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

UBC East Mall Redesign Detailed Design Report

Per requested by UBC SEEDS Sustainability Program, a redesign on the East Mall segment between Agronomy Road and W 16th Avenue is prompted to achieve two goals: 1) Address current traffic issues such as speeding, lack of safety for pedestrians and cyclists, insufficient supply of temporary parking, etc.; 2) Improve the surrounding area with betterment such as tie-in with the Thunderbird Stadium Neighborhood, weather protection at Agronomy Road, greenspace increment and etc. The final detailed design is developed based on the preliminary design, with new features added. The final report includes design key components, design criteria, construction and maintenance plan, detailed cost estimate, construction schedule as well as the IFC drawings package and construction specification. Different modelling softwares such as Excel, AutoCAD and Synchro were applied to visualize the design components and analyze the design outcome. An updated class-B cost estimate is conducted, with the total of 14 main tasks defined in the detailed stage broken down into 35 subtasks. The project is estimated to be $11,432,982 CAD. The estimated cost covers permitting fee, construction cost, direct operation cost and maintenance cost. Based on estimated project schedule, actual construction will start on May 1st, 2021, and will attain substantial completion by Aug 22nd, 2021. Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”Applied Science, Faculty ofCivil Engineering, Department ofUnreviewedUndergraduat

Preclinical Evaluation of GS-9160, a Novel Inhibitor of Human Immunodeficiency Virus Type 1 Integrase▿ †

GS-9160 is a novel and potent inhibitor of human immunodeficiency virus type 1 (HIV-1) integrase (IN) that specifically targets the process of strand transfer. It is an authentic inhibitor of HIV-1 integration, since treatment of infected cells results in an elevation of two-long terminal repeat circles and a decrease of integration junctions. GS-9160 has potent and selective antiviral activity in primary human T lymphocytes producing a 50% effective concentration (EC50) of ∼2 nM, with a selectivity index (50% cytotoxic concentration/EC50) of ∼2,000. The antiviral potency of GS-9160 decreased by 6- to 10-fold in the presence of human serum. The antiviral activity of GS-9160 is synergistic in combination with representatives from three different classes of antiviral drugs, namely HIV-1 protease inhibitors, nonnucleoside reverse transcriptase inhibitors, and nucleotide reverse transcriptase inhibitors. Viral resistance selections performed with GS-9160 yielded a novel pattern of mutations within the catalytic core domain of IN; E92V emerged initially, followed by L74M. While E92V as a single mutant conferred 12-fold resistance against GS-9160, L74M had no effect as a single mutant. Together, these mutations conferred 67-fold resistance to GS-9160, indicating that L74M may potentiate the resistance caused by E92V. The pharmacokinetic profile of GS-9160 in healthy human volunteers revealed that once-daily dosing was not likely to achieve antiviral efficacy; hence, the clinical development of this compound was discontinued

Heterostructure Interface Construction of Cobalt/Nickle Diselenides Hybridized with sp²–sp³ Bonded Carbon to Boost Internal/External Sodium and Potassium Storage Dynamics

Metal selenides exhibit great potential in energy storage systems owing to their diversified species, large interlayer spaces, and high theoretical specific capacity according to multiple ion-storage behaviors. In this work, heterostructured CoSe2/NiSe2 coupled with sp3 bonded N-doped carbon coating layers and interconnected with sp2 bonded carbon nanotubes is synthesized through a room-temperature wet-chemistry approach and a selenization route with Co–Ni Prussian blue analogues as the precursor. The hybrid exhibits enhanced energy storage properties when utilized as an anode material for sodium- and potassium-ion batteries. The excellent performance of the hybrid can be indexed to the delicately design of the CoSe2/NiSe2 heterostructure and the hybridization of it with sp2 and sp3 bonded carbonaceous materials synchronously. Experimental and theoretical calculation results demonstrate the heterostructure is constructed to acquire charge transfer driving forces to boost internal reaction dynamics. And there is a combination of the dual advantages of sp3 and sp2 bonded carbon, possessing not only the exceptional mechanics buffer capability of N-doped carbon coating layers but also the excellent electrical characteristics of carbon nanotubes to promote external reaction dynamics. In addition, to elucidate the differential sodium/potassium storage capability of the hybrid, theoretical calculations are further performed to indagate the adsorption energy of sodium and potassium on the CoSe2/NiSe2 heterointerface by establishing five Na/K adsorption sites. The research provides an effective strategy for the melioration of internal/external reaction dynamics to deliver ions durably and efficiently in energy storage regions

Early inner plexiform layer thinning and retinal nerve fiber layer thickening in excitotoxic retinal injury using deep learning-assisted optical coherence tomography

Abstract Excitotoxicity from the impairment of glutamate uptake constitutes an important mechanism in neurodegenerative diseases such as Alzheimer’s, multiple sclerosis, and Parkinson's disease. Within the eye, excitotoxicity is thought to play a critical role in retinal ganglion cell death in glaucoma, diabetic retinopathy, retinal ischemia, and optic nerve injury, yet how excitotoxic injury impacts different retinal layers is not well understood. Here, we investigated the longitudinal effects of N-methyl-D-aspartate (NMDA)-induced excitotoxic retinal injury in a rat model using deep learning-assisted retinal layer thickness estimation. Before and after unilateral intravitreal NMDA injection in nine adult Long Evans rats, spectral-domain optical coherence tomography (OCT) was used to acquire volumetric retinal images in both eyes over 4 weeks. Ten retinal layers were automatically segmented from the OCT data using our deep learning-based algorithm. Retinal degeneration was evaluated using layer-specific retinal thickness changes at each time point (before, and at 3, 7, and 28 days after NMDA injection). Within the inner retina, our OCT results showed that retinal thinning occurred first in the inner plexiform layer at 3 days after NMDA injection, followed by the inner nuclear layer at 7 days post-injury. In contrast, the retinal nerve fiber layer exhibited an initial thickening 3 days after NMDA injection, followed by normalization and thinning up to 4 weeks post-injury. Our results demonstrated the pathological cascades of NMDA-induced neurotoxicity across different layers of the retina. The early inner plexiform layer thinning suggests early dendritic shrinkage, whereas the initial retinal nerve fiber layer thickening before subsequent normalization and thinning indicates early inflammation before axonal loss and cell death. These findings implicate the inner plexiform layer as an early imaging biomarker of excitotoxic retinal degeneration, whereas caution is warranted when interpreting the ganglion cell complex combining retinal nerve fiber layer, ganglion cell layer, and inner plexiform layer thicknesses in conventional OCT measures. Deep learning-assisted retinal layer segmentation and longitudinal OCT monitoring can help evaluate the different phases of retinal layer damage upon excitotoxicity

Exploration of Major Cognitive Deficits in Medication-Free Patients With Major Depressive Disorder

Background: Major depressive disorder (MDD) is associated with a wide range of cognitive deficits. However, it remains unclear whether there will be a major cognitive deficit independently caused by depression at acute episodes of MDD. Method: A comprehensive neurocognitive test battery was used to assess the executive function, processing speed, attention, and memory in 162 MDD patients and 142 healthy controls (HCs). A multivariate analysis of variance, hierarchical regression analyses and general linear regression analyses were used to explore the possible major cognitive deficits and their predictor variables. Results: MDD patients showed extensive impairment in all four cognitive domains. Impairment of executive function and processing speed were found to persist even with other cognitive domains and clinical variables being accounted for. Executive function and processing speed were further predicted by total disease duration and depression severity, respectively. Conclusions: Executive function and processing speed may be two distinct major deficits at acute episodes of MDD. Furthermore, the executive function is likely originated from the cumulative effect of disease duration and processing speed is possibly derived from the temporary effect of current depressive episode.</p