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Effects of asymmetries on the behaviour of two polymers confined to a boxlike cavity
No full textThe behaviour of systems of confined polymers has been the topic of much recent research. The
information from these studies may help guide the development and optimization of nanofluidic
devices as well as provide insight into the mechanism for segregation of DNA chromosomes in
prokaryotic cells. Some recent experiments examined two DNA molecules confined to a box-like
cavity with strong confinement in one dimension. The researchers examined the effect of
asymmetries in the cross-section of the box and polymer length. In this study, we use computer
simulations to examine the effect of such asymmetries on the behaviour of confined-polymer
systems. We employ a simplistic bead-spring-chain model in computer simulations to obtain
information about the behaviour of the system. We find that asymmetries in the cross-section of
the box tend to promote segregation of the polymers along the long axis of the box. We further
find that in cases where the polymers are different lengths, the longer polymer tends to have a
strong preference for the centre of the box while the smaller polymer is pushed away from the
centre. The information obtained from this study is then used to obtain insight into the trends
observed in the experiments
Tissue processing and optimal visualization of cerebral infarcts following sub-acute focal ischemia in rats
No full textTransient cerebral ischemia followed by reperfusion in an infarcted brain comes with predictable acute and chronic morphological alterations in neuronal and non-neuronal cells. An accurate delineation of the cerebral infarct is not a simple task due to the complex shapes and indistinct borders of the infarction. Thus, an exact macroscopic histological approach for infarct volume estimation can lead to faster and more reliable preclinical research results. This study investigated the effect(s) of confounding factors such as fixation and tissue embedding on the quality of macroscopic visualization of focal cerebral ischemia by anti-microtubule-associated-protein-2 antibody (MAP2) with conventional Hematoxylin and Eosin (HE) staining serving as the control. The aim was to specify the most reliable macroscopic infarct size estimation method after sub-acute focal cerebral ischemia based on the qualitative investigation. Our results showed that the ischemic area on the MAP2-stained sections could be identified macroscopically on both cryo-preserved and paraffin-embedded sections from both immersion- and perfusion-fixed brains. The HE staining did not clearly depict an infarct area for macroscopic visualization. Therefore both immersion-fixed and perfused-fixed-MAP2 stained sections can be used reliably to quantify cerebral infarcts.Independent Research Fund Denmar
Encephalitozoon pogonae–Associated Systemic Vasculitis in a Central Bearded Dragon (Pogona vitticeps)
No full textA 4-yr-old female central bearded dragon (Pogona vitticeps) with a history of tenesmus was found dead 1 month after surgical debulking of a palpable caudal coelomic mass. At necropsy, a 2.5-cm-diameter, firm, lobulated, tan–yellow mass was associated with the wall of the pelvic canal and bilateral masses were present in the caudal pharynx (0.6 and 3.0 cm in diameter), the largest of which was soft and dark red. Histologically, the mass within the pelvic canal arose from the coelomic wall and consisted primarily of fibrocollagen with myxoid to cystic regions, and mixed inflammatory infiltrates. Additional findings included granulomatous dermatitis, myositis/cellulitis, coelomitis, encephalitis, and pneumonia. Vasculitis was detected in multiple organs, and in the pharynx resulted in aneurysmal dilation and perivascular hemorrhage leading to masslike lesions. Within all lesions, scattered macrophages contained oval, weakly basophilic, Gram-positive, slightly refractile, 1–2 µm-diameter ovoid organisms consistent with microsporidia. A diagnosis of systemic microsporidiosis characterized by lymphohistiocytic and heterophilic vasculitis with medial hypertrophy and fibrinoid necrosis was made. Using DNA sequencing, the organism was identified as Encephalitozoon pogonae. Encephalitozoon pogonae should be considered a differential diagnosis for vasculitis and aneurysms in bearded dragons
Glioma segmentation of optimized 3D U-net and prediction of multi-modal survival time
No full textIt is difficult to segment Glioma and its internal structure because the Glioma boundaries have edemas and complex internal structures. This paper proposes a new optimized, integrated 3D U-Net network to achieve accurate segmentation of Glioma and internal subareas. The contribution of this paper is twofold, it studies the clinical path of patients with Glioma and constructs an optimized 3D U-Net deep learning algorithm by combining them with the radiologic feature set. The proposed model was validated in the published Glioma operation data set of multi-modal MRI resonance images and clinicians manual segmentation data. The model can accurately segment the MRI multi-modality images of Glioma and intra-tumour nodes and achieve the multi-modality prediction of the overall survival period of patients. The experimental results further indicated that the segmentation accuracy of the proposed method was higher than other sophisticated methods. The Dice similarity coefficients of the whole tumor (WT) region, the core tumor (CT) region, and the augmentation / enhanced tumor (ET) region, were 0.9632, 0.8763, and 0.8421, respectively, which are better than the clinical experts’ manual segmentation results. Hence, this research can effectively promote the development of deep learning clinical precise diagnosis and medical technology for Glioma
Evaluation of antimicrobial prescriptions in dogs with suspected bacterial urinary tract disease
No full textBackground: Antimicrobials are commonly used to treat urinary tract disease in dogs. Understanding antimicrobial use is a critical component of antimicrobial stewardship efforts. Hypothesis/Objectives: To evaluate antimicrobial prescriptions for dogs diagnosed with acute cystitis, recurrent cystitis, and pyelonephritis. Animals: Dogs prescribed antimicrobials for urinary tract disease at veterinary practices in the United States and Canada. Materials and Methods: A retrospective review of antimicrobial prescriptions was performed. Results: The main clinical concerns were sporadic bacterial cystitis (n = 6582), recurrent cystitis (n = 428), and pyelonephritis (n = 326). Amoxicillin/clavulanic acid (2702, 41%), cefpodoxime (1024, 16%), and amoxicillin (874, 13%) were most commonly prescribed for sporadic bacterial cystitis. The median prescribed duration was 12 days (range, 3‐60 days; interquartile range [IQR], 4 days). Shorter durations were used in 2018 (median, 10 days; IQR, 4 days) compared to both 2016 and 2017 (both median, 14 days; IQR, 4 days; P ≤.0002). Amoxicillin/clavulanic acid (146, 33%), marbofloxacin (95, 21%), and cefpodoxime (65, 14%) were most commonly used for recurrent cystitis; median duration of 14 days (range, 3‐77 days; IQR, 10.5 days). Amoxicillin/clavulanic acid (86, 26%), marbofloxacin (56, 17%), and enrofloxacin (36, 11%) were most commonly prescribed for pyelonephritis; however, 93 (29%) dogs received drug combinations. The median duration of treatment was 14 days (range, 3‐77 days; IQR, 11 days). Conclusions and Clinical Importance: Decreases in duration and increased use of recommended first‐line antimicrobials were encouraging. Common drug choices and durations should still be targets for antimicrobial stewardship programs that aim to optimize antimicrobial use, concurrently maximizing patient benefits while minimizing antimicrobial use and use of higher tier antimicrobials
Bayesian estimation of diagnostic accuracy of somatic cell counts history and on-farm milk culture using Petrifilm® to identify quarters or cows that should be treated with antimicrobials in selective treatment protocols at dry off
No full textBayesian latent class models were used to estimate the test accuracy (sensitivity (Se), specificity (Sp), and predictive values (NPV and PPV)) of cow-level somatic cell counts (SCC) data, quarter-level Petrifilm® on-farm milk culture, and quarter-level standard milk bacteriology for the identification of quarters that should possibly be treated with antimicrobials at dry off in dairy cows. Data of 282 cows from 9 dairy herds in Québec, Canada, with bulk tank SCC < 250,000 cells/mL were used. Estimated median herd-prevalence of infections that should be treated was 16.2 % (95 % credibility interval (CI): 11.0--22.7). Se and Sp estimates for quarter-milk culture using Petrifilm® were 82.2 % (95 %CI: 74.0--89.5) and 62.0 % (95 %CI: 58.6--65.6), respectively. Se and Sp for quarter-milk standard bacteriology were 67.4 % (95 %CI: 55.8--81.2) and 79.6 % (95 %CI: 76.4--83.0), respectively. Se and Sp of different SCC scenarios and thresholds were estimated. For first parity cows, using only the last Dairy Herd Improvement (DHI) test SCC with a threshold of 100,000 cells/mL appeared quite accurate, with Se, Sp, PPV, NPV and reduction of antimicrobial usage of 85.6 % (95 %CI: 69.6--95.6), 86.0 % (95 %CI: 80.0--91.7), 58.0 % (95 %CI: 42.3--74.2), 96.4 % (95 %CI: 91.3--99.0), and 75.3 % (95 %CI: 70.7--79.3), respectively. For cows of [greater than or equal to] 2nd parity, using only the last DHI test SCC with a threshold of 200,000 cells/mL resulted in Se, Sp, PPV, NPV and reduction of antimicrobial usage of 75.3 % (95 %CI: 55.8--87.3), 84.0 % (95 %CI: 78.8--89.3), 47.2 % (95 %CI: 32.0--63.7), 94.7 % (95 %CI: 89.0--97.6), and of 77.0 % (95 %CI: 73.3--80.3), respectively. Adding quarter-level milk culture using Petrifilm® to cows identified as unhealthy using cow-level SCC data improved the test accuracy (mainly the PPV) and further reduced the use of antimicrobials. For instance, in [greater than or equal to] 2nd parity cows, using only the last DHI SCC with a threshold of 200,000 cells/mL, adding a subsequent Petrifilm® test increased the reduction from 77.0 % (95 %CI: 73.3--80.3) to 89.5 % (95 %CI: 86.7--91.8). Considering the availability of SCC data, the easiness of using just the last DHI test, and the high NPV that could be achieved, producers may consider using just the last DHI test as a potential tool to identify cows that should be treated with antimicrobials at dry off. It may be used alone or in combination with quarter-level on-farm Petrifilm® milk culture on high SCC cows to further reduce the use of antimicrobials by identifying quarters that need to be treated
RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis)
No full textBackground: The lace plant (Aponogeton madagascariensis) is an aquatic monocot that develops leaves with uniquely formed perforations through the use of a developmentally regulated process called programmed cell death (PCD). The process of perforation formation in lace plant leaves is subdivided into several developmental stages: pre-perforation, window, perforation formation, perforation expansion and mature. The first three emerging "imperforate leaves" do not form perforations, while all subsequent leaves form perforations via developmentally regulated PCD. PCD is active in cells called "PCD cells" that do not retain the antioxidant anthocyanin in spaces called areoles framed by the leaf veins of window stage leaves. Cells near the veins called "NPCD cells" retain a red pigmentation from anthocyanin and do not undergo PCD. While the cellular changes that occur during PCD are well studied, the gene expression patterns underlying these changes and driving PCD during leaf morphogenesis are mostly unknown. We sought to characterize differentially expressed genes (DEGs) that mediate lace plant leaf remodelling and PCD. This was achieved performing gene expression analysis using transcriptomics and comparing DEGs among different stages of leaf development, and between NPCD and PCD cells isolated by laser capture microdissection. Results: Transcriptomes were sequenced from imperforate, pre-perforation, window, and mature leaf stages, as well as PCD and NPCD cells isolated from window stage leaves. Differential expression analysis of the data revealed distinct gene expression profiles: pre-perforation and window stage leaves were characterized by higher expression of genes involved in anthocyanin biosynthesis, plant proteases, expansins, and autophagy-related genes. Mature and imperforate leaves upregulated genes associated with chlorophyll development, photosynthesis, and negative regulators of PCD. PCD cells were found to have a higher expression of genes involved with ethylene biosynthesis, brassinosteroid biosynthesis, and hydrolase activity whereas NPCD cells possessed higher expression of auxin transport, auxin signalling, aspartyl proteases, cysteine protease, Bag5, and anthocyanin biosynthesis enzymes. Conclusions: RNA sequencing was used to generate a de novo transcriptome for A. madagascariensis leaves and revealed numerous DEGs potentially involved in PCD and leaf remodelling. The data generated from this investigation will be useful for future experiments on lace plant leaf development and PCD in plantaNatural Science and Engineering Research Council of CanadaDalhousie Universit
Streamflow prediction using an integrated methodology based on convolutional neural network and long short-term memory networks
No full textStreamfow (Qfow) prediction is one of the essential steps for the reliable and robust water resources
planning and management. It is highly vital for hydropower operation, agricultural planning, and food
control. In this study, the convolution neural network (CNN) and Long-Short-term Memory network
(LSTM) are combined to make a new integrated model called CNN-LSTM to predict the hourly Qfow
(short-term) at Brisbane River and Teewah Creek, Australia. The CNN layers were used to extract the
features of Qfow time-series, while the LSTM networks use these features from CNN for Qfow time
series prediction. The proposed CNN-LSTM model is benchmarked against the standalone model CNN,
LSTM, and Deep Neural Network models and several conventional artifcial intelligence (AI) models.
Qfow prediction is conducted for diferent time intervals with the length of 1-Week, 2-Weeks, 4-Weeks,
and 9-Months, respectively. With the help of diferent performance metrics and graphical analysis
visualization, the experimental results reveal that with small residual error between the actual and
predicted Qfow, the CNN-LSTM model outperforms all the benchmarked conventional AI models as
well as ensemble models for all the time intervals. With 84% of Qfow prediction error below the range
of 0.05 m3
s−1, CNN-LSTM demonstrates a better performance compared to 80% and 66% for LSTM
and DNN, respectively. In summary, the results reveal that the proposed CNN-LSTM model based on
the novel framework yields more accurate predictions. Thus, CNN-LSTM has signifcant practical value
in Qfow prediction.University of Southern Queenslan
Mesograzer interactions with a unique strain of Irish moss Chondrus crispus: colonization, feeding, and algal condition-related effects
No full textMarine macroalgae are exposed to multiple sources of stress. As a result, perennial macroalga habitats have become depleted in many coastlines. Here, we investigated the role of mesograzers in the sharp decline of a unique strain of Chondrus crispus (the giant Irish moss) found solely in a lagoon in Atlantic Canada. This study was prompted by damage resembling grazing scars that appeared on the fronds as the population declined, for which no grazer had been identified. We identified potential grazers of the seaweed by deploying 4 types of experimental clumps of giant Irish moss and sampling the epifauna that colonized them. Laboratory assays were then run with an abundant species, the amphipod Gammarus oceanicus, to measure feeding rates and test whether this mesograzer is capable of consuming the alga and creating measurable damage. G. oceanicus readily consumed the Irish moss at a grazing rate of 5.24 mg amphipod-1 d-1 and created deep lateral grazing wounds similar to those observed in the field. An additional experiment was conducted to assess whether a co-acting stressor in the lagoon, the accumulation of fine sediments, could explain the appearance and spatially patchy distribution of the damage in the population. Giant Irish moss fronds that had been buried under sediment lost twice as much biomass as those that had not. These results suggest that grazer activity and declining conditions in the lagoon have a negative and additive effect on this unique strain of Irish moss, with clear implications for its restoration
Spatial distribution and sustainability implications of the Canadian groundwater resources under changing climate
No full textGroundwater availability, utilization, sustainability, and climate change implications were assessed at regional and provincial scales of Canada. It remains an unexplored resource, estimated to be renewing between 380 and 625 km3/year. However, the provinces have initiated developing their quantitative and qualitative databases for their accurate inventory. Sustainable groundwater availability at the national scale was estimated as 19,832 m3/person/year (750 km3/year), with high regional variations ranging from 3949 in the densely populated Prince Edward Island (PEI) province to 87,899 in the thinly populated Newfoundland and Labrador (NFL). It fulfills 82%, 43%, and 14% of water requirements of the rural population, irrigation, and industry, respectively. It is the potable water source for more than 9 million people countrywide (24% of the population), and provinces of Quebec, and Ontario (1.3 million people), and PEI (0.15 million people) particularly depend on it. It is mostly a free or nominally charged commodity, but its utilization was found to be well under sustainable limits (40% of recharge) at the provincial scales, i.e., under 4% for all the provinces except New Brunswick (NB), which also had just 8% extraction of sustainable availability. Nevertheless, localized issues of quantitative depletion and qualitative degradation were found at scattered places, particularly in Ontario and Quebec. Climate change impacts of warming and changing precipitations on groundwater underscored its stability with some temporal shifts in recharge patterns. In general, increased recharge in late winters and springs was observed due to reduced frost and more infiltration, and was somewhat decreasing in summers due to more intense rainfall events.Natural Sciences and Engineering Research Council of CanadaPEI Department of Environment, Energy, and Climate Actio