans Knight, it would be an error to always interpret the rules so broadly. Courts should consider Parliament's purpose in using a bright-line test before applying GAAR, and ask how arbitrary and potentially manipulable the line is.
Journal Article