Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden.

Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.

Xrs2/NBS1 promote end-bridging activity of the MRE11-RAD50 complex.

DNA double strand breaks (DSBs) can be detrimental to the cell and need to be efficiently repaired. A first step in DSB repair is to bring the free ends in close proximity to enable ligation by non-homologous end-joining (NHEJ), while the more precise, but less available, repair by homologous recombination (HR) requires close proximity of a sister chromatid. The human MRE11-RAD50-NBS1 (MRN) complex, Mre11-Rad50-Xrs2 (MRX) in yeast, is involved in both repair pathways. Here we use nanofluidic channels to study, on the single DNA molecule level, how MRN, MRX and their constituents interact with long DNA and promote DNA bridging. Nanofluidics is a suitable method to study reactions on DNA ends since no anchoring of the DNA end(s) is required. We demonstrate that NBS1 and Xrs2 play important, but differing, roles in the DNA tethering by MRN and MRX. NBS1 promotes DNA bridging by MRN consistent with tethering of a repair template. MRX shows a "synapsis-like" DNA end-bridging, stimulated by the Xrs2 subunit. Our results highlight the different ways MRN and MRX bridge DNA, and the results are in agreement with their key roles in HR and NHEJ, respectively, and contribute to the understanding of the roles of NBS1 and Xrs2 in DSB repair.

Peeling mechanism of tomato induced by HHAIB: Microscopic, ultrastructure, chemical, physical and mechanical properties perspectives.

In order to better manage the peeling degree and avoid unnecessary losses, the current work aimed to explore the peeling mechanism of a novel peeling technology, high-humidity hot air impingement blanching (HHAIB). The relationships between HHAIB peeling performance and the changes in skin temperature, skin structure, water state, pectin fractions content, and skin mechanical properties of tomatoes were analyzed. Results showed, after HHAIB treatment, the epicuticular wax was disrupted, the skin exhibited more and longer random cracks, the degradation of inner skin tissue was observed by transmission electron microscopy, the free water percentage increased resulting in water loss in the whole tomato, the water-soluble pectin contents decreased in tomato fleshes, while the contents of chelate-soluble pectin and sodium-carbonate-soluble pectin increased. HHAIB heating reduced the elongation at break, and increased Young's Modulus of tomato peel. This study revealed the HHAIB peeling mechanism and provided new insights for developing HHAIB peeling technology.

Artificial Neural Network Modeling and Genetic Algorithm Multiobjective Optimization of Process of Drying-Assisted Walnut Breaking.

This study combined an artificial neural network (ANN) with a genetic algorithm (GA) to obtain the model and optimal process parameters of drying-assisted walnut breaking. Walnuts were dried at different IR temperatures (40 °C, 45 °C, 50 °C, and 55 °C) and air velocities (1, 2, 3, and 4 m/s) to different moisture contents (10%, 15%, 20%, and 25%) by using air-impingement technology. Subsequently, the dried walnuts were broken in different loading directions (sutural, longitudinal, and vertical). The drying time (DT), specific energy consumption (SEC), high kernel rate (HR), whole kernel rate (WR), and shell-breaking rate (SR) were determined as response variables. An ANN optimized by a GA was applied to simulate the influence of IR temperature, air velocity, moisture content, and loading direction on the five response variables, from which the objective functions of DT, SEC, HR, WR, and SR were developed. A GA was applied for the simultaneous maximization of HR, WR, and SR and minimization of DT and SEC to determine the optimized process parameters. The ANN model had a satisfactory prediction ability, with the coefficients of determination of 0.996, 0.998, 0.990, 0.991, and 0.993 for DT, SEC, HR, WR, and SR, respectively. The optimized process parameters were found to be 54.9 °C of IR temperature, 3.66 m/s of air velocity, 10.9% of moisture content, and vertical loading direction. The model combining an ANN and a GA was proven to be an effective method for predicting and optimizing the process parameters of walnut breaking. The predicted values under optimized process parameters fitted the experimental data well, with a low relative error value of 2.51-3.96%. This study can help improve the quality of walnut breaking, processing efficiency, and energy conservation. The ANN modeling and GA multiobjective optimization method developed in this study provide references for the process optimization of walnut and other similar commodities.

Changes in, and correlation analysis of, volatile compounds, key enzymes, and fatty acids in lemon juice vesicles during freeze drying and hot-air drying.

BACKGROUND: Lemon juice vesicles are distinguished by their unique and abundant volatile flavor compounds, which can undergo complex changes during drying. In this study, integrated freeze drying (IFD), conventional freeze drying (CFD), and hot-air drying (AD) were used to dry lemon juice vesicles to investigate the changes in, and correlations among volatile compounds, fatty acids, and key enzyme activity during the drying process. RESULTS: Twenty-two volatile compounds were detected during the drying processes. Compared with fresh samples, seven compounds were lost in the dried samples after IFD, seven after CFS, and six after AD, and the loss rates of the total content of volatile compounds in the dried samples were 82.73% in CFD, more than 71.22% in IFD, and more than 28.78% in AD. In total, 1.015 mg/g of seven fatty acids were detected in the fresh samples; the content loss rates of total fatty acids after drying were 67.68% in AD, more than 53.00% in CFD, and more than 36.95% in IFD, respectively. During the three drying processes, IFD retained relatively higher enzyme activity in the samples. CONCLUSION: Many positive and negative correlations (P < 0.05) were observed among the key enzyme effects, fatty acids, and volatile compounds, showing close associations. The current work provides information that is important for the selection of suitable drying techniques for lemon juice vesicles and suggests how to control their flavor during the drying process. © 2023 Society of Chemical Industry.

Pulsed Vacuum Drying of Persimmon Slices: Drying Kinetics, Physicochemical Properties, Microstructure and Antioxidant Capacity.

In order to explore an alternative drying method to enhance the drying process and quality of persimmon slices, pulsed vacuum drying (PVD) was employed and the effects of different drying temperatures (60, 65, 70, and 75 °C) on drying kinetics, color, rehydration ratio (RR), microstructure, bioactive compounds, and the antioxidant capacity of sliced persimmons were investigated in the current work. Results showed that the rehydration ratio (RR) of the samples under PVD was significantly higher than that of the traditional hot air-dried ones. Compared to the fresh samples, the dried persimmon slices indicated a decrease in the bioactive compounds and antioxidant capacity. The total phenolic content (TPC) of PVD samples at 70 °C was 87.96% higher than that of the hot air-dried persimmon slices at 65 °C. Interestingly, at 70 °C, the soluble tannin content and TPC of the PVD samples reached the maximum values of 6.09 and 6.97 mg GAE/g, respectively. The findings in the current work indicate that PVD is a promising drying method for persimmon slices as it not only enhances the drying process but also the quality attributes.

A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data.

In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and development to the regulation of biological networks and pathways, both under homeostatic and pathological states like cancer.Despite their immense importance as key regulators of cellular processes, accurate and reliable estimation of miRNAs using Next Generation Sequencing is challenging, largely due to the limited availability of robust computational tools/methods/pipelines. Here, we introduce miRPipe, an end-to-end computational framework for the identification, characterization, and expression estimation of small RNAs, including the known and novel miRNAs and previously annotated pi-RNAs from small-RNA sequencing profiles. Our workflow detects unique novel miRNAs by incorporating the sequence information of seed and non-seed regions, concomitant with clustering analysis. This approach allows reliable and reproducible detection of unique novel miRNAs and functionally same miRNAs (paralogues). We validated the performance of miRPipe with the available state-of-the-art pipelines using both synthetic datasets generated using the newly developed miRSim tool and three cancer datasets (Chronic Lymphocytic Leukemia, Lung cancer, and breast cancer). In the experiment over the synthetic dataset, miRPipe is observed to outperform the existing state-of-the-art pipelines (accuracy: 95.23% and F 1-score: 94.17%). Analysis on all the three cancer datasets shows that miRPipe is able to extract more number of known dysregulated miRNAs or piRNAs from the datasets as compared to the existing pipelines.

Design, development and model analysis of lower extremity Exo-skeleton.

Over the past few years the growth and development of exo-skeleton has dramatically raised with the development of precise control elements and actuation systems. Many exo-skeleton systems have been designed, developed and tested for performance optimization. In the recent years, the significance of exo-skeleton in medical fields have got increased and are used in providing therapy and rehabilitation to the patients. With this development there comes the importance for analysis and control of the exo-skeleton for precise functioning and to avoid malfunction of the system in the later part. Dynamic analysis of limb joints is essential to better facilitate a deeper understanding of the exo-skeleton limb during various environmental conditions like varied loading. The dynamic model so developed will assist in choosing an apt actuation system based on the torque requirement of the model.This paper focusses on the analysis of a 2DOF lower limb active control exo-skeleton system and makes a torque calculation for actuator selection for the lower limb to provide rehabilitation to the patients as wearable walking aid. The work also makes a trajectory planning for the lower limb to move in sequence for making a walking cycle with angular limitations to avoid damage to the user's limbs. The motion analysis for the developed lower limb Exoskeleton as per the analysis is 52.055 Nm at hip joint 11.677 Nm at knee joint.

A mathematical model captures the role of adenyl cyclase Cyr1 and guanidine exchange factor Ira2 in creating a growth-to-hyphal bistable switch in Candida albicans.

Recent biochemical experiments have indicated that in Candida albicans, a commensal fungal pathogen, the Ras signaling pathway plays a significant role in the yeast-to-hyphal transition; specifically, two enzymes in this pathway, Adenyl Cyclase Cyr1 and GTPase activating protein Ira2, facilitate this transition, in the presence of energy sensor ATP. However, the precise mechanism by which protein interactions between Ira2 and Cyr1 and the energy sensor ATP result in the yeast-to-hyphal transition and create a switch-like process are unknown. We propose a new set of biochemical reaction steps that captures all the essential interactions between Ira2, Cyr1, and ATP in the Ras pathway. With the help of chemical reaction network theory, we demonstrate that this set of biochemical reaction steps results in bistability. Further, bifurcation analysis of the differential equations based on this set of reaction steps supports the existence of a bistable switch, and this switch may act as a checkpoint mechanism for the promotion of growth-to-hyphal transition in C. albicans.

Correlation of changes in subclonal architecture with progression in the MMRF CoMMpass study.

Multiple myeloma (MM) is a heterogeneous plasma cell proliferative disorder that arises from its premalignant precursor stages through a complex cascade of interactions between clonal mutations and co-evolving microenvironment. The temporo-spatial evolutionary trajectories of MM are established early during myelomatogenesis in precursor stages and retained in MM. Such molecular events impact subsequent disease progression and clinical outcomes. Identification of clonal sweeps of actionable gene targets in MM could reveal potential vulnerabilities that may exist in early stages and thus potentiate prognostication and customization of early therapeutic interventions. We have evaluated clonal evolution at multiple time points in 76 MM patients enrolled in the MMRF CoMMpass study. The major findings of this study are (a) MM progresses predominantly through branching evolution, (b) there is a heterogeneous spectrum of mutational landscapes that include unique actionable gene targets at diagnosis compared to progression, (c) unique clonal gains/ losses of mutant driver genes can be identified in patients with different cytogenetic aberrations, (d) there is a significant correlation between co-occurring oncogenic mutations/ co-occurring subclones e.g., with mutated TP53+SYNE1, NRAS+MAGI3, and anticorrelative dependencies between FAT3+FCGBP gene pairs. Such co-trajectories may synchronize molecular events of drug response, myelomatogenesis and warrant future studies to explore their potential for early prognostication and development of risk stratified personalized therapies in MM.

Guidelines on reporting treatment conditions for emerging technologies in food processing.

In the last decades, different non-thermal and thermal technologies have been developed for food processing. However, in many cases, it is not clear which experimental parameters must be reported to guarantee the experiments' reproducibility and provide the food industry a straightforward way to scale-up these technologies. Since reproducibility is one of the most important science features, the current work aims to improve the reproducibility of studies on emerging technologies for food processing by providing guidelines on reporting treatment conditions of thermal and non-thermal technologies. Infrared heating, microwave heating, ohmic heating and radiofrequency heating are addressed as advanced thermal technologies and isostatic high pressure, ultra-high-pressure homogenization sterilization, high-pressure homogenization, microfluidization, irradiation, plasma technologies, power ultrasound, pressure change technology, pulsed electric fields, pulsed light and supercritical CO2 are approached as non-thermal technologies. Finally, growing points and perspectives are highlighted.

A comprehensive review on innovative and advanced stabilization approaches of anthocyanin by modifying structure and controlling environmental factors.

Anthocyanins are pigments abundant in fruits and vegetables, and commonly applied in foods due to attractive colour and health-promoting benefits. However, instability of anthocyanins leads to their easy degradation, reduced bioactivity, and colour fading in food processing, limiting their application and causing economic losses. Stability of anthocyanins depends on their own structures and environmental factors. For structural factors, modification including copigmentation, acylation and biosynthesis is a potential solution to increase anthocyanin stability due to forming stable structures. With regard to environmental factors, encapsulation such as microencapsulation, liposome and nanoparticles has been shown effectively to enhance the stability. We proposed the potential challenges and perspectives for the diversification of anthocyanin-rich products for food application, particularly, introduction of hazards, technical limitations, interaction with other ingredients in food system and exploration of pyranoanthocyanins. The integrated strategies are warranted for improving anthocyanin stabilization for promoting their further application in food industry.

Effect of seed layer thickness on the Ta crystalline phase and spin Hall angle.

Heavy metal-ferromagnet bilayer structures have attracted great research interest for charge-to-spin interconversion. In this work, we investigated the effect of the permalloy (Py) seed layer on the tantalum (Ta) polycrystalline phase and its spin Hall angle. Interestingly, for the same deposition rates the crystalline phase of Ta deposited on the Py seed layer strongly depends on the thickness of the seed layer. We observed a phase transition from α-Ta to (α + ß)-Ta while increasing the Py seed layer thickness. The observed phase transition is attributed to the strain at the interface between the Py and Ta layers. Ferromagnetic resonance-based spin pumping studies reveal that the spin-mixing conductance in the (α + ß)-Ta is relatively higher as compared to the α-Ta. Spin Hall angles of α-Ta and (α + ß)-Ta are obtained from the inverse spin Hall effect (ISHE) measurements. The spin Hall angle of (α + ß)-Ta is estimated to be θSH = -0.15 ± 0.009 which is relatively higher than that of the α-Ta. Our systematic results connecting the phase of Ta with the seed layer and its effect on the efficiency of spin to charge conversion might resolve ambiguities across various literature and open up new functionalities based on the growth process for emerging spintronic devices.

Structural characterization and antioxidant activities of one neutral polysaccharide and three acid polysaccharides from Ziziphus jujuba cv. Hamidazao: A comparison.

A neutral polysaccharide (HJP-1a) and three acid polysaccharides (HJP-2, HJP-3 and HJP-4) were obtained from Z. jujuba cv. Hamidazao. HJP-1a was mainly composed of arabinose and galactose in a ratio of 56.9:20.0, with an average molecular weight of 3.115 × 104 g/mol. HJP-2, HJP-3 and HJP-4 were homogeneous heteropolysaccharides mainly containing galacturonic acid, arabinose and galactose, with average molecular weights of 4.590 × 104, 6.986 × 104 and 1.951 × 105 g/mol, respectively. Structural characterization indicated that the backbone of HJP-3 appeared to be mainly composed of →4)-α-d-GalpA (1→ and →2,4)-α-l-Rhap (1→ residues with some branches consisting of →5)-α-l-Araf (1→ residues and terminals of T-α-l-Araf (1→ and T-ß-d-Galp residues. The four purified fractions displayed dose-dependent radical scavenging activity on ABTS+ radicals and reducing capacity, as well as excellent protective effect on H2O2-induced HepG2 cells and metronidazole-damaged zebrafish embryos, especially HJP-2 in vitro and HJP-1a in vivo. Therefore, the polysaccharides from Z. jujuba cv. Hamidazao could be used as a potential antioxidant in functional foods.

Improving Biosecurity Procedures to Minimize the Risk of Spreading Pathogenic Infections Agents After Carcass Recycling.

Animal proteins are essential elements of human and animal feed chain and improving the safety of human and animal feed requires understanding and controlling of the transmission of infectious agents in food chain. Many pathogenic infectious agents, such as prion protein is known to damage the central nervous system in the cattle. Bovine spongiform encephalopathy (BSE) results from infection agent (prion), and affects number of species such as cattle, human, and cats. In addition, Salmonella, pathogenic E. coli O157:H7, and Listeria monocytogenes were found in animal by-products used in the human and animal feed production. Increased interest in controlling microbial risks in human and animal feed is evidenced by a large number of publications, which highlights the need for examining the animal disposal method such as rendering process and provides a broader perspective of rendering process. While existing practices help greatly in controlling microbial contamination, this overview study showed that additional biosafety measures are necessary to ensure microbial safety in animal feed.

Characterization and management strategies for process discharge streams in California industrial tomato processing.

The California tomato industry is the leading processor of tomatoes in the world. Accordingly, it produces a large amount of solid and liquid byproducts during processing. Some of these byproducts are under-utilized and discarded. There is increasing demand for the conversion of tomato byproducts into value-added products. This study reviews the characteristics of solid residue and process water discharge streams generated at different stages of tomato processing in addition to their current management strategies. Furthermore, relevant policy that governs management of solid and liquid organic byproducts for California tomato processors is discussed. Finally, recommendations for novel and sustainable management strategies are explored.

Emerging chemical and physical disinfection technologies of fruits and vegetables: a comprehensive review.

With a growing demand for safe, nutritious, and fresh-like produce, a number of disinfection technologies have been developed. This review comprehensively examines the working principles and applications of several emerging disinfection technologies. The chemical treatments, including chlorine dioxide, ozone, electrolyzed water, essential oils, high-pressure carbon dioxide, and organic acids, have been improved as alternatives to traditional disinfection methods to meet current safety standards. Non-thermal physical treatments, such as UV-light, pulsed light, ionizing radiation, high hydrostatic pressure, cold plasma, and high-intensity ultrasound, have shown significant advantages in improving microbial safety and maintaining the desirable quality of produce. However, using these disinfection technologies alone may not meet the requirement of food safety and high product quality. Several hurdle technologies have been developed, which achieved synergistic effects to maximize lethality against microorganisms and minimize deterioration of produce quality. The review also identifies further research opportunities for the cost-effective commercialization of these technologies.

Multi-scale modeling of the circadian modulation of learning and memory.

We propose a multi-scale model to explain the time-of-day effects on learning and memory. We specifically model the circadian variation of hippocampus (HC) dependent long-term potentiation (LTP), depression (LTD), and the fear conditioning paradigm in amygdala. The model we built has both Goodwin type circadian gene regulatory network (GRN) and the conductance model of Morris-Lecar (ML) type to explain the spontaneous firing patterns (SFR) in suprachiasmatic nucleus (SCN). In the conductance model, we also include N-Methyl-D-aspartic acid receptor (NMDAR) to study the circadian dependent changes in LTP/LTD in hippocampus and include both NMDAR and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) dynamics to explain the circadian modulation of fear conditioning paradigm in memory acquisition, recall, and extinction as seen in amygdala. Our multi-scale model captures the essential dynamics seen in the experiments and strongly supports the circadian time-of-the-day effects on learning and memory.

Hilbert transform-based time-series analysis of the circadian gene regulatory network.

In this work, the authors propose the Hilbert transform (HT)-based numerical method to analyse the time series of the circadian rhythms. They demonstrate the application of HT by taking both deterministic and stochastic time series that they get from the simulation of the fruit fly model Drosophila melanogaster and show how to extract the period, construct phase response curves, determine period sensitivity of the parameters to perturbations and build Arnold tongues to identify the regions of entrainment. They also derive a phase model that they numerically simulate to capture whether the circadian time series entrains to the forcing period completely (phase locking) or only partially (phase slips) or neither. They validate the phase model, and numerics with the experimental time series forced under different temperature cycles. Application of HT to the circadian time series appears to be a promising tool to extract the characteristic information about circadian rhythms.

Application of Exactly Linearized Error Transport Equations to Sonic Boom Prediction Workshop.

The computational fluid dynamics (CFD) prediction workshops sponsored by the AIAA have created invaluable opportunities to discuss the predictive capabilities of CFD in areas in which it has struggled, e.g., sonic boom prediction. While there are many factors that contribute to disagreement between simulated and experimental results, such as modeling or discretization errors, quantifying the errors contained in a simulation is important for those who make decisions based on the computational results. The linearized error transport equations (ETE) combined with a truncation error estimate is a method to quantify one source of error. The ETE are implemented with a complex-step method to provide an exact linearization with minimal source code modifications to CFD and multidisciplinary analysis methods including atmospheric propagation of sonic boom signatures. Uniformly refined grids from the 2nd AIAA Sonic Boom Prediction Workshop demonstrate the utility of ETE for multidisciplinary analysis with a connection between estimated discretization error and (resolved or under-resolved) flow features.