The Architecture of SARS-CoV-2 Transcriptome.

SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 genome was reported recently, its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous discontinuous transcription events. In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif, AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the modification and the 3' tail. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2.

The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction, the FSE-arch, that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure-based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses and will aid future efforts to develop antiviral strategies.

Stress-activated friction in sheared suspensions probed with piezoelectric nanoparticles.

A hallmark of concentrated suspensions is non-Newtonian behavior, whereby the viscosity increases dramatically once a characteristic shear rate or stress is exceeded. Such strong shear thickening is thought to originate from a network of frictional particle-particle contact forces, which forms under sufficiently large stress, evolves dynamically, and adapts to changing loads. While there is much evidence from simulations for the emergence of this network during shear thickening, experimental confirmation has been difficult. Here, we use suspensions of piezoelectric nanoparticles and exploit the strong local stress focusing within the network to activate charge generation. This charging can then be detected in the measured ac conductance and serve as a signature of frictional contact formation. The direct link between stress-activated frictional particle interactions and piezoelectric suspension response is further demonstrated by tracking the emergence of structural memory in the contact network under oscillatory shear and by showing how stress-activated friction can drive mechano-transduction of chemical reactions with nonlinear reaction kinetics. Taken together, this makes the ac conductance of piezoelectric suspensions a sensitive in-situ reporter of the micromechanics associated with frictional interactions.

How does a hyperuniform fluid freeze?

All phase transitions can be categorized into two different types: continuous and discontinuous phase transitions. Discontinuous phase transitions are normally accompanied with significant structural changes, and nearly all of them have the kinetic pathway of nucleation and growth, if the system does not suffer from glassy dynamics. Here, in a system of barrier-controlled reactive particles, we find that the discontinuous freezing transition of a nonequilibrium hyperuniform fluid into an absorbing state does not have the kinetic pathway of nucleation and growth, and the transition is triggered by long-wavelength fluctuations. The transition rate decreases with increasing the system size, which suggests that the metastable hyperuniform fluid could be kinetically stable in an infinitely large system. This challenges the common understanding of metastability in discontinuous phase transitions. Moreover, we find that the "metastable yet kinetically stable" hyperuniform fluid features a scaling in the structure factor [Formula: see text] in 2D, which is the third dynamic hyperuniform state in addition to the critical hyperuniform state with [Formula: see text] and the nonequilibrium hyperuniform fluid with [Formula: see text].

Development and characterization of discontinuous atmospheric pressure interface - Dual pressure chamber miniature mass spectrometer.

Miniaturized mass spectrometers have become increasingly prevalent for real-time detection and analysis, owing to their compact size and portability. The pursuit of performance enhancement in these instruments is a pivotal objective within the domain of mass spectrometry miniaturization. This study introduces a novel miniature mass spectrometer featuring a discontinuous atmospheric pressure interface and a dual pressure chamber. Compared to conventional single-chamber, discontinuous sampling interface mass spectrometers, the newly developed instrument demonstrates a more than tenfold improvement in detection efficiency. This significant enhancement is achieved without the need for complex control of switch coupling time series, thereby streamlining the circuit design and improving the instrument's fault tolerance. Furthermore, by capitalizing on the benefits of discontinuous sampling, the instrument reduces the operational pressure relative to traditional continuous sampling in differential pressure vacuum chambers. It accommodates larger inlet capillary (0.38 mm) and skimmer (0.5 mm) diameters, leading to a ninefold increase in response strength for risperidone and lowering the detection limit to 0.5 ppb. The instrument's capacity for rapid drug detection, along with enhanced resolution and detection limits, underscores its potential utility. Additionally, it facilitates the use of smaller mechanical pumps, significantly diminishing both the instrument's volume and power consumption. This presents a promising avenue for further miniaturization of mass spectrometers.

Nickel augmented biochar for sustaining produced water treatment to decarbonize oil and gas industrial waste using anaerobic-aerobic granular cylindrical periodic discontinuous batch reactors.

This study assessed the efficacy of granular cylindrical periodic discontinuous batch reactors (GC-PDBRs) for produced water (PW) treatment by employing eggshell and waste activated sludge (WAS) derived Nickel (Ni) augmented biochar. The synthesized biochar was magnetized to further enhance its contribution towards achieving carbon neutrality due to carbon negative nature, Carbon dioxide (CO2) sorption, and negative priming effects. The GC-PDBR1 and GC-PDBR2 process variables were optimized by the application of central composite design (CCD). This is to maximize the decarbonization rate. Results showed that the systems could reduce total phosphorus (TP) and chemical oxygen demand (COD) by 76-80% and 92-99%, respectively. Optimal organic matter and nutrient removals were achieved at 80% volumetric exchange ratio (VER), 5 min settling time and 3000 mg/L mixed liquor suspended solids (MLSS) concentration with desirability values of 0.811 and 0.954 for GC-PDBR1 and GC-PDBR2, respectively. Employing four distinct models, the biokinetic coefficients of the GC-PDBRs treating PW were calculated. The findings indicated that First order (0.0758-0.5365) and Monod models (0.8652-0.9925) have relatively low R2 values. However, the Grau Second-order model and Modified Stover-Kincannon model have high R2 values. This shows that, the Grau Second Order and Modified Stover-Kincannon models under various VER, settling time, and MLSS circumstances, are more suited to explain the removal of pollutants in the GC-PDBRs. Microbiological evaluation demonstrated that a high VER caused notable rises in the quantity of several microorganisms. Under high biological selective pressure, GC-PDBR2 demonstrated a greater percentage of nitrogen removal via autotrophic denitrification and a greater number of nitrifying bacteria. The overgrowth of bacteria such as Actinobacteriota spp. Bacteroidota spp, Gammaproteobacteria, Desulfuromonas Mesotoga in the phylum, class, and genus, has positively impacted on granule formation and stability. Taken together, our study through the introduction of intermittent aeration GC-PDBR systems with added magnetized waste derived biochar, is an innovative approach for simultaneous aerobic sludge granulation and PW treatment, thereby providing valuable contributions in the journey toward achieving decarbonization, carbon neutrality and sustainable development goals (SDGs).

Predicting adequate segmental lordosis correction in lumbar spinal stenosis patients undergoing oblique lumbar interbody fusion: a focus on the discontinuous segment.

PURPOSE: To identify the factors associated with a correction of the segmental angle (SA) with a total change greater than 10° in each level following minimally invasive oblique lumbar interbody fusion (MIS-OLIF). METHODS: Patients with lumbar spinal stenosis who underwent single- or two-level MIS-OLIF were reviewed. Segments with adequate correction of the SA >10° after MIS-OLIF in immediate postoperative radiograph were categorized as discontinuous segments (D segments), whereas those without such improvement were assigned as continuous segments (C segments). Clinical and radiological parameters were compared, and multivariate logistic regression analysis was performed to identify factors associated with SA correction >10° after MIS-OLIF. RESULTS: Of 211 segments included, 38 segments (18.0%) were classified as D segments. Compared with C segments, D segments demonstrated a significantly smaller preoperative SA (mean ± standard deviation [SD], - 1.1° ± 6.7° vs. 6.6° ± 6.3°, p < 0.001), larger change of SA (mean ± SD, 13.5° ± 3.4° vs. 3.1° ± 3.9°, p < 0.001), and a higher rate of presence of facet effusion (76.3% vs. 48.6%, p = 0.002). Logistic regression revealed preoperative SA (odds ratio (OR) [95% confidence interval (CI)]:0.733 [0.639-0.840], p < 0.001) and facet effusion (OR [95% CI]:14.054 [1.758-112.377], p = 0.027) as significant predictors for >10° SA correction after MIS-OLIF. CONCLUSION: Preoperative kyphotic SA and facet effusion can predict SA correction >10° following MIS-OLIF. For patients with lordotic SA and no preoperative facet effusion, supplemental procedures, such as anterior column release or posterior osteotomy, should be prepared for additional lumbar lordosis correction required for remnant global sagittal imbalance after MIS-OLIF.

Transcatheter recanalisation for absent intra-pericardial pulmonary arteries.

Unilateral absence of intra-pericardial pulmonary artery is a rare congenital malformation. If untreated, it can lead to morbidity and mortality in adulthood. Early intervention and restoration of physiologic pulmonary blood flow is necessary. Transcatheter stenting as initial intervention has been rarely reported. We present transcatheter recanalisation and stenting of the obliterated ductus in two newborns with unilateral absence of intra-pericardial pulmonary artery with cross-sectional imaging, procedural details, angiography, and follow up to surgical repair. We believe that such procedure promotes ipsilateral pulmonary vasculature growth to facilitate unifocalization surgery at a later age.

Discontinuous Deformation Monitoring of Smart Aerospace Structures Based on Hybrid Reconstruction Strategy and Fiber Bragg Grating.

A hybrid enhanced inverse finite element method (E-iFEM) is proposed for real-time intelligent sensing of discontinuous aerospace structures. The method can improve the flight performance of intelligent aircrafts by feeding back the structural shape information to the control system. Initially, the presented algorithm combines rigid kinematics with the classical iFEM to discretize the aerospace structures into elastic parts and rigid parts, which will effectively overcome structural complexity due to fluctuating bending stiffness and a special aerodynamic section. Subsequently, the rigid parts provide geometric constraints for the iFEM in the shape reconstruction method. Meanwhile, utilizing the Fiber Bragg grating (FBG) strain sensor to obtain real-time strain information ensures lightweight and anti-interference of the monitoring system. Next, the strain data and the geometric constraints are processed by the iFEM for monitoring the full-field elastic deformation of the aerospace structures. The whole procedure can be interpreted as a piecewise sensing technology. Overall, the effectiveness and reliability of the proposed method are validated by employing a comprehensive numerical simulation and experiment.

Generalized Pulse Width Modulation Switch Model for Converters Based on the Multistate Switching Cell in Discontinuous Conduction Mode.

This work introduces a generalized version of the pulse width modulation (PWM) switch model applied in the small-signal modeling of converters based on the multistate switching cell (MSSC) operating in discontinuous conduction mode (DCM). It consists of extending the concept formerly introduced by Vorperian for the representation of multiphase converters in DCM, yielding a circuit-based approach that does not rely on matrix manipulations unlike state-space averaging (SSA). The derived dc and ac models are valid for any number of switching states and any operating region defined in terms of the duty cycle, thus allowing for determining the voltage gain and distinct transfer functions. A thorough discussion of results is presented to demonstrate the applicability of the derived models to represent distinct configurations of the MSSC.

Cut-and-paste for impulsive gravitational waves with Λ: the mathematical analysis.

Impulsive gravitational waves are theoretical models of short but violent bursts of gravitational radiation. They are commonly described by two distinct spacetime metrics, one of local Lipschitz regularity and the other one even distributional. These two metrics are thought to be 'physically equivalent' since they can be formally related by a 'discontinuous coordinate transformation'. In this paper we provide a mathematical analysis of this issue for the entire class of nonexpanding impulsive gravitational waves propagating in a background spacetime of constant curvature. We devise a natural geometric regularisation procedure to show that the notorious change of variables arises as the distributional limit of a family of smooth coordinate transformations. In other words, we establish that both spacetimes arise as distributional limits of a smooth sandwich wave taken in different coordinate systems which are diffeomorphically related.

Estranged and Unhappy? Examining the Dynamics of Personal and Relationship Well-Being Surrounding Infidelity.

Although relationship theories often describe infidelity as a damaging event in a couple's life, it remains unclear whether relationship problems actually follow infidelity, precede it, or both. The analyses of dyadic panel data of adults in Germany including about 1,000 infidelity events showed that infidelity was preceded (but not followed) by a gradual decrease in relationship functioning in perpetrators and victims. There was little evidence of rebound effects in the aftermath of infidelity, with the exception of unfaithful women and individuals with lower initial relationship commitment who returned to the pre-event level of well-being or even exceeded it, providing support to the expectancy violation theory (vs. the investment model of infidelity). By showing that well-being starts to decline before infidelity happens, this study provides a differentiated view on the temporal dynamics of infidelity and well-being and contributes to the literature on romantic relationship dynamics and major life events.

Tunnelling Dynamics of Kicked Systems: A Route to Tunnelling Control.

The effects of discontinuously time-varying perturbations on the dynamics of a particle moving in harmonic, symmetric double well and symmetric triple well potentials, are investigated both classically and quantum mechanically. The quantum dynamics is followed using the time-dependent Fourier grid Hamiltonian (TDFGH) method while the classical dynamics is analyzed within the framework of classical Hamiltonian mechanics. Depending on the spatial symmetry of the perturbation and the characteristic features of the reversal time τ r ${\left( {\tau _r } \right)}$ , different types of 'phase space' structures are observed in each of the potentials. For symmetric double and triple well potentials, quantum dynamics reveals that complete destruction of tunnelling (CDT) can be achieved in the presence of a time-dependent spatially asymmetric perturbing field that is continuous in time. Any discontinuity in time-variation of the perturbation may induce over the barrier transition. The relevance of these results in the context of (i) tunnelling control and (ii) quantum computing with 3-state or 2-state quantum registers is briefly discussed.

Enhancing the expression of multi-antigen chimeric TGAGS/BST protein from Toxoplasma gondii in Escherichia coli BL 21 Star during batch cultivation.

Toxoplasmosis, despite advances in science and technology, is a disease that requires attention since there is no vaccine capable of immunizing humans and animals against all isolated types of Toxoplasma gondii. Thus, the use of chimeric proteins, which can contain multiple antigens, is a very promising alternative for the process of obtaining a vaccine and diagnostic test for toxoplasmosis due to the great diversity of antigens presented by T. gondii. In this context, the present study evaluates batch culture strategies in the production of the multi-antigenic chimeric protein TgAGS/BsT from Toxoplasma gondii. Several exploratory cultures were initially carried out to observe the kinetic behavior of E. coli BL21 Star in five different medium compositions without the addition of IPTG (inducer). Cultures of E. coli B21 Star were carried out with 1.0 mM IPTG at different times of initiation of induction (0.5, 1, and 6 h) to evaluate the effects on cell growth, production of the protein of interest, culture pH, and acetic acid formation. The results showed that among the culture media evaluated, 2xTY and TB supplemented with glycerol had the best cell concentration values of 3.42 ± 0.05 g/L and 5.48 ± 0.05 g/L, respectively. In the assays induced by IPTG, a higher expression of TgAGS/BsT protein was observed, with induction beginning within 6 h of culture, with a maximum concentration of protein of interest of 1.82 ± 0.02 g/L for the 2xTY and 2.49 ± 0.03 g/L for the TB medium. In addition, later induction by IPTG provided greater stability of plasmid pET-TgAGS, remaining with values above 90% at the end of culture.

Gas exchange patterns for a small, stored-grain insect pest, Tribolium castaneum.

Insects breathe using one or a combination of three gas exchange patterns; continuous, cyclic and discontinuous, which vary in their rates of exchange of oxygen, carbon dioxide and water. In general, there is a trade-off between lowering gas exchange using discontinuous exchange that limits water loss at the cost of lower metabolic rate. These patterns and hypotheses for the evolution of discontinuous exchange have been examined for relatively large insects (>20 mg) over relatively short periods (<4 h), but smaller insects and longer time periods have yet to be examined. We measured gas exchange patterns and metabolic rates for adults of a small insect pest of grain, the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae), using flow-through respirometry in dry air for 48 h. All adults survived the desiccating measurement period; initially they used continuous gas exchange, then after 24 h switched to cyclic gas exchange with a 27% decrease in metabolic rate, and then after 48 h switched to discontinuous gas exchange with increased interburst duration and further decrease in metabolic rate. The successful use of the Qubit, a lower cost and so more common gas analyser, to measure respiration in the very small T. castaneum, may prompt more flow-through respirometry studies of small insects. Running such studies over long durations may help to better understand the evolution of respiration physiology and thus suggest new methods of pest management.

Dichorionic Diamniotic Twin Pairs with Complex Congenital Heart Disease.

Complex congenital heart disease (CHD) in each of dichorionic diamniotic (DiDi) twin pairs is extremely rare and has not been well characterized. Four DiDi twin pairs were included in this multi-institutional case series. The congenital cardiac abnormalities noted included tetralogy of Fallot (ToF) with pulmonary atresia and collaterals (n = 1), ToF with absent pulmonary valve (n = 1), ToF (n = 2), discontinuous right pulmonary artery (RPA) (n = 1), tricuspid atresia (TA) with normally related great arteries and pulmonary valve stenosis or atresia (n = 2) and coarctation of aorta (CoA) with bicuspid aortic valve (BAV) and borderline left-sided structures (n = 1). Genetic testing was obtained on seven of the eight twins but did not reveal any causal abnormality. A comprehensive review of literature yielded another 8 DiDi twin pairs with complex CHD. The CHD noted in these twin pairs included ToF (n = 2), CoA (n = 4), corrected transposition of great arteries (ccTGA) (n = 2), truncus arteriosus (n = 2), complete common atrioventricular canal (CCAVC) (n = 2), hypoplastic left heart syndrome (HLHS) (n = 2), Shone's complex (n = 1), and hypoplastic right heart syndrome (HRHS) (n = 1). Limited genetic testing was obtained on 4 of these twins and revealed trisomy 21 in a twin pair. Conotruncal abnormalities (42%), CoA (21%), and abnormalities of the right ventricle, the right ventricular outflow tract and pulmonary arteries (17%) are more prevalent in DiDi twins with complex CHD. Clustering of these abnormalities suggests a possible genetic basis; however, genetic testing was obtained on eleven of the twins, and except for trisomy 21 in a twin pair both of whom had CCAVC, did not reveal any causal abnormality. A major direct genetic contribution is therefore unlikely and like other CHD, the underlying etiopathological basis is likely multifactorial.

Autonomous Planning of Discontinuous Terrain-Dependent Crawling for Space Dobby Robots.

Complex space missions require more space robotic extravehicular operations required to crawl on spacecraft surfaces with discontinuous features at the graspable point, greatly increasing the difficulty of space robot motion manipulation. Therefore, this paper proposes an autonomous planning method for space dobby robots based on dynamic potential fields. This method can realize the autonomous crawling of space dobby robots in discontinuous environments while considering the task objectives and the self-collision problem of robotic arms when crawling. In this method, a hybrid event-time trigger with event triggering as the main trigger is proposed by combining the working characteristics of space dobby robots and improving the gait timing trigger; the dynamic potential field function is designed to adjust the space robot robotic arm grasping point adaptively according to the space robot state. Simulation results verify the effectiveness of the proposed autonomous planning method.

Physics-Constrained Data-Driven Variational Method for Discrepancy Modeling.

This paper presents a data-driven discrepancy modeling method that variationally embeds measured data in the modeling and analysis framework. The proposed method exploits the residual between the first-principles theory and sensor-based measurements from the dynamical system, and it augments the physics-based model with a variationally derived loss function that is comprised of this residual. The method was first developed in the context of linear elasticity (Masud and Goraya, J. Appl. Mech. 89 (11), 111001 (2022)) wherein the relation between the discrepancy model and loss terms was derived to show that the data embedding terms behave like residual-based least-squares regression functions. An interpretation of the stabilization tensor as a kernel function was formally established and its role in assimilating a-priori knowledge of the problem in the modeling method was highlighted. The present paper employs linear elastodynamics as a model problem where the Data-Driven Variational (DDV) method incorporates high-fidelity data into the forward simulations, thereby driving the problem with not only the boundary and initial conditions, but also by measurement data that is taken at only a small subset of the total domain. The effect of the loss function on the time-dependent response of the system is investigated under a variety of loading conditions and model discrepancies. The energy and Morlet wavelet analyses reveal that the problem with embedded data recovers the energy and the fundamental frequency band of the target system. Time histories of strain energy and kinetic energy of a cantilever beam undergoing damped oscillations are recovered by including known data in an undamped model to highlight the data-driven discrepancy modeling feature of the method under the combined effect of parameter and model discrepancy.

An Optimized Schwarz Method for the Optical Response Model Discretized by HDG Method.

An optimized Schwarz domain decomposition method (DDM) for solving the local optical response model (LORM) is proposed in this paper. We introduce a hybridizable discontinuous Galerkin (HDG) scheme for the discretization of such a model problem based on a triangular mesh of the computational domain. The discretized linear system of the HDG method on each subdomain is solved by a sparse direct solver. The solution of the interface linear system in the domain decomposition framework is accelerated by a Krylov subspace method. We study the spectral radius of the iteration matrix of the Schwarz method for the LORM problems, and thus propose an optimized parameter for the transmission condition, which is different from that for the classical electromagnetic problems. The numerical results show that the proposed method is effective.

An "epitomic" analysis of the specificity of conformation-dependent, anti-Aß amyloid monoclonal antibodies.

Antibodies against Aß amyloid are indispensable research tools and potential therapeutics for Alzheimer's disease. They display several unusual properties, such as specificity for aggregated forms of the peptide, the ability to distinguish polymorphic aggregate structures, and the ability to recognize generic aggregation-related epitopes formed by unrelated amyloid sequences. Understanding the mechanisms underlying these unusual properties and the structures of their corresponding epitopes is crucial for the understanding why antibodies display different therapeutic activities and for the development of more effective therapeutic agents. Here we employed a novel "epitomic" approach to map the fine structure of the epitopes of 28 monoclonal antibodies against amyloid-beta using immunoselection of random sequences from a phage display library, deep sequencing, and pattern analysis to define the critical sequence elements recognized by the antibodies. Although most of the antibodies map to major linear epitopes in the amino terminal 1 to 14 residues of Aß, the antibodies display differences in the target sequence residues that are critical for binding and in their individual preferences for nontarget residues, indicating that the antibodies bind to alternative conformations of the sequence by different mechanisms. Epitomic analysis also identifies discontinuous, nonoverlapping sequence Aß segments that may constitute the conformational epitopes that underlie the aggregation specificity of antibodies. Aggregation-specific antibodies recognize sequences that display a significantly higher predicted propensity for forming amyloid than antibodies that recognize the monomer, indicating that the ability of random sequences to aggregate into amyloid is a critical element of their binding mechanism.