An in-situ conductometric apparatus for physicochemical characterization of solutions and in-line monitoring of separation processes at elevated temperatures and pressures

Specific conductance and frequency-dependent resistance (impedance) data are widely utilized for understanding the physicochemical characteristics of aqueous and non-aqueous fluids and for evaluating the performance of chemical processes. However, the implementation of such an in-situ probe in high-temperature and high-pressure environments is not trivial. This work provides a description of both the hardware and software associated with implementing a parallel-type in-situ electrochemical sensor. The sensor can be used for in-line monitoring of thermal desalination processes and for impedance measurements in fluids at high temperature and pressure. A comparison between the experimental measurements on the specific conductance in aqueous sodium chloride solutions and the conductance model demonstrate that the methodology yields reasonable agreement with both the model and literature data. A combination of hardware components, a softwarebased correction for experimental artifacts, and computational fluid dynamics (CFD) calculations used in this work provide a sound basis for implementing such in-situ electrochemical sensors to measure frequency-dependent resistance spectra.

JUMPER Enables Discontinuous Transcript Assembly in Coronaviruses

Genes in SARS-CoV-2 and other viruses in the order of Nidovirales are expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes and produces subgenomic RNAs that express different viral genes. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLY problem of finding transcripts T and their abundances c given an alignment R of paired end short reads under a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient progressive heuristic that uses mixed integer linear program. We show using simulations that our method, JUMPER, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses of Nidovirales transcriptomes under varying conditions.

Jumper Enables Discontinuous Transcript Assembly in Coronaviruses

Genes in SARS-CoV-2 and, more generally, in viruses in the order of Nidovirales are expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes, rendering current transcript assembly methods unsuitable to Nidovirales sequencing samples. Here, we introduce the Discontinuous Transcript Assembly problem of finding transcripts and their abundances c given an alignment under a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient mixed integer linear program. We show using simulations that our method, Jumper, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1 and SARS-CoV-2 samples, we find that Jumper not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. Jumper enables detailed analyses of Nidovirales transcriptomes.Code availabilitySoftware is available at https://github.com/elkebir-group/Jumper

A Three-Phase Fundamental Diagram from Three-Dimensional Traffic Data

This paper uses empirical traffic data collected from three locations in Europe and the US to reveal a three-phase fundamental diagram with two phases located in the uncongested regime. Model-based clustering, hypothesis testing and regression analyses are applied to the speed–flow–occupancy relationship represented in the three-dimensional space to rigorously validate the three phases and identify their gaps. The finding is consistent across the aforementioned different geographical locations. Accordingly, we propose a three-phase macroscopic traffic flow model and a characterization of solutions to the Riemann problems. This work identifies critical structures in the fundamental diagram that are typically ignored in first- and higher-order models and could significantly impact travel time estimation on highways.

Physico-chemical Characterization of Solutions from Cooked Beans and Their Comparison with Human Urine: Fertilizer and Food?

The present paper aims to highlight the chemical characteristics of solutions from cooked beans and to compare them with human urine. Solutions of cooked beans were produced by cooking variety of Phaseolus vulgaris L. known as “Meringue” without salts. After this stage, samples of those solutions and samples of the water used for the cooking process were collected for laboratory analysis. A solution from cooked beans is rich in mineral salts, particularly major macro elements (N and K) and minor macro elements (Ca, S, Mg). Concerning the third major macro element, notably the phosphorous, it is present in low amounts. The advantage of this fluid consists in its low amounts of sodium and chlorides, coupled to its low electric conductivity. This fluid has a pH of 6.31. It is made of about 90% of water. A deep parallelism can be established between the human urine and solutions from cooked beans. In fact, these two fluids are rich in nitrogen and potassium, and mainly made of water. But, in the detail, some particularities are present. Human urine has high amounts of sodium and chlorides, this coupled with a high electric conductivity. Concerning solutions from cooked beans, it has high amounts of calcium and magnesium, and a quite nil electric conductivity. The solutions from cooked beans do not require a dilution, but a ridging directly after its application in other to avoid the loose of sulfur and nitrogen through gas emanation. Moreover, the numerous nutrients contained in solutions from cooked beans can be gainfully recycled as soup after flavoring.

Chemotaxis on networks: Analysis and numerical approximation

We consider the Keller–Segel model of chemotaxis on one-dimensional networks. Using a variational characterization of solutions, positivity preservation, conservation of mass, and energy estimates, we establish global existence of weak solutions and uniform bounds. This extends related results of Osaki and Yagi to the network context. We then analyze the discretization of the system by finite elements and an implicit time-stepping scheme. Mass lumping and upwinding are used to guarantee the positivity of the solutions on the discrete level. This allows us to deduce uniform bounds for the numerical approximations and to establish order optimal convergence of the discrete approximations to the continuous solution without artificial smoothness requirements. In addition, we prove convergence rates under reasonable assumptions. Some numerical tests are presented to illustrate the theoretical results.