In situ correction of liquid meniscus in cell culture imaging system based on parallel Fourier ptychographic microscopy (96 Eyes)

We collaborated with Amgen and spent five years in designing and fabricating next generation multi-well plate imagers based on Fourier ptychographic microscopy (FPM). A 6-well imager (Emsight) and a low-cost parallel microscopic system (96 Eyes) based on parallel FPM were reported in our previous work. However, the effect of liquid meniscus on the image quality is much stronger than anticipated, introducing obvious wavevector misalignment and additional image aberration. To this end, an adaptive wavevector correction (AWC-FPM) algorithm and a pupil recovery improvement strategy are presented to solve these challenges in situ. In addition, dual-channel fluorescence excitation is added to obtain structural information for microbiologists. Experiments are demonstrated to verify their performances. The accuracy of angular resolution with our algorithm is within 0.003 rad. Our algorithms would make the FPM algorithm more robust and practical and can be extended to other FPM-based applications to overcome similar challenges

Antibiotic resistance : from pig to meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health

In situ correction of liquid meniscus in cell culture imaging system based on parallel Fourier ptychographic microscopy (96 Eyes)

We collaborated with Amgen and spent five years in designing and fabricating next generation multi-well plate imagers based on Fourier ptychographic microscopy (FPM). A 6-well imager (Emsight) and a low-cost parallel microscopic system (96 Eyes) based on parallel FPM were reported in our previous work. However, the effect of liquid meniscus on the image quality is much stronger than anticipated, introducing obvious wavevector misalignment and additional image aberration. To this end, an adaptive wavevector correction (AWC-FPM) algorithm and a pupil recovery improvement strategy are presented to solve these challenges in situ. In addition, dual-channel fluorescence excitation is added to obtain structural information for microbiologists. Experiments are demonstrated to verify their performances. The accuracy of angular resolution with our algorithm is within 0.003 rad. Our algorithms would make the FPM algorithm more robust and practical and can be extended to other FPM-based applications to overcome similar challenges

Stabilization of swine fecal samples influences taxonomic and functional results in microbiome analyses

Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals’ microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80 °C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing

Neutron and proton drip lines using the modified Bethe-Weizsacker mass formula

Proton and neutron separation energies have been calculated using the extended Bethe-Weizsacker mass formula. This modified Bethe-Weizsacker mass formula describes minutely the positions of all the old and the new magic numbers. It accounts for the disappearance of some traditional magic numbers for neutrons and provides extra stability for some new neutron numbers. The neutron and proton drip lines have been predicted using this extended Bethe-Weizsacker mass formula. The implications of the proton drip line on the astrophysical rp-process and of the neutron drip line on the astrophysical r-process have been discussed.Comment: 5 pages, 2 figure

Feasibility of shear wave sonoelastography to detect endoleak and evaluate thrombus organization after endovascular repair of abdominal aortic aneurysm

Purpose To investigate the feasibility of shear wave sonoelastography (SWS) for endoleak detection and thrombus characterization of abdominal aortic aneurysm (AAA) after endovascular repair (EVAR). Materials and methods Participants who underwent EVAR were prospectively recruited between November 2014 and March 2016 and followed until March 2019. Elasticity maps of AAA were computed using SWS and compared to computed tomography angiography (CTA) and color Doppler ultrasound (CDUS). Two readers, blinded to the CTA and CDUS results, reviewed elasticity maps and B-mode images to detect endoleaks. Three or more CTAs per participant were analyzed: pre-EVAR, baseline post-EVAR, and follow-ups. The primary endpoint was endoleak detection. Secondary endpoints included correlation between total thrombus elasticity, proportion of fresh thrombus, and aneurysm growth between baseline and reference CTAs. A 3-year follow-up was made to detect missed endoleaks, EVAR complication, and mortality. Data analyses included Cohen’s kappa; sensitivity, specificity, and positive predictive value (PPV); Pearson coefficient; and Student’s t tests. Results Seven endoleaks in 28 participants were detected by the two SWS readers (k = 0.858). Sensitivity of endoleak detection with SWS was 100%; specificity and PPV averaged 67% and 50%, respectively. CDUS sensitivity was estimated at 43%. Aneurysm growth was significantly greater in the endoleak group compared to sealed AAAs. No correlation between growth and thrombus elasticity or proportion of fresh thrombus in AAAs was found. No new endoleaks were observed in participants with SWS negative studies. Conclusion SWS has the potential to detect endoleaks in AAA after EVAR with comparable sensitivity to CTA and superior sensitivity to CDUS

The SCottish Alcoholic Liver disease Evaluation: a population-level matched cohort study of hospital-based costs, 1991-2011

Studies assessing the costs of alcoholic liver disease are lacking. We aimed to calculate the costs of hospitalisations before and after diagnosis compared to population controls matched by age, sex and socio-economic deprivation. We aimed to use population level data to identify a cohort of individuals hospitalised for the first time with alcoholic liver disease in Scotland between 1991 and 2011.Incident cases were classified by disease severity, sex, age group, socio-economic deprivation and year of index admission. 5 matched controls for every incident case were identified from the Scottish population level primary care database. Hospital costs were calculated for both cases and controls using length of stay from morbidity records and hospital-specific daily rates by specialty. Remaining lifetime costs were estimated using parametric survival models and predicted annual costs. 35,208 incident alcoholic liver disease hospitalisations were identified. Mean annual hospital costs for cases were 2.3 times that of controls pre diagnosis (£804 higher) and 10.2 times (£12,774 higher) post diagnosis. Mean incident admission cost was £6,663. Remaining lifetime cost for a male, 50-59 years old, living in the most deprived area diagnosed with acoholic liver disease was estimated to be £65,999 higher than the matched controls (£12,474 for 7.43 years remaining life compared to £1,224 for 21.8 years). In Scotland, alcoholic liver disease diagnosis is associated with significant increases in admissions to hospital both before and after diagnosis. Our results provide robust population level estimates of costs of alcoholic liver disease for the purposes of health-care delivery, planning and future cost-effectiveness analyses

Parallel Fourier ptychographic microscopy for high-throughput screening with 96 cameras (96 Eyes)

We report the implementation of a parallel microscopy system (96 Eyes) that is capable of simultaneous imaging of all wells on a 96-well plate. The optical system consists of 96 microscopy units, where each unit is made out of a four element objective, made through a molded injection process, and a low cost CMOS camera chip. By illuminating the sample with angle varying light and applying Fourier Ptychography, we can improve the effective brightfield imaging numerical aperture of the objectives from 0.23 to 0.3, and extend the depth of field from ±5 μm to ±15 μm. The use of Fourier Ptychography additionally allows us to computationally correct the objectives’ aberrations out of the rendered images, and provides us with the ability to render phase images. The 96 Eyes acquires raw data at a rate of 0.7 frame per second (all wells) and the data are processed with 4 cores of graphical processing units (GPUs; GK210, Nvidia Tesla K80, USA). The system is also capable of fluorescence imaging (excitation = 465 nm, emission = 510 nm) at the native resolution of the objectives. We demonstrate the capability of this system by imaging S1P_1-eGFP-Human bone osteosarcoma epithelial (U2OS) cells