Observe Locally, Classify Globally: Using GNNs to Identify Sparse Matrix Structure

The performance of sparse matrix computation highly depends on the matching of the matrix format with the underlying structure of the data being computed on. Different sparse matrix formats are suitable for different structures of data. Therefore, the first challenge is identifying the matrix structure before the computation to match it with an appropriate data format. The second challenge is to avoid reading the entire dataset before classifying it. This can be done by identifying the matrix structure through samples and their features. Yet, it is possible that global features cannot be determined from a sampling set and must instead be inferred from local features. To address these challenges, we develop a framework that generates sparse matrix structure classifiers using graph convolutional networks. The framework can also be extended to other matrix structures using user-provided generators. The approach achieves 97% classification accuracy on a set of representative sparse matrix shapes

Bridging the Gap between Sparse Matrix Computation and Graph Models

Sparsity manifests itself in a multitude of modern High-Performance Computing applications including graph neural networks, network analytics, and scientific computing. In sparse matrices, the majority of values are zeros. Traditional methods of storing and processing dense data are unsuitable for the new nature of sparse data, as they end up wasting storage and compute on zeros. Hence, a variety of sparse data formats that store only the non-zero elements were proposed in literature to provide a compact representation of sparse data. Performance of operations on sparse data mainly depends on the sparse data format used for storing the data, as the algorithm needs to closely match the sparse data format. However, choosing the optimal sparse data format for the input sparse matrix is non-trivial, as the optimal format depends on the sparsity pattern of the input sparse matrix. For example, in sparse matrix-vector multiplication (SpMV), for the same input sparse matrix, using different sparse data formats can yield highly variant performance. The best format being the one that closely matches how the non-zeros are arranged within the matrix. Additionally, performance prediction for operations involving sparse matrices is not as straightforward as it used to be for the dense case. For dense computations, dimensions and strides suffice for performance predictions as they provide a sense of the number of floating point operations (FLOPs) to be performed, and how this number compares to the architecture properties (peak FLOPs, number of processing elements, etc.). On the other hand, sparse matrix dimensions do not directly convey useful information about the total number of operations to be performed, since the majority of elements are zeros and do not contribute to the total number of FLOPs. Moreover, existing work on sparse operations optimizations mainly depends on a discrete set of matrices, limiting the ability to generalize observations. To address these challenges, we identify the sparsity pattern as the main driving factor for performance. First, we propose an extensible classifier framework to automatically identify the sparsity pattern of the input sparse matrix. This framework uses graph neural networks (GNNs) by representing the input sparse matrix as a graph, and then learning the structural relationship between nodes in the matrix (graph). Our framework achieves up to 98% classification accuracy on full graphs, the same accuracy for scrambled matrices, and 92% accuracy for small random subsamples taken out of original graphs. Second, we use graph models as a proxy to generate large-scale synthetic sparse matrices. We propose another modular framework to study the correlation between the graph model parameters, and the structure of the resulting graph and its tolerance to noise during the generation step. Third, we also use graph models for a performance evaluation framework that can assist in finding the best sparse format for a given graph model on a given architecture, utilizing the graph model parameters as a representative set of features to predict performance, and providing a more robust way of visualizing sparse matrix operations performance. This framework also takes into consideration noise in the matrix generation step, and evaluates the extent of noise to which performance can still be predictable based on the graph model parameters. Our results show that sparse computations need richer models to categorize sparse matrices in terms of structure, study the sensitivity of such models even for one structure, and tie performance to a more descriptive set of parameters

Effect of postharvest exogenous edible coating treatments on inhibitor browning and maintaining quality of fresh mushroom

The shelf-life of fresh mushrooms is limited to 1-3 days at ambient conditions and antioxidant characters are reduced and acquire a brown colour during post-harvest storage. Therefore, the present study was conducted to investigate the effect of some postharvest exogenous edible coating treatments of immersed in six different solutions for 5 min of calcium chloride (2%, 4%), chitosan (1%, 2%), CMC (1%, 2%) and control (distilled water) on reducing the browning, microbial load and maintaining quality during storage for 15 days at 4 ± 1 °C and 95% RH, during two successive seasons of 2021 and 2022 in 4th and 6th of January in the first and second seasons respectively. The obtained results revealed that dipping mushroom plants in a solution of chitosan 2% or calcium chloride 4% was the best treatment for reducing weight loss, while chitosan 2% for 5 min was the most effective treatment in reducing browning, PPO activity, total phenolic, flavonoids contents and inhibiting microbial counts for 12 days at 4 ± 1 °C and 95% RH

Autologous Pericardial Band for Tricuspid Valve Annuloplasty: Midterm Results

Background: Even though tricuspid regurgitation (TR) is a frequent cardiac valve disorder, and tricuspid valve annuloplasty (TVA) has been evolved to manage TR for more than 50 years, there is still a substantial controversy regarding the best durable method for TVA. We reported our midterm (3 years) outcomes of TVA using autologous pericardial (AP) band comparing it with DeVega annuloplasty for the management of functional TR. Methods: Between January 2017 and November 2018, about 175 cases with moderate or more TR underwent TVA as a part of primary left-sided valve replacement surgery. Autologous pericardial (AP) TVA was performed in 100 patients, and DeVega TVA in 75 patients. Results: Both groups are comparable as regards preoperative characteristics. Immediate postoperatively, regarding NYHA class, degree of TR, ejection fraction, and pulmonary artery systolic pressure, there was a marked improvement within the 2 groups compared to the preoperative values, without a significant difference between both groups. 94% of patients completed the follow-up period. In hospital death was 2% in the AP group, and 1% in the DeVega group. The AP group showed a marked improvement in the mean degree of TR at the same follow-up period compared to the DeVega group, 12% patients of the AP group and 21% patients of the De Vega group had 3+ or 4+ TR at 3 years postoperative follow up. There was a marked improvement in the Diastolic tricuspid annuloplasty diameter in the AP group compared to the DeVega group. There were 6.3% late deaths in our study. Conclusion:  TVA with an AP was more durable than the DeVega in avoiding postoperative TR progression on the midterm results

Genotoxic and Anatomical Deteriorations Associated with Potentially Toxic Elements Accumulation in Water Hyacinth Grown in Drainage Water Resources

Potentially toxic elements (PTEs)-induced genotoxicity on aquatic plants is still an open question. Herein, a single clone from a population of water hyacinth covering a large distribution area of Nile River (freshwater) was transplanted in two drainage water resources to explore the hazardous effect of PTEs on molecular, biochemical and anatomical characters of plants compared to those grown in freshwater. Inductivity Coupled Plasma (ICP) analysis indicated that PTEs concentrations in water resources were relatively low in most cases. However, the high tendency of water hyacinth to bio-accumulate and bio-magnify PTEs maximized their concentrations in plant samples (roots in particular). A Random Amplified Polymorphic DNA (RAPD) assay showed the genotoxic effects of PTEs on plants grown in drainage water. PTEs accumulation caused substantial alterations in DNA profiles including the presence or absence of certain bands and even the appearance of new bands. Plants grown in drainage water exhibited several mutations on the electrophoretic profiles and banding pattern of total protein, especially proteins isolated from roots. Several anatomical deteriorations were observed on PTEs-stressed plants including reductions in the thickness of epidermis, cortex and endodermis as well as vascular cylinder diameter. The research findings of this investigation may provide some new insights regarding molecular, biochemical and anatomical responses of water hyacinth grown in drainage water resources.</jats:p

Influence of some chemicals and solvents on the lytic activity and the adsorption of bacteriophages on Pectobacterium carotovoroum Subsp. carotovorum

Recently, bacteriophages have been used to control hazardous bacterial soft rot disease on crops. However, agricultural plants are frequently treated with different chemicals (fertilizers, pesticides and solvents), so we assessed the effect of some commonly used chemicals and solvents on the lytic activity of tested bacteriophages and their adsorption potential. This study reports the isolation of three specific phages against the Pectobacterium carotovorum subsp. carotovorum DSM 30170 strain, designated as ?PC1, ?PC2 and ?PC3, then partially characterized using electron microscopy and genome size. The 3 isolated phages belong to the Myoviridae family. The results obtained were based on the plaque-forming unit observed after incubation. By increasing the chemical concentrations (from 0.1 to 0.5 mM), calcium chloride (CaCl2) and potassium chloride (KCl) showed a significant increase in the lytic activity of the phages. Copper sulphate (CuSO4) and copper chloride (CuCl2) showed a substantial decrease in the activity of ?PC3; however, such a decrease was insignificant for ?PC1 and ?PC2. By increasing the solvent concentrations (from 30 % v/v to 70 % v/v), propanol, ethanol and methanol showed a significant decrease in the count of the three isolated phages, ?PC1, ?PC2 and ?PC3, compared to the control. Chloroform was the only solvent that did not reduce the phage titer. Our findings offer significant information for developing a strategy to combat the P. carotovorum subsp. carotovorum caused bacterial soft rot disease. avoiding copper compounds and alcoholic solvents such as propanol, ethanol and methanol in plots where phages are applied seems advisable

Cardiac Myxomas: A single center experience and ten-years follow up

Background: Cardiac myxoma is a benign tumor that carries the risk of embolization and obstruction of the blood flow. The ideal surgical approach is still debatable. We present our experience in the surgical treatment of cardiac myxomas and its ideal surgical approach.Methods: We retrospectively analyzed the data for all patients who underwent surgical excision of cardiac myxoma at our institution over 11 years starting from January 2006 to December 2016. Descriptive statistics were used to present preoperative, operative and postoperative data and Kaplan Meier curve to plot long-term survival.Results: Twenty-one patients had surgical excision of a primary, single and sporadic cardiac myxoma. Thirteen patients (62 %) were females, and the mean age at operation was 55.2 years (range: 28 – 71 years). The location of myxomas was in the left atrium in 17 patients (81%) and right atrium in 4 patients (19 %). Dyspnea was the main presenting symptom (71.4%) followed by constitutional symptoms (28%), palpitations (23.8%), syncope (14.2%) and stroke (14.2%). A right atrial trans-septal incision was used in 76.5% of left atrial myxoma cases. Five patients had concomitant operative procedures (coronary artery bypass grafting (n=2), tricuspid valve repair (n=1), mitral valve replacement (n=1) and bullectomy (n=1)). Postoperative complications were reported in six patients (28.6%) (supraventricular arrhythmia (n=2), temporary conduction deficit (n=2), pulmonary atelectasis (n=1), and postoperative bleeding (n=1)). Early postoperative mortality occurred in one patient (4.76 %), and there were no late deaths related to myxoma.Conclusion: Surgical treatment of cardiac myxoma is safe with low morbidity and mortality. The right atrial trans-septal incision is the recommended surgical approach

Essential oil constituents and secondary metabolites of Mentha viridis under tissue culture technique using violet visible light emitting diodes (LEDs)

This study aimed to propagate the valuable medicinal plant Mentha viridis through in vitro culture of nodal segments measuring approximately 1-1.5 cm. Two different types of light-emitting diode (LED) systems were used to apply three different concentrations of two different cytokinins: 6-benzylaminopurine (BAP) and thidiazuron (TDZ) at 0, 1, or 2 mg/L. The LED systems were white as a control and violet, which is a 1:1 ratio of red and blue light. After a 30-day incubation period, the results revealed significant improvements in the survival rate and the number of shoots per explant across the various treatment groups. With MS medium supplemented with 2 mg/L TDZ and illuminated by white and violet LEDs, the highest values were obtained, yielding survival rates of 93.3% and 13.3 shoots per explant, respectively. Moreover, the treatment involving 2 mg/L TDZ under violet LEDs illumination exhibited superior outcomes in terms of leaf count per explant, callus formation, and callus size. Notably, no callus formation was observed in response to BAP treatments. All treatments resulted in a significant increase in antioxidant enzyme activity and the accumulation of various compounds, such as anthocyanin, ascorbic acid, phenols, flavonoids, peroxidase, and polyphenol oxidase, when compared to the control in a broader context, the levels of IAA, kinetin, and zeatin increased, while GA3 and ABA decreased in response to the applied treatments, as compared to the control. Additionally, ten compounds were consistently found in all treatments by GC/MS analysis of the micro-propagated Mentha, with carvone accounting for the highest proportion (43.5%) and being the predominant component. Among all treatments, nodal segments that were exposed to violet LEDs and grown on MS medium supplemented with 1 mg/L TDZ had the highest carvone content

Integrating soil mulching and subsurface irrigation for optimizing deficit irrigation effectiveness as a water-rationing strategy in tomato production

Irrigated agriculture from now on should be implemented under water scarcity. Hence, this research was designed to determine the optimal interaction between irrigation water-rationing strategy (deficit irrigation), irrigation techniques, and soil mulching to improve water use efficiency and maintaining plant performance as well as yield productivity of tomatoes. The experiment was set up during the 2020-2021 and 2021-2022 growing seasons. Three factors were studied: two drip irrigation techniques, surface (SI) and subsurface (SSI) irrigation, and two irrigation rates, 100% ETc for full irrigation (FI) and 60% ETc for deficit-irrigation (DI) along with three treatments of soil mulching, bare soil (BS), organic mulch (OrM) and black polyethylene mulch (BPE). The results demonstrated that applying the absolute regular DI regime significantly reduced vegetative growth, fruit yield, and yield component along with water productivity. Also, it reduced the physiological function measures, and nutrient content of the tomato leaf. Meanwhile, applying the DI regime via the SSI technique and integrated with BPE soil mulching proved the best optimization of the DI negative effect followed by applying the DI regime through either SSI or SI technique combined with OrM or BPE soil mulching, respectively. As a result, it is advisable to use the integration of DI via the SSI accompanied by BPE soil mulching since this is considered a good method for conserving irrigation water from being lost by both evaporation and seepage out of the root zone improving water use efficiency without significantly reducing tomato yield

Treatment of Sweet Pepper with Stress Tolerance-Inducing Compounds Alleviates Salinity Stress Oxidative Damage by Mediating the Physio-Biochemical Activities and Antioxidant Systems

Salinity stress occurs due to the accumulation of high levels of salts in soil, which ultimately leads to the impairment of plant growth and crop loss. Stress tolerance-inducing compounds have a remarkable ability to improve growth and minimize the effects of salinity stress without negatively affecting the environment by controlling the physiological and molecular activities in plants. Two pot experiments were carried out in 2017 and 2018 to study the influence of salicylic acid (1 mM), yeast extract (6 g L−1), and proline (10 mM) on the physiological and biochemical parameters of sweet pepper plants under saline conditions (2000 and 4000 ppm). The results showed that salt stress led to decreasing the chlorophyll content, relative water content, and fruit yields, whereas electrolyte leakage, malondialdehyde (MDA), proline concentration, reactive oxygen species (ROS), and the activities of antioxidant enzymes increased in salt-stressed plants. The application of salicylic acid (1 mM), yeast extract (6 g L−1), and proline (10 mM) markedly improved the physiological characteristics and fruit yields of salt-stressed plants compared with untreated stressed plants. A significant reduction in electrolyte leakage, MDA, and ROS was also recorded for all treatments. In conclusion, our results reveal the important role of proline, SA, and yeast extracts in enhancing sweet pepper growth and tolerance to salinity stress via modulation of the physiological parameters and antioxidants machinery. Interestingly, proline proved to be the best treatment.</jats:p