Analytical Study of Unsteady Nested Groundwater Flow Systems

Two analytical solutions using segregation variable method to calculate the hydraulic head under steady and unsteady flow conditions based on Tóth’s classical model were developed. The impacts of anisotropy ratio, hydraulic conductivity (K), and specific yield (μs) on the flow patterns were analyzed. It was found that the area of the equal velocity region increases and the penetrating depth of the flow system decreases at steady state with anisotropy ratio increases, which is defined as ε=Kx/Kz. In addition, stagnant zones can be found in the flow field where the streamlines have opposite directions. These stagnant zones move toward the surface as the horizontal hydraulic conductivity increases. The results of the study on transient flow indicate that a relative increase in hydraulic conductivity produces a positive impact on hydraulic head and a relative enhancement in specific yield produces a negative effect on hydraulic head at early times

rSeqTU—A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units

A transcription unit (TU) is composed of one or multiple adjacent genes on the same strand that are co-transcribed in mostly prokaryotes. Accurate identification of TUs is a crucial first step to delineate the transcriptional regulatory networks and elucidate the dynamic regulatory mechanisms encoded in various prokaryotic genomes. Many genomic features, for example, gene intergenic distance, and transcriptomic features including continuous and stable RNA-seq reads count signals, have been collected from a large amount of experimental data and integrated into classification techniques to computationally predict genome-wide TUs. Although some tools and web servers are able to predict TUs based on bacterial RNA-seq data and genome sequences, there is a need to have an improved machine learning prediction approach and a better comprehensive pipeline handling QC, TU prediction, and TU visualization. To enable users to efficiently perform TU identification on their local computers or high-performance clusters and provide a more accurate prediction, we develop an R package, named rSeqTU. rSeqTU uses a random forest algorithm to select essential features describing TUs and then uses support vector machine (SVM) to build TU prediction models. rSeqTU (available at https://s18692001.github.io/rSeqTU/) has six computational functionalities including read quality control, read mapping, training set generation, random forest-based feature selection, TU prediction, and TU visualization

Transcriptome Analysis of Oleoresin-Producing Tree Sindora Glabra and Characterization of Sesquiterpene Synthases

Terpenes serve important physiological and ecological functions in plants. Sindora glabra trees accumulate copious amounts of sesquiterpene-rich oleoresin in the stem. A transcriptome approach was used to determine the unique terpene biosynthesis pathway and to explore the different regulatory mechanisms responsible for the variation of terpene content among individuals. Analysis of de novo-assembled contigs revealed a complete set of genes for terpene biosynthesis. A total of 23,261 differentially expressed unigenes (DEGs) were discovered between high and low oil-yielding plants. DEG enrichment analysis suggested that the terpene biosynthesis process and the plant hormone signal transduction pathway may exert a major role in determining terpene variation in S. glabra. The expression patterns of candidate genes were further verified by quantitative RT-PCR experiments. Key genes involved in the terpene biosynthesis pathway were predominantly expressed in phloem and root tissues. Phylogenetic analysis and subcellular localization implied that S. glabra terpene synthases may evolve from a common ancestor. Furthermore, two sesquiterpene synthase genes, SgSTPS1 and SgSTPS2, were functionally characterized. SgSTPS1 mainly generated β-caryophyllene from farnesyl pyrophosphate. SgSTPS2 is a versatile enzyme that catalyzes the formation of 12 sequiterpenes from farnesyl pyrophosphate and synthesis of three monoterpenes using geranyl pyrophosphate. Together, these results provide large reservoir for elucidating the molecular mechanism of terpene biosynthesis and for exploring the ecological function of sesquiterpenes in S. glabra

Fractional quantum Hall effect in the absence of Landau levels

It has been well-known that topological phenomena with fractional excitations, i.e., the fractional quantum Hall effect (FQHE) \cite{Tsui1982} will emerge when electrons move in Landau levels. In this letter, we report the discovery of the FQHE in the absence of Landau levels in an interacting fermion model. The non-interacting part of our Hamiltonian is the recently proposed topologically nontrivial flat band model on the checkerboard lattice \cite{sun}. In the presence of nearest-neighboring repulsion ($U$), we find that at 1/3 filling, the Fermi-liquid state is unstable towards FQHE. At 1/5 filling, however, a next-nearest-neighboring repulsion is needed for the occurrence of the 1/5 FQHE when $U$ is not too strong. We demonstrate the characteristic features of these novel states and determine the phase diagram correspondingly.Comment: 6 pages and 4 figure

Nondissipative Drag Conductance as a Topological Quantum Number

We show in this paper that the boundary condition averaged nondissipative drag conductance of two coupled mesoscopic rings with no tunneling, evaluated in a particular many-particle eigenstate, is a topological invariant characterized by a Chern integer. Physical implications of this observation are discussed.Comment: 4 pages, no figure. Title modified and significant revision made to the text. Final version appeared in PR

Development of a novel PCV2 and PCV3 vaccine using virus-like vesicles incorporating Venezuelan equine encephalomyelitis virus-containing vesicular stomatitis virus glycoprotein

Porcine circovirus disease (PCV) causes substantial economic losses in the pig industry, primarily from porcine circovirus type 2 (PCV2) and porcine circovirus type 3 (PCV3). Novel vaccines are necessary to prevent and control PCV infections. PCV coat proteins are crucial for eliciting immunogenic proteins that induce the production of antibodies and immune responses. A vaccine platform utilizing Semliki Forest virus RNA replicons expressing vesicular stomatitis virus glycoprotein (VSV-G), was recently developed. This platform generates virus-like vesicles (VLVs) containing VSV-G exclusively, excluding other viral structural proteins. In our study, we developed a novel virus-like vesicle vaccine by constructing recombinant virus-like vesicles (rVLVs) that also express EGFP. These rVLVs were created using the RNA replicon of Venezuelan equine encephalomyelitis (VEEV) and New Jersey serotype VSV-G. The rVLVs underwent characterization and safety evaluation in vitro. Subsequently, rVLVs expressing PCV2d-Cap and PCV3-Cap proteins were constructed. Immunization of C57 mice with these rVLVs led to a significant increase in anti-porcine circovirus type 2 and type 3 capsid protein antibodies in mouse serum. Additionally, a cellular immune response was induced, as evidenced by high production of IFN-γ and IL-4 cytokines. Overall, this study demonstrates the feasibility of developing a novel porcine circovirus disease vaccine based on rVLVs

A Characterization of Topological Insulators: Chern Numbers for a Ground State Multiplet

We propose to use generic Chern numbers for a characterization of topological insulators. It is suitable for a numerical characterization of low dimensional quantum liquids where strong quantum fluctuations prevent from developing conventional orders. By twisting parameters of boundary conditions, the non-Abelian Chern number are defined for a few low lying states near the ground state in a finite system, which is a ground state multiplet with a possible (topological) degeneracy. We define the system as a topological insulator when energies of the multiplet are well separated from the above. Translational invariant twists up to a unitary equivalence are crutial to pick up only bulk properties without edge states. As a simple example, the setup is applied for a two-dimensional $XXZ$-spin system with an ising anisotropy where the ground state multiplet is composed of doubly almost degenerate states. It gives a vanishing Chern number due to a symmetry. Also Chern numbers for the generic fractional quantum Hall states are discussed shortly.Comment: 2 figure

Association between the risk of heart failure hospitalization and end-stage renal disease with digoxin usage in patients with cardiorenal syndrome: A population-based study

BackgroundThe management of the coexistence of heart disease and kidney disease is increasingly challenging for clinicians. Chronic kidney disease (CKD) is not only a prevalent comorbidity of patients with heart failure but has also been identified as a noteworthy risk factor for all-cause mortality and poor clinical outcomes. Digoxin is one of the commonest treatments for heart disease. There are few trials investigating the role of digoxin in patients with cardiorenal syndrome (CRS). This study aims to examine the association between digoxin usage and clinical outcomes in patients with CRS in a nationwide cohort.MethodWe conducted a population-based study that included 705 digoxin users with CRS; each patient was age, sex, comorbidities, and medications matched with three non-users who were randomly selected from the CRS population. Cox proportional hazards regression analysis was conducted to estimate the effects of digoxin on the incidence of all-cause mortality, congestive heart failure (CHF) hospitalization, coronary artery disease (CAD) hospitalization, and end-stage renal disease (ESRD).ResultsThe all-cause mortality rate was significantly higher in digoxin users than in non-users (adjusted hazard ratio [aHR] = 1.26; 95% confidence interval [CI] = 1.09–1.46, p = 0.002). In a subgroup analysis, there was significantly high mortality in the 0.26–0.75 defined daily dose (DDD) subgroup of digoxin users (aHR = 1.49; 95% CI = 1.23–1.82, p<0.001). Thus, the p for trend was 0.013. With digoxin prescription, the CHF hospitalization was significantly higher [subdistribution HR (sHR) = 1.17; 95% CI = 1.05–1.30, p = 0.004], especially in the >0.75 DDD subgroup (sHR = 1.19; 95% CI = 1.01–1.41, p = 0.046; p for trend = 0.006). The digoxin usage lowered the coronary artery disease (CAD) hospitalization in the > 0.75 DDD subgroup (sHR = 0.79; 95% CI = 0.63–0.99, p = 0.048). In renal function progression, more patients with CRS entered ESRD with digoxin usage (sHR = 1.34; 95% CI = 1.16–1.54, p<0.001). There was a significantly greater incidence of ESRD in the < 0.26 DDD and 0.26–0.75 DDD subgroups of digoxin users (sHR = 1.32; 95% CI = 1.06–1.66, p = 0.015; sHR = 1.44; 95% CI = 1.18–1.75; p for trend<0.001).ConclusionDigoxin should be prescribed with caution to patients with CRS

The RCK1 domain of the human BK_(Ca) channel transduces Ca^(2+) binding into structural rearrangements

Large-conductance voltage- and Ca^(2+)-activated K^+ (BK_(Ca)) channels play a fundamental role in cellular function by integrating information from their voltage and Ca2+ sensors to control membrane potential and Ca^(2+) homeostasis. The molecular mechanism of Ca^(2+)-dependent regulation of BKCa channels is unknown, but likely relies on the operation of two cytosolic domains, regulator of K^+ conductance (RCK)1 and RCK2. Using solution-based investigations, we demonstrate that the purified BK_(Ca) RCK1 domain adopts an α/β fold, binds Ca^(2+), and assembles into an octameric superstructure similar to prokaryotic RCK domains. Results from steady-state and time-resolved spectroscopy reveal Ca^(2+)-induced conformational changes in physiologically relevant [Ca^(2+)]. The neutralization of residues known to be involved in high-affinity Ca^(2+) sensing (D362 and D367) prevented Ca^(2+)-induced structural transitions in RCK1 but did not abolish Ca^(2+) binding. We provide evidence that the RCK1 domain is a high-affinity Ca^(2+) sensor that transduces Ca^(2+) binding into structural rearrangements, likely representing elementary steps in the Ca^(2+)-dependent activation of human BK_(Ca) channels