An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming.

The great demographic pressure brings tremendous volume of beef demand. The key to solve this problem is the growth and development of Chinese cattle. In order to find molecular markers conducive to the growth and development of Chinese cattle, sequencing was used to determine the position of copy number variations (CNVs), bioinformatics analysis was used to predict the function of ZNF146 gene, real-time fluorescent quantitative polymerase chain reaction (qPCR) was used for CNV genotyping and one-way analysis of variance was used for association analysis. The results showed that there exists CNV in Chr 18: 47225201-47229600 (5.0.1 version) of ZNF146 gene through the early sequencing results in the laboratory and predicted ZNF146 gene was expressed in liver, skeletal muscle and breast cells, and was amplified or overexpressed in pancreatic cancer, which promoted the development of tumour through bioinformatics. Therefore, it is predicted that ZNF146 gene affects the proliferation of muscle cells, and then affects the growth and development of cattle. Furthermore, CNV genotyping of ZNF146 gene was three types (deletion type, normal type and duplication type) by Real-time fluorescent quantitative PCR (qPCR). The association analysis results showed that ZNF146-CNV was significantly correlated with rump length of Qinchuan cattle, hucklebone width of Jiaxian red cattle and heart girth of Yunling cattle. From the above results, ZNF146-CNV had a significant effect on growth traits, which provided an important candidate molecular marker for growth and development of Chinese cattle.

Active skin-friction reduction in a turbulent boundary layer (TBL) is experimentally studied based on time-periodic blowing through one array of streamwise slits. The control parameters investigated include the blowing amplitude A+ and frequency f+, which, expressed in wall units, range from 0 to 2 and from 0.007 to 0.56, respectively. The maximum local friction reduction downstream of the slits reaches more than 70 %; friction does not fully recover to the state of the natural TBL until 500 wall units behind the slits. A positive net power saving is possible, and 4.01 % is measured with a local friction drag reduction (DR) of 49 %. A detailed analysis based on hot-wire, particle image velocimetry and smoke-wire flow visualization data is performed to understand the physical mechanisms involved. Spectral analysis indicates weakened near-wall large-scale structures. Flow visualizations show stabilized streaky structures and a locally relaminarized flow. Two factors are identified to contribute to the DR. Firstly, the jets from the slits create streamwise vortices in the near-wall region, preventing the formation of near-wall streaks and interrupting the turbulence generation cycle. Secondly, the zero-streamwise-momentum fluid associated with the jets also accounts for the DR. A closed-loop opposing control system is developed, along with an open-loop desynchronized control scheme, to quantify the two contributions. The latter is found to account for 77 % of the DR, whereas the former is responsible for 23 %. An empirical scaling of the DR is also proposed, which provides valuable insight into the TBL control physics.

This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to coronavirus disease 2019 (COVID-19) with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplementary materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.

The fatty acid composition of chicken’s meat is largely influenced by dietary lipids, which are often used as supplements to increase dietary caloric density. The underlying key metabolites and pathways influenced by dietary oils remain poorly known in chickens. The objective of this study was to explore the underlying metabolic mechanisms of how diets supplemented with mixed or a single oil with distinct fatty acid composition influence the fatty acid profile in breast muscle of Qingyuan chickens. Birds were fed a corn-soybean meal diet supplemented with either soybean oil (control, CON) or equal amounts of mixed edible oils (MEO; soybean oil : lard : fish oil : coconut oil = 1 : 1 : 0.5 : 0.5) from 1 to 120 days of age. Growth performance and fatty acid composition of muscle lipids were analysed. LC-MS was applied to investigate the effects of CON v. MEO diets on lipid-related metabolites in the muscle of chickens at day 120. Compared with the CON diet, chickens fed the MEO diet had a lower feed conversion ratio (P < 0.05), higher proportions of lauric acid (C12:0), myristic acid (C14:0), palmitoleic acid (C16:1n-7), oleic acid (C18:1n-9), EPA (C20:5n-3) and DHA (C22:6n-3), and a lower linoleic acid (C18:2n-6) content in breast muscle (P < 0.05). Muscle metabolome profiling showed that the most differentially abundant metabolites are phospholipids, including phosphatidylcholines (PC) and phosphatidylethanolamines (PE), which enriched the glycerophospholipid metabolism (P < 0.05). These key differentially abundant metabolites – PC (14:0/20:4), PC (18:1/14:1), PC (18:0/14:1), PC (18:0/18:4), PC (20:0/18:4), PE (22:0/P-16:0), PE (24:0/20:5), PE (22:2/P-18:1), PE (24:0/18:4) – were closely associated with the contents of C12:0, C14:0, DHA and C18:2n-6 in muscle lipids (P < 0.05). The content of glutathione metabolite was higher with MEO than CON diet (P < 0.05). Based on these results, it can be concluded that the diet supplemented with MEO reduced the feed conversion ratio, enriched the content of n-3 fatty acids and modified the related metabolites (including PC, PE and glutathione) in breast muscle of chickens.

It is difficult to separate an age-dependent fall in nitrogen use efficiency (NUE; N balance/N intake) in growing ruminants from a progressively decrease in animal protein requirements over time. This study examined the effect of dietary protein content on N partitioning, digestibility and N isotopic discrimination between the animal and its diet (Δ15Nanimal-diet) evaluated at two different fattening periods (early v. late). Twenty-four male Romane lambs (age: 19 ± 4.0 days; BW: 8.3 ± 1.39 kg) were equally allocated to three dietary CP treatments (15%, 17% and 20% CP on a DM basis). Lambs were reared with their mothers until weaning, thereafter housed in individual pens until slaughter (45 kg BW). During the post-weaning period, lambs were allocated twice (early fattening (30 days post-weaning) and late fattening (60 days post-weaning)) to metabolic cages for digestibility and N balance study. When diet CP content increased, the average daily gain of lambs increased (P < 0.05) while the age at slaughter decreased (P = 0.01), but no effect was observed on feed efficiency (P > 0.10). Diet CP content had limited effect on lamb carcass traits. Higher fibre digestibility was observed at the early v. late fattening period (P < 0.001). The N intake and the urinary N excretion increased when diet CP content increased (P < 0.001) and when shifting from early to late fattening period (P < 0.001). Faecal N excretion (P = 0.14) and N balance (P > 0.10) were not affected by diet CP content. Nitrogen digestibility increased (P < 0.001) as the diet CP content increased and on average it was greater at late v. early fattening period (P = 0.02). The NUE decreased (P = 0.001) as the diet CP content increased and as the lamb became older (P < 0.001). However, the age-dependent fall in NUE observed was lower at high v. low dietary CP content (CP × age interaction; P = 0.04). The Δ15Nanimal-diet was positively correlated (P < 0.05) with N intake (r = 0.59), excretion of faecal N (r = 0.41), urinary N (r = 0.69) and total manure N (r = 0.64), while negatively correlated with NUE (r = −0.57). Overall, the experiment showed NUE was lower in older lambs and when lambs were fed high diet CP content, and that Δ15Nanimal-diet was a useful indicator not only for NUE but also for urinary N excretion, which is a major environmental pollution factor on farm.

Copy number variations (CNVs), as an important source of genetic variation, can affect a wide range of phenotypes by diverse mechanisms. The somatostatin receptor 2 (SSTR2) gene plays important roles in cell proliferation and apoptosis. Recently, this gene was mapped to a CNV region, which encompasses quantitative trait loci of cattle economic traits including body weight, marbling score, etc. Therefore, SSTR2 CNV may exhibit phenotypic effects on cattle growth traits. In the current study, distribution of SSTR2 gene CNVs was investigated in six Chinese cattle breeds (XN, QC, NY, JA, LX and PN), and the results showed higher CNV polymorphisms in XN, QC and NY cattle. Next, association analysis between growth traits and SSTR2 CNV was performed for XN, QC and NY cattle. In NY, individuals with fewer copies showed better performance than those with more copies. Further, the effects of SSTR2 CNV on the SSTR2 mRNA level were also investigated, but revealed no significant correlation in either muscle or adipose tissue of adult NY cattle. The results suggested the potential for use of SSTR2 CNV as a marker for the molecular breeding of NY cattle.

We describe the case of an 11-month-old girl with a rare cerebellar glioblastoma driven by a NACC2-NTRK2 (Nucleus Accumbens Associated Protein 2-Neurotrophic Receptor Tyrosine Kinase 2) fusion. Initial workup of our case demonstrated homozygous CDKN2A deletion, but immunohistochemistry for other driver mutations, including IDH1 R132H, BRAF V600E, and H3F3A K27M were negative, and ATRX was retained. Tissue was subsequently submitted for personalized oncogenomic analysis, including whole genome and whole transcriptome sequencing, which demonstrated an activating NTRK2 fusion, as well as high PD-L1 expression, which was subsequently confirmed by immunohistochemistry. Furthermore, H3 and IDH demonstrated wildtype status. These findings suggested the possibility of treatment with either NTRK- or immune checkpoint- inhibitors through active clinical trials. Ultimately, the family pursued standard treatment that involved Head Start III chemotherapy and proton radiotherapy. Notably, at most recent follow upapproximately two years from initial diagnosis, the patient is in disease remission and thriving, suggesting favorable biology despite histologic malignancy. This case illustrates the value of personalized oncogenomics, as the molecular profiling revealed two actionable changes that would not have been apparent through routine diagnostics. NTRK fusions are known oncogenic drivers in a range of cancer types, but this is the first report of a NACC2-NTRK2 fusion in a glioblastoma.

Various individual diet and lifestyle factors are associated with mortality. Investigating these factors collectively may help clarify whether dietary and lifestyle patterns contribute to life expectancy. We investigated the association of previously described evolutionary-concordance and Mediterranean diet pattern scores and a novel evolutionary-concordance lifestyle pattern score with all-cause and cause-specific mortality in the prospective Iowa Women’s Health Study (1986–2012). We created the diet pattern scores from Willett FFQ responses, and the lifestyle pattern score from self-reported physical activity, BMI and smoking status, and assessed their associations with mortality, using multivariable Cox proportional hazards regression. Of the 35 221 55- to 69-year-old cancer-free women at baseline, 18 687 died during follow-up. The adjusted hazard ratios (HR) and 95 % CI for all-cause, all CVD, and all-cancer mortality among participants in the highest relative to the lowest quintile of the evolutionary-concordance lifestyle score were, respectively, 0·52 (95 % CI 0·50, 0·55), 0·53 (95 % CI 0·49, 0·57) and 0·51 (95 % CI 0·46, 0·57). The corresponding findings for the Mediterranean diet score were HR 0·85 (95 % CI 0·82, 0·90), 0·83 (95 % CI 0·76, 0·90) and 0·93 (95 % CI 0·84, 1·03), and for the evolutionary-concordance diet score they were close to null and not statistically significant. The lowest estimated risk was among those in the highest joint quintile of the lifestyle score and either diet score (both Pinteraction <0·01). Our findings suggest that (1) a more Mediterranean-like diet pattern and (2) a more evolutionary-concordant lifestyle pattern, alone and in interaction with a more evolutionary-concordant or Mediterranean diet pattern, may be inversely associated with mortality.

The response of soil microbial communities to soil quality changes is a sensitive indicator of soil ecosystem health. The current work investigated soil microbial communities under different fertilization treatments in a 31-year experiment using the phospholipid fatty acid (PLFA) profile method. The experiment consisted of five fertilization treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice (Oryza sativa L.) straw residue and chemical fertilizer (RF), low manure rate and chemical fertilizer (LOM), and high manure rate and chemical fertilizer (HOM). Soil samples were collected from the plough layer and results indicated that the content of PLFAs were increased in all fertilization treatments compared with the control. The iC15:0 fatty acids increased significantly in MF treatment but decreased in RF, LOM and HOM, while aC15:0 fatty acids increased in these three treatments. Principal component (PC) analysis was conducted to determine factors defining soil microbial community structure using the 21 PLFAs detected in all treatments: the first and second PCs explained 89.8% of the total variance. All unsaturated and cyclopropyl PLFAs except C12:0 and C15:0 were highly weighted on the first PC. The first and second PC also explained 87.1% of the total variance among all fertilization treatments. There was no difference in the first and second PC between RF and HOM treatments. The results indicated that long-term combined application of straw residue or organic manure with chemical fertilizer practices improved soil microbial community structure more than the mineral fertilizer treatment in double-cropped paddy fields in Southern China.

Introduction: The 2015 CanMEDS framework requires all residency programs to increase their focus on Quality Improvement and Patient Safety (QIPS). We created a longitudinal (4-year), modular QIPS curriculum for FRCP emergency medicine residents at the University of Toronto (UT) using multiple educational methods. The curriculum addresses three levels of QIPS training: knowledge, practical skills at the microsystem level, and practical skills at the organization level. Aim Statement: To increase the UT FRCP emergency medicine residents absolute score on the QIKAT-R (Quality Improvement Knowledge Application Tool Revised) by 10% after the completion of the QIPS curriculum. Methods: Physicians and other healthcare professionals with QI expertise collaboratively designed and taught the curriculum. We used the QIKAT-R as the outcome measure to evaluate QI knowledge and its applicability. The QIKAT-R is a validated measure that assesses an individuals ability to decipher a QI issue within the healthcare context, and propose a change initiative to address it. The first cohort of residents completed the QIKAT-R prior to the first session in 2014 (pre) and at the completion of the curriculum in 2017 (post). Each response was anonymized and scored by physicians with QI expertise. The QIKAT-R scores and comments from course evaluations are used to make yearly iterative curriculum changes. Results: The QIPS curriculum was implemented in September 2014. All nine residents in the first cohort completed the curriculum; they demonstrated an absolute increase of 19.6% (5.3/27) in the mean QIKAT-R score (13.0 +/− 3.3 pre vs. 18.3 +/− 3.8 post, p=0.001). Of the pre-test responses, 26% were categorized as poor, 70% as good, and 4% as excellent, whereas of the post-test 11% of responses were categorized as poor, 37% as good, and 52% as excellent (p<0.001). Two iterative curriculum changes were made at the end of each academic year since 2014: (1) The time between sessions were decreased to promote knowledge retention, and (2) different PGY3 QI practical project options were provided to suit residents individual QI interests. QIKAT-R scores and resident feedback were used to evaluate the impact of the curriculum changes. Conclusion: A collaborative, modular, longitudinal QIPS curriculum for UT FRCP emergency medicine residents that met CanMEDS requirements was created using multiple educational methods. The first resident cohort that completed the curriculum demonstrated an absolute increase in QI knowledge and its applicability (as measured by the QIKAT-R) by 19.6%. Two PDSA cycles were completed to improve the curriculum with the change ideas generated from resident feedback. Ongoing challenges include limited staff availability to teach and supervise resident QI projects. Future directions include incentivising staff participation and providing mentorship for residents with a career interest in QI beyond what is offered by the curriculum.

Introduction: With the current opioid crisis in Canada, presentations of acute opioid withdrawal (AOW) to emergency departments (ED) are increasing. Undertreated symptoms may result in relapse, overdose and death. Buprenorphine/naloxone (bup/nal) is a partial opioid agonist/antagonist used to mitigate symptoms of AOW, approved by Health Canad in 2007 for opioid use disorder. It is superior to clonidine, and increases follow up with addiction treatment programs when initiated in the ED. Nevertheless, in our inner-city ED in 2014, bup/nal was rarely prescribed. We aimed to increase ED physician prescribing of bup/nal for AOW by 50% over a 26-month period. Methods: Commencing in 2014, an interprofessional team of ED physicians, nurses (RN), pharmacists and QI specialists collaborated to improve the care of patients with AOW. PDSA cycles included: (1) needs assessment of emergency physicians knowledge and practices in 2014; (2) Grand Rounds and a web based information sheet in 2015; (3) ED stocking of bup/nal; (4) convenience order set to standardize AOW management; (5) Grand Rounds in 2016 and (6) peer-coaching for RNs, including case-based discussions and pocket card cognitive aids. The outcome was the number of times bup/nal was prescribed per month by ED physicians between Sept, 2015 and Oct, 2017. Data included the prescriber and use of order set as the process measure. The balancing measure was the number of patients referred to the Addiction Medicine Team who subsequently received bup/nal. Results: Bup/nal was prescribed by ED physicians 70 times, and 14 times by the Addiction Medicine Team. With each PDSA cycle, there was an increase in prescribing, with no significant shifts or trends. By all physicians, the median number of prescriptions per month was 3, and increased from 2 to 4 prescriptions/month after nursing education. There was a smaller increase in the median from 2 to 3 prescriptions/month by ED physicians alone. The order set was used 97% of the time. Conclusion: Bup/nal is safe, effective, and increases follow up with addiction programs for comprehensive assessment and treatment planning. We met our goal of increasing bup/nal prescribing in the ED for AOW by 50%. Moreover, prescribing increased by 100% with the addition of patients who received bup/nal after a referral to the Addiction Medicine Team. The intervention with the greatest impact was RN education, demonstrating that peer-coaching and teaching by an interprofessional team is key to changing practice. Unfortunately, overall prescribing remains low, and ED physicians may still be hesitant to prescribe bup/nal and defer to the specialists. It is unclear if this is due to a low number of patients presenting with AOW, patients with contraindications to bup/nal, or ED physician factors. The next step is an audit of all patients with AOW to see what percentage of those eligible are treated with bup/nal. A follow up survey to determine ongoing barriers will inform further PDSA cycles.

Here a compact three orthogonal planes high-energy electron radiography system was proposed. One of the critical technologies, the ultra-fast beam bunches split from the bunch train are studied. The separated bunches could be transported to the three orthogonal planes of the target for dynamic radiography diagnostics. The key elements of the ultra-fast bunches split system are transverse deflecting cavity (TDC) and the twin septum magnet (TSM). The principle of TDC and TSM are briefly introduced. An example of the beam bunches split system for test experiment (40 MeV electron beam) with TDC and TSM is designed and studied by particle-tracking simulation and it confirms this method is valid and feasible. Especially with TSM, a compact three orthogonal planes radiography system can be realized. The evolution of the beam parameters along the beam line from simulation are investigated. The detailed design of the beam split system and beam dynamics simulation study are presented in this paper.

Bacillary dysentery continues to be a major health issue in developing countries and ambient temperature is a possible environmental determinant. However, evidence about the risk of bacillary dysentery attributable to ambient temperature under climate change scenarios is scarce. We examined the attributable fraction (AF) of temperature-related bacillary dysentery in urban and rural Hefei, China during 2006–2012 and projected its shifting pattern under climate change scenarios using a distributed lag non-linear model. The risk of bacillary dysentery increased with the temperature rise above a threshold (18·4 °C), and the temperature effects appeared to be acute. The proportion of bacillary dysentery attributable to hot temperatures was 18·74% (95 empirical confidence interval (eCI): 8·36–27·44%). Apparent difference of AF was observed between urban and rural areas, with AF varying from 26·87% (95% eCI 16·21–36·68%) in urban area to −1·90% (95 eCI −25·03 to 16·05%) in rural area. Under the climate change scenarios alone (1–4 °C rise), the AF from extreme hot temperatures (>31·2 °C) would rise greatly accompanied by the relatively stable AF from moderate hot temperatures (18·4–31·2 °C). If climate change proceeds, urban area may be more likely to suffer from rapidly increasing burden of disease from extreme hot temperatures in the absence of effective mitigation and adaptation strategies.

There has been wide-spread use of plane wave theory in muffler design in industry. However, This has led to an underestimation of acoustical performances at higher frequencies. To overcome the above drawback, the finite element and boundary element methods have been developed. Nevertheless, the time consumed in calculating the noise level is unacceptable. Moreover, considering the acoustical effect and necessity of space-constrained situation in industry, a compact design of reverse mufflers which may improve the acoustical efficiency is then proposed.

In this paper, a numerical assessment of rectangular mufflers hybridized with straight/reverse chambers using eigen function, four-pole matrix, and genetic algorithm under limited space is developed. Before the optimization is performed, an accuracy check of the mathematical models for the muffler will be carried out. Results reveal that the noise reduction will increase when the number of chambers increases. In addition, the acoustical performance of the mufflers is reversely proportional to the diameter of the inlet/outlet tubes. Also, the TL of the mufflers will be improved when using more number of target tones in the objective function. Consequently, a successful approach in searching optimal shaped rectangular straight/reverse mufflers using an eigen function and a genetic algorithm method within a constrained space has been demonstrated.