bluuebunny/crossref_metadata_2025 huggingface dataset:
Lumped and distributed‐parameter pipe model framework for thermal transients: State‐space and transfer function theory and application to multi‐energy systems
Authors: Liu Xiu , Strunz Kai
Published: July 2022

The accurate prediction and simulation of thermal transients in district heating networks is essential for the meaningful analysis of combined heat and power systems. For this purpose, the focus of this paper lies on the development of a consistent and comprehensive modelling framework that links diverse pipe model categories to specific applications where flows are driven by forced convection. The framework considers pipe modelling based on lumped and distributed parameters. Related state‐space and transfer function representations are formulated, and model performances are validated. The comparative analysis of the distributed‐parameter versus the lumped‐parameter categories is shown to be insightful. For the latter category, thermal transients in the form of changing temperature distributions may be observed along the spatial extension of the pipe. In the distributed‐parameter pipe model, only the input and output temperatures are presented. On the other hand, the distributed‐parameter pipe model offers higher computational efficiency. This is confirmed by the equivalent floating‐point operation (eFLOP) count that is newly introduced to quantify the integer multiple of computation time needed for a mathematical operation with respect to the time needed for an elementary addition. The application of the models is illustrated for a combined heat and power network involving diverse transients.
Artificial intelligence technology in electronic communication engineering for medical applications
Authors: Lin Youwen , Zhang Zhijie , Jagota Vishal , Rakhra Manik , Singh Bhupesh Kumar
Published: July 2022

In order to solve the problem of high frame error rate in electronic communication engineering, the application of artificial intelligence technology in electronic communication engineering is proposed. Taking LPWAN technology in artificial intelligence technology as an example, a new architecture is proposed to improve the security of wireless communication system of internet of things. The architecture is mainly composed of business layer, data processing layer, terminal access layer and communication technology layer. The experimental results show that the system configuration sends four kinds of information transmission instructions of “temperature, light, air pressure and humidity” every 30 s, and the receiving port collects the above command data continuously for 4 h, compared with the traditional architecture (15.6%), and the packet loss rate is 4%, which can effectively improve the throughput and processing efficiency of the system. The designed architecture runs stably, has low bit error rate, and can better support the wireless communication. It is proved that the new architecture with LPWAN technology as an example has large overall capacity and excellent performance of its electronic communication engineering interface. The frame number error rate is greatly reduced and the result of signal frame number is more accurate.
Direct simulation Monte Carlo of the gas-adsorption of particles in gas–particle flows
Authors: Yu Hsinchen , Zhang Xiaoping , He Peishan
Published: July 2022

The acceleration and heating of particles in gas–particle flows represents a general question in fluid mechanics and has been widely studied since the 1920s. However, studies on the gas adsorption–desorption process of a particle in a gas–particle flow are still lacking. In this paper, we aim to introduce a framework with which to explain the gas adsorption–desorption kinetic equilibrium of a spherical particle in a gas–particle flow. We also explore the potential influences of gas adsorption and desorption on the heating and acceleration of a particle in such a flow. We study the gas adsorption–desorption process using the Langmuir adsorption model and the flow method presented by Brancher in a Direct Simulation Monte Carlo simulation. We develop a new model to consider the gas adsorption–desorption kinetic equilibrium on the surfaces of spherical particles in the calculation of the Thermal Accommodation Coefficient. We observe from the simulations that the trend of gas adsorption is opposite to that of the particle surface temperature. We also find that the efficiency of the convective heat transfer and acceleration of a particle is higher for a particle with a higher adsorption probability on its surface. This paper provides a new framework with which to study the gas adsorption–desorption processes of particles in gas–particle flows. It also inspires for future work on the potential applications of the particle gas adsorption–desorption model in astrophysics.
Laser light-induced deformation of free surface of oil due to thermocapillary Marangoni phenomenon: Experiment and computational fluid dynamics simulations
Authors: Bełej Monika , Grześkiewicz Katarzyna , Miniewicz Andrzej
Published: July 2022

Remote light-induced free liquid surface deformation has been studied in various systems for decades. One of the mechanisms able to do this task is driven by the thermocapillary Marangoni effect. The strength of the light–matter interaction, which is usually weak, here is amplified by the light absorption and heat production that changes surface tension. Here, we report on an experimental study aimed at dynamical aspects of the deformation induced under conditions of chopped laser excitation light. The light-induced deformations are usually in the range of several micrometers. Therefore, we applied the interferometric technique to measure deformation profiles in real time. Experiments were performed in the shallow bath of the rapeseed oil with an azo-dye and excited with 514.5 nm and probed with 650 nm coherent laser beams, respectively. The mechanism of deformation driven by Marangoni effect was carefully modeled in 3D by computational fluid dynamic numerical simulations within the COMSOL Multiphysics package. The adaptive mesh technique used in the simulation together with solving the time-dependent coupled Navier–Stokes and heat transport differential equations allowed us to replicate the experimental findings. A satisfactory agreement between the results of the simulations and those of the experiment in terms of the dynamics, shape, and depth of the deformation has been obtained. The toroidal-like whirls accompanying the thermocapillary Marangoni effect were identified by the simulation results. We then experimentally proved that these toroidal-like vortices, which accompany laser heating in dyed oil, formed a kind of novel hydrodynamic trap, in the center of their quiet zone, in which microcrystals can be trapped.
Flow-induced noise sources and reduction methods in centrifugal pumps: A literature review
Authors: Gangipamula Rajavamsi , Ranjan Pritanshu , Patil Ranjit S.
Published: July 2022

This Review describes the research work conducted by many researchers in the field of hydro-acoustics of centrifugal pumps. This study aims to understand the flow induced noise mechanism, factors affecting it, and available methods to attenuate the same in centrifugal pumps. In general, the noise generated by a pump is interpreted in terms of pressure pulsations and can be represented in the frequency domain as a combination of discrete components and broadband components. In the discrete frequency noise component, the major emphasis is given on blade pass frequency noise and its relation to the rotor–stator interaction in pumps. The intensified rotor–stator interaction results in high pressure pulsations, thus strong flow induced noise. The effect of various geometrical parameters on the rotor–stator interaction and available methods to mitigate it to reduce noise are discussed in detail. Apart from the rotor–stator interaction, the importance of energy loss mechanisms, such as flow recirculation, flow-separation, and jet-wakes occurrence in pumps, which affect the blade pass frequency component, are also discussed. One of the other discrete noise components, the rotating stall mechanism with its physical mechanism, was also explored in detail. Subsequently, two major phenomena of broadband noise components, turbulence and cavitation, are explained. For cavitation, the phenomenon is elaborated in detail as well as various methods explored by the researchers to predict the existence of the cavitation phenomenon using the acoustic spectrum. Conclusions are also drawn for each source by describing the major events. In the end, the possible future scope of work that can be explored is given.
Numerical investigation of an insect-scale flexible wing with a small amplitude flapping kinematics
Authors: Guo Yueyang , Yang Wenqing , Dong Yuanbo , Xuan Jianlin
Published: July 2022

To maintain flight, insect-scale air vehicles must adapt to their low Reynolds number flight conditions and generate sufficient aerodynamic force. Researchers conducted extensive studies to explore the mechanism of high aerodynamic efficiency on such a small scale. In this paper, a centimeter-level flapping wing is used to investigate the mechanism and feasibility of whether a simple motion with a certain frequency can generate enough lift. The unsteady numerical simulations are based on the fluid structure interaction (FSI) method and dynamic mesh technology. The flapping motion is in a simple harmonic law of small amplitude with high frequency, which corresponds to the flapping wing driven by a piezoelectric actuator. The inertial and aerodynamic forces of the wing can cause chordwise torsion, thereby generating the vertical aerodynamic force. The concerned flapping frequency refers to the structural modal frequency and FSI modal frequency. According to the results, we find that under the condition that frequency ratio is 1.0, that is, when the wing flaps at the first-order structural modal frequency, the deformation degree of the wing is the highest, but it does not produce good aerodynamic performance. However, under the condition that frequency ratio is 0.822, when the wing flaps at the first-order FSI modal frequency, the aerodynamic efficiency achieve the highest and is equal to 0.273. Under the condition that frequency ratio is 0.6, that is, when the wing flaps at a frequency smaller than the first-order FSI modal frequency, the flapping wing effectively utilizes the strain energy storage and release mechanism and produces the maximum vertical coefficient which is equal to 4.86. The study shows that this flapping motion can satisfy the requirements of lift to sustain the flight on this scale.
Modeling of the compartmentalization effect induced by leading-edge tubercles
Authors: Cai Chang , Zhou Teng , Liu Shuhong , Zuo Zhigang , Zhang Yinan , Li Qing'an
Published: July 2022

As a passive flow control technique, the use of leading-edge tubercles inspired by humpback whale flippers has attracted much interest. It is believed that one of the flow control mechanisms of leading-edge tubercles is compartmentalization, which is similar to the way in which wing fences act. However, to date, there has been no direct evidence for this belief. In view of this, the present work aims to verify and quantitatively describe the compartmentalization effect induced by leading-edge tubercles. Numerical simulation is performed to investigate the flow structures on a wavy airfoil with leading-edge tubercles, and the results reveal the presence of typical biperiodic flow patterns when a critical angle of attack is exceeded. Based on the flow characteristics of the wavy airfoil, special fences paired in a diverging configuration are designed and positioned on the baseline airfoil. A modeling method is developed to determine the main parameters of the fence configurations. It is found that the fenced airfoils designed using this method are able to reproduce the typical flow characteristics of the wavy airfoil under different inflow conditions. The spanwise distributions of the sectional airfoil performance under flow control by leading-edge tubercles and by the specially designed fences are very similar. A combined mechanism mainly including the lifting-line theory and the compartmentalization theory is proposed to provide a more comprehensive picture of the flow dynamic of leading-edge tubercles. This work provides strong evidence to confirm the compartmentalization mechanism of action of leading-edge tubercles, as well as developing a quantitative modeling method, both of which are important for fully understanding the underlying mechanism and guiding further optimization of this passive flow control technique.
Modeling the squeeze flow of droplet over a step
Authors: Mehboudi Aryan , Singhal Shrawan , Sreenivasan S. V.
Published: July 2022

In this paper, we study the squeeze flow of a droplet confined between two plates in the presence of a step. Understanding this fluid mechanics problem is of the utmost importance particularly for nanoimprint lithography, wherein the photoresist droplets are dispensed on a substrate and imprinted and cured into a desired pattern. Often, the desired pattern includes various steps and trenches, and the droplets need to flow over. Here, we use the lubrication theory to find the instantaneous pressure and velocity fields. A volume-of-fluid advection algorithm is also used for evolving the volume fraction in time. The obtained results reveal that for step sizes comparable to the gap between plates, the squeeze flow characteristics become quite distinct across the step. Under such circumstances, the fluid finds it less expensive to reverse its flow direction toward the deep region to pass through the low-resistance zone, which leads to a net mass flow rate across the step from a shallow to deep region. Such a mass transfer is found to be enhanced by applying larger squeezing forces. This phenomenon becomes less noticeable for liquid film thicknesses much larger than the step size. As a result, it takes large droplets a longer time to reach to the regime wherein a substantial mass flow rate occurs. In addition, the results suggest that the dimensionless characteristic features, such as the ratios of volume and area of liquid in the deep (or shallow) region to those of the total liquid, collapse onto their corresponding master curves.
The pappus angle as a key factor in the entire separation of a vortex ring from a dandelion seed’s pappus
Authors: Qiu Fu-Sheng , Qian Hui-Yuan , Du Yi-Ming , Li Cheng-Jun
Published: July 2022

A separated vortex ring is the main aerodynamic feature of the dandelion seed which enables its flight. However, recent research on simply modeled dandelion seeds with a pappus angle of 180° (flat porous disk) shows that the vortex ring is not entirely separated from the pappus. This significantly differs from what is observed in a real dandelion seed and would prevent us from fully understanding its flight mechanism. In this work, the two key structural features of the pappus that are considered in the work of others, i.e., the circular disk-like geometry and the porosity, were expected to be insufficient to form an entirely separated vortex ring. Therefore, refined numerical simulations were conducted on model pappi with different pappus angles, which are more similar to real dandelion seeds than flat porous disks. A stable and entirely separated vortex ring and a small vortex ring above the central disk were observed. The lower pappus angle increases the radial pressure gradient toward the central axis between the root of the filaments. When the net effect of this pressure gradient is large enough to overcome the effect of the pressure gradient away from the central axis below the pappus, the streamlines near the root of the filaments deflect to the central axis and the vortex ring is lifted and separates entirely. It is concluded that an appropriate pappus angle is another key feature for forming an entirely separated vortex ring. This more in-depth flow mechanism is of considerable reference value for future research.
An extensive scope of flow loops with a focus on particle transport
Authors: Martin Brown Nickolas , Dejam Morteza
Published: July 2022

All the oil and natural gas wells from underground reservoirs to the surface resemble flow loops. Over the past couple of decades, a variety of flow loops have been established in order to create real field environments in the laboratories. The flow loops help to further advance the efficiency of drilling, production, and hydraulic fracturing operations. This can be achieved by better understanding the mechanisms behind particle transport within the flow loops such as fluid velocity and rheology, particle size and concentration, acting forces on particles, and pressure drop. The objective of the current review is to critically investigate several flow loops with different applications addressing transportation of particles such as cuttings, sands, condensate droplets, hydrates, and proppants.
Inertial instabilities of stratified jets: Linear stability theory
Authors: Harris M. W. , Poulin F. J. , Lamb K. G.
Published: July 2022

This paper uses a linear stability analysis to investigate instabilities of barotropic and baroclinic jets that satisfy the necessary condition for inerital instabilities within the context of a rotating, stratified Boussinesq model. First, we review the different types of instabilities that can occur in these jets and the conditions that make the jet subject to inertial instability but stable to Rayleigh–Taylor instability. Second, we numerically solve one-dimensional and two-dimensional eigenvalue problems for the linear stability problems and examine the dependence of the growth rates on the Rossby number, Burger number, the aspect ratio, and the Reynolds number. We find that there are two critical Reynolds numbers where there is a transition between what type of instability has the largest growth rate. Finally, we examine the characteristics of inertial instabilities in more detail for three selected parameter sets: a low Reynolds number regime, a high Reynolds number regime, and a regime with low Reynolds number and larger aspect ratio. The most unstable mode in the low Reynolds number regime is a barotropic–baroclinic instability and has a barotropic spatial structure. In contrast, the most unstable mode in the high Reynolds number regime is an inertial instability and its spatial structure is independent of the along-flow direction. Modes with this property are commonly referred to as symmetric instabilities. In the intermediate regime, the flow can be unstable to both barotropic–baroclinic and inertial instabilities, possibly with comparable growth rates.
A kinetic model for multicomponent gas transport in shale gas reservoirs and its applications
Authors: Wang Shihao , Zhang Yanbin , Wu Haiyi , Lee Seong H. , Qiao Rui , Wen Xian-Huan
Published: July 2022

An accurate gas transport model is of vital importance to the simulation and production optimization of unconventional gas reservoirs. Although great success has been achieved in the development of single-component transport models, limited progress has been made in multicomponent systems. The major challenge of developing non-empirical multicomponent gas transport models lies in the absence of the quantification of the concentration impact on the fluid dynamic properties. To fill such a gap, this work presents a comprehensive transport model for multicomponent gas transport in shale and tight reservoirs. In developing the model, we first conducted molecular dynamic simulations to qualitatively understand the differential release of hydrocarbons from unconventional shale and tight reservoirs. It is found that the gas slippage, differential adsorption, and surface diffusion are the primary transport mechanisms in the working range of Knudsen number during reservoir production. Based on the molecular dynamic study, a quantitative transport model has been developed and validated, which extends existing models from single-component systems to multiple-component systems. The kinetic theory of gases is adopted and modified to model the multicomponent slippage effect. A generalized Maxwell–Stefan formulation with extended Langmuir adsorption isotherm is used to model the multicomponent surface diffusion process. The accuracy of the proposed model is above 90% for low to moderate Knudsen numbers in modeling the differential release phenomenon in unconventional reservoirs.
Optimizing the mean swimming velocity of a model two-sphere swimmer
Authors: Felderhof B. U.
Published: July 2022

The swimming of a two-sphere system oscillating in a viscous fluid is studied on the basis of simplified equations of motion which take account of both friction and inertial effects. In the model, the friction follows from an Oseen approximation to the mobility matrix, and the inertial effects follow from a dipole approximation to the added mass matrix. The resulting mean swimming velocity is evaluated analytically in a first harmonics approximation. For specific choices of the parameters, this is compared with the exact result following from a numerical calculation including higher harmonics. The Oseen-dipole model is compared with the simpler Oseen* model, in which the added mass effects are approximated by just the effective mass of the single spheres and dipole interactions are neglected. The expression for the mean swimming velocity can be reduced to a dimensionless scaling form. For given viscosity and mass density of the fluid, the frequency of the stroke and the ratio of radii can be chosen such that the swimming velocity is optimized.
Host diversity positively affects the temporal stability of foliar fungal diseases in a Tibetan alpine meadow
Authors: Liu Xiang , Lu Yawen , Huang Mengjiao , Zhou Shurong
Published: July 2022

Background and Aims

Plant disease can dramatically affect population dynamics, community composition and ecosystem functions. However, most empirical studies focus on diseases at a certain time point and largely ignore their temporal stability, which directly affects our ability to predict when and where disease outbreaks will occur.

Methods

Using a removal experiment that manipulates plant diversity (i.e. a plant biodiversity and ecosystem function experiment) and a fertilization experiment in a Tibetan alpine meadow, we investigated how different plant biodiversity indices and nitrogen fertilization affect the temporal stability of foliar fungal diseases (measured as the mean value of community pathogen load divided by its standard deviation) over seven consecutive years.

Key Results

We found that the temporal stability of foliar fungal diseases increased with plant diversity indices in the plant biodiversity and ecosystem function experiment. Meanwhile, we observed a weakly positive relationship between host diversity and temporal stability in the fertilization experiment. However, the nitrogen treatment did not affect temporal stability, given that fertilization increased both the mean and standard deviation of pathogen load by roughly the same magnitude.

Conclusions

We conclude that host diversity regulates the temporal stability of pathogen load, but we note that this effect may be attenuated under rapid biodiversity loss in the Anthropocene.
Nonverbal Neurocognitive Assessment during the Coronavirus Disease of 2019 Pandemic: the Effect of Personal Protective Equipment
Authors: Lichtenstein Jonathan , Niemczak Christopher , Bowers Caitlin , Magohe Albert , Fellows Abigail , Ealer Christin , Massawe Enica , Moshi Ndeserua , Buckey Jay
Published: July 2022

Objective

The coronavirus disease of 2019 pandemic has increased personal protective equipment (PPE) use in medical settings. The current study examined the effect of PPE on a nonverbal measure of neurocognitive functioning.

Methods

The Leiter International Performance Scale, Third Edition (Leiter-3) was administered to 125 children between the ages of three and eight. Fifty-nine children were assessed twice without any PPE and 66 were assessed once without and once with PPE. Group differences on composite scores were evaluated using a repeated measures design, accounting for sex, school attendance, socioeconomic status, and HIV status.

Results

Nonverbal IQ scores increased significantly between test administrations for both groups, but no significant interaction between PPE group and scores on Leiter-3 composites was found.

Conclusions

No main effect of PPE on Leiter-3 outcomes was found. These results suggest clinical and research work using a nonverbal neurocognitive assessment can be completed when PPE is required.
Multiomics technologies: role in disease biomarker discoveries and therapeutics
Authors: Dar Mashooq Ahmad , Arafah Azher , Bhat Kaisar Ahmad , Khan Andleeb , Khan Mosin Saleem , Ali Aarif , Ahmad Syed Mudasir , Rashid Shahzada Mudasir , Rehman Muneeb U
Published: July 2022

Medical research has been revolutionized after the publication of the full human genome. This was the major landmark that paved the way for understanding the biological functions of different macro and micro molecules. With the advent of different high-throughput technologies, biomedical research was further revolutionized. These technologies constitute genomics, transcriptomics, proteomics, metabolomics, etc. Collectively, these high-throughputs are referred to as multi-omics technologies. In the biomedical field, these omics technologies act as efficient and effective tools for disease diagnosis, management, monitoring, treatment and discovery of certain novel disease biomarkers. Genotyping arrays and other transcriptomic studies have helped us to elucidate the gene expression patterns in different biological states, i.e. healthy and diseased states. Further omics technologies such as proteomics and metabolomics have an important role in predicting the role of different biological molecules in an organism. It is because of these high throughput omics technologies that we have been able to fully understand the role of different genes, proteins, metabolites and biological pathways in a diseased condition. To understand a complex biological process, it is important to apply an integrative approach that analyses the multi-omics data in order to highlight the possible interrelationships of the involved biomolecules and their functions. Furthermore, these omics technologies offer an important opportunity to understand the information that underlies disease. In the current review, we will discuss the importance of omics technologies as promising tools to understand the role of different biomolecules in diseases such as cancer, cardiovascular diseases, neurodegenerative diseases and diabetes.

Summary Points
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA
Authors: Danilevsky Artem , Polsky Avital Luba , Shomron Noam
Published: July 2022

Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful technique to solve many complex computational tasks. ‘Adaptive sequencing’ is an implementation of selective sequencing, intended for use on the nanopore sequencing platform. In this study, we demonstrated an alternative method of software-based selective sequencing that is performed in real time by combining nanopore sequencing and deep learning. Our results showed the feasibility of using deep learning for classifying signals from only the first 200 nucleotides in a raw nanopore sequencing signal format. This was further demonstrated by comparing the accuracy of our deep learning classification model across data from several human cell lines and other eukaryotic organisms. We used custom deep learning models and a script that utilizes a ‘Read Until’ framework to target mitochondrial molecules in real time from a human cell line sample. This achieved a significant separation and enrichment ability of 2.3-fold. In a series of very short sequencing experiments (10, 30 and 120 min), we identified genomic and mitochondrial reads with accuracy above 90%, although mitochondrial DNA comprised only 0.1% of the total input material. The uniqueness of our method is the ability to distinguish two groups of DNA even without a labeled reference. This contrasts with studies that required a well-defined reference, whether of a DNA sequence or of another type of representation. Additionally, our method showed higher correlation to the theoretically possible enrichment factor, compared with other published methods. We believe that our results will lay the foundation for rapid and selective sequencing using nanopore technology and will pave the approach for clinical applications that use nanopore sequencing data.
SYSMut: decoding the functional significance of rare somatic mutations in cancer
Authors: Khalighi Sirvan , Joseph Peronne , Babu Deepak , Singh Salendra , LaFramboise Thomas , Guda Kishore , Varadan Vinay
Published: July 2022

Current tailored-therapy efforts in cancer are largely focused on a small number of highly recurrently mutated driver genes but therapeutic targeting of these oncogenes remains challenging. However, the vast number of genes mutated infrequently across cancers has received less attention, in part, due to a lack of understanding of their biological significance. We present SYSMut, an extendable systems biology platform that can robustly infer the biologic consequences of somatic mutations by integrating routine multiomics profiles in primary tumors. We establish SYSMut’s improved performance vis-à-vis state-of-the-art driver gene identification methodologies by recapitulating the functional impact of known driver genes, while additionally identifying novel functionally impactful mutated genes across 29 cancers. Subsequent application of SYSMut on low-frequency gene mutations in head and neck squamous cell (HNSC) cancers, followed by molecular and pharmacogenetic validation, revealed the lipidogenic network as a novel therapeutic vulnerability in aggressive HNSC cancers. SYSMut is thus a robust scalable framework that enables the discovery of new targetable avenues in cancer.
High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands
Authors: Yang Tong , Gao Feng
Published: July 2022

The pan-genome analysis of bacteria provides detailed insight into the diversity and evolution of a bacterial population. However, the genomes involved in the pan-genome analysis should be checked carefully, as the inclusion of confounding strains would have unfavorable effects on the identification of core genes, and the highly similar strains could bias the results of the pan-genome state (open versus closed). In this study, we found that the inclusion of highly similar strains also affects the results of unique genes in pan-genome analysis, which leads to a significant underestimation of the number of unique genes in the pan-genome. Therefore, these strains should be excluded from pan-genome analysis at the early stage of data processing. Currently, tens of thousands of genomes have been sequenced for Escherichia coli, which provides an unprecedented opportunity as well as a challenge for pan-genome analysis of this classical model organism. Using the proposed strategies, a high-quality E. coli pan-genome was obtained, and the unique genes was extracted and analyzed, revealing an association between the unique gene clusters and genomic islands from a pan-genome perspective, which may facilitate the identification of genomic islands.
RNAloops: a database of RNA multiloops
Authors: Wiedemann Jakub , Kaczor Jacek , Milostan Maciej , Zok Tomasz , Blazewicz Jacek , Szachniuk Marta , Antczak Maciej
Published: July 2022

Motivation

Knowledge of the 3D structure of RNA supports discovering its functions and is crucial for designing drugs and modern therapeutic solutions. Thus, much attention is devoted to experimental determination and computational prediction targeting the global fold of RNA and its local substructures. The latter include multi-branched loops—functionally significant elements that highly affect the spatial shape of the entire molecule. Unfortunately, their computational modeling constitutes a weak point of structural bioinformatics. A remedy for this is in collecting these motifs and analyzing their features.

Results

RNAloops is a self-updating database that stores multi-branched loops identified in the PDB-deposited RNA structures. A description of each loop includes angular data—planar and Euler angles computed between pairs of adjacent helices to allow studying their mutual arrangement in space. The system enables search and analysis of multiloops, presents their structure details numerically and visually, and computes data statistics.

Availability and implementation

RNAloops is freely accessible at https://rnaloops.cs.put.poznan.pl.

Supplementary information

Supplementary data are available at Bioinformatics online.
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing
Authors: Breitenbach Tim , Schmitt Matthias Jürgen , Dandekar Thomas
Published: July 2022

Motivation

A recent approach to perform genetic tracing of complex biological problems involves the generation of synthetic deoxyribonucleic acid (DNA) probes that specifically mark cells with a phenotype of interest. These synthetic locus control regions (sLCRs), in turn, drive the expression of a reporter gene, such as fluorescent protein. To build functional and specific sLCRs, it is critical to accurately select multiple bona fide cis-regulatory elements from the target cell phenotype cistrome. This selection occurs by maximizing the number and diversity of transcription factors (TFs) within the sLCR, yet the size of the final sLCR should remain limited.

Results

In this work, we discuss how optimization, in particular integer programing, can be used to systematically address the construction of a specific sLCR and optimize pre-defined properties of the sLCR. Our presented instance of a linear optimization problem maximizes the activation potential of the sLCR such that its size is limited to a pre-defined length and a minimum number of all TFs deemed sufficiently characteristic for the phenotype of interest is covered. We generated an sLCR to trace the mesenchymal glioblastoma program in patients by solving our corresponding linear program with the software optimizer Gurobi. Considering the binding strength of transcription factor binding sites (TFBSs) with their TFs as a proxy for activation potential, the optimized sLCR scores similarly to an sLCR experimentally validated in vivo, and is smaller in size while having the same coverage of TFBSs.

Availability and implementation

We provide a Python implementation of the presented framework in the Supplementary Material with which an optimal selection of cis-regulatory elements can be calculated once the target set of TFs and their binding strength with their TFBSs is known.

Supplementary information

Supplementary data are available at Bioinformatics online.
DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma
Authors: Chen Yang , Chen Shue , Lei Elissa P
Published: July 2022

Motivation

ChIP-seq detects protein–DNA interactions within chromatin, such as that of chromatin structural components and transcription machinery. ChIP-seq profiles are often noisy and variable across replicates, posing a challenge to the development of effective algorithms to accurately detect differential peaks. Methods have recently been designed for this purpose but sometimes yield conflicting results that are inconsistent with the underlying biology. Most existing algorithms perform well on limited datasets. To improve differential analysis of ChIP-seq, we present a novel Differential analysis method for ChIP-seq based on Limma (DiffChIPL).

Results

DiffChIPL is adaptive to asymmetrical or symmetrical data and can accurately report global differences. We used simulated and real datasets for transcription factors (TFs) and histone modification marks to validate and benchmark our algorithm. DiffChIPL shows superior performance in sensitivity and false positive rate in different simulations and control datasets. DiffChIPL also performs well on real ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq datasets. DiffChIPL is an accurate and robust method, exhibiting better performance in differential analysis for a variety of applications including TF binding, histone modifications and chromatin accessibility.

Availability and implementation

https://github.com/yancychy/DiffChIPL.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evaluating causes of effects by posterior effects of causes
Authors: Lu Zitong , Geng Zhi , Li Wei , Zhu Shengyu , Jia Jinzhu
Published: July 2022

For the case with a single causal variable, Dawid et al. (2014) defined the probability of causation, and Pearl (2000) defined the probability of necessity to assess the causes of effects. For a case with multiple causes that could affect each other, this paper defines the posterior total and direct causal effects based on the evidence observed for post-treatment variables, which could be viewed as measurements of causes of effects. Posterior causal effects involve the probabilities of counterfactual variables. Thus, as with the probability of causation, the probability of necessity and direct causal effects, the identifiability of posterior total and direct causal effects requires more assumptions than the identifiability of traditional causal effects conditional on pre-treatment variables. We present assumptions required for the identifiability of posterior causal effects and provide identification equations. Further, when the causal relationships between multiple causes and an endpoint can be depicted by causal networks, we can simplify both the required assumptions and the identification equations of the posterior total and direct causal effects. Finally, using numerical examples, we compare the posterior total and direct causal effects with other measures for evaluating the causes of effects and the population attributable risks.
Reciprocal Contributions between People and Nature: A Conceptual Intervention
Authors: Ojeda Jaime , Salomon Anne K , Rowe James K , Ban Natalie C
Published: July 2022

Throughout human history, Indigenous and local communities have stewarded nature. In the present article, we revisit the ancestral principle of reciprocity between people and nature and consider it as a conceptual intervention to the current notion of ecosystem services commonly used to inform sustainability transformation. We propose the concept of reciprocal contributions to encompass actions, interactions, and experiences between people and other components of nature that result in positive contributions and feedback loops that accrue to both, directly or indirectly, across different dimensions and levels. We identify reciprocal contributions and showcase examples that denote the importance of reciprocity for our ecological legacy and its relevance for biocultural continuity. We suggest that the concept of reciprocal contribution can support transformation pathways by resituating people as active components of nature and restructuring institutions so that ethical principles and practices from Indigenous and local communities can redirect policy approaches and interventions worldwide.
Secondary Sclerosing Cholangitis Following Coronavirus Disease 2019 (COVID-19): A Multicenter Retrospective Study
Authors: Hunyady Peter , Streller Lea , Rüther Darius F , Groba Sara Reinartz , Bettinger Dominik , Fitting Daniel , Hamesch Karim , Marquardt Jens U , Mücke Victoria T , Finkelmeier Fabian , Sekandarzad Asieb , Wengenmayer Tobias , Bounidane Ayoub , Weiss Felicitas , Peiffer Kai-Henrik , Schlevogt Bernhard , Zeuzem Stefan , Waidmann Oliver , Hollenbach Marcus , Kirstein Martha M , Kluwe Johannes , Kütting Fabian , Mücke Marcus M
Published: July 2022

Background

Secondary sclerosing cholangitis (SSC) is a rare disease with poor prognosis. Cases of SSC have been reported following coronavirus disease 2019 (COVID-SSC). The aim of this study was to compare COVID-SSC to SSC in critically ill patients (SSC-CIP) and to assess factors influencing transplant-free survival.

Methods

In this retrospective, multicenter study involving 127 patients with SSC from 9 tertiary care centers in Germany, COVID-SSC was compared to SSC-CIP and logistic regression analyses were performed investigating factors impacting transplant-free survival.

Results

Twenty-four patients had COVID-SSC, 77 patients SSC-CIP, and 26 patients other forms of SSC. COVID-SSC developed after a median of 91 days following COVID-19 diagnosis. All patients had received extensive intensive care treatment (median days of mechanical ventilation, 48). Patients with COVID-SSC and SSC-CIP were comparable in most of the clinical parameters and transplant-free survival was not different from other forms of SSC (P = .443, log-rank test). In the overall cohort, the use of ursodeoxycholic acid (UDCA) (odds ratio [OR], 0.36 [95% confidence interval {CI}, .16–.80], P = .013; log-rank P < .001) and high serum albumin levels (OR, 0.40 [95% CI, .17–.96], P = .040) were independently associated with an increased transplant-free survival, while the presence of liver cirrhosis (OR, 2.52 [95% CI, 1.01–6.25], P = .047) was associated with worse outcome. Multidrug-resistant organism (MDRO) colonization or infection did not impact patients’ survival.

Conclusions

COVID-SSC and CIP-SSC share the same clinical phenotype, course of the disease, and risk factors for its development. UDCA may be a promising therapeutic option in SSC, though future prospective trials are needed to confirm our findings.
Universal behaviour of the growth method and importance of local hubs in cascading failure
Authors: Jeong Wonhee , Yu Unjong
Published: July 2022

We introduce hub centrality and study the relation between hub centrality and the degree of each node in the networks. We discover and verify a universal relation between them in various networks generated by the growth method, but the relation is not applied to real-world networks due to the rich-club phenomenon and the presence of local hubs. Through the study of a targeted attack and overload cascading failure, we prove that hub centrality is a meaningful parameter that gives extra insight beyond degree in real-world networks. Especially, we show that the local hubs occupy key positions in real-world networks with higher probabilities to incur global cascading failure. Therefore, we conclude that networks generated by the growth method, which do not include local hubs, have inevitable limitations to describe real-world networks.
Cardiovascular magnetic resonance in autoimmune rheumatic diseases: a clinical consensus document by the European Association of Cardiovascular Imaging
Authors: Mavrogeni S , Pepe A , Nijveldt R , Ntusi N , Sierra-Galan L M , Bratis K , Wei J , Mukherjee M , Markousis-Mavrogenis G , Gargani L , Sade L E , Ajmone-Marsan N , Seferovic P , Donal E , Nurmohamed M , Cerinic M Matucci , Sfikakis P , Kitas G , Schwitter J , Lima J A C , Dawson Dana , Dweck Marc , Haugaa Kristina H , Keenan Niall , Moon James , Stankovic Ivan , Donal Erwan , Cosyns Bernard
Published: July 2022

Autoimmune rheumatic diseases (ARDs) involve multiple organs including the heart and vasculature. Despite novel treatments, patients with ARDs still experience a reduced life expectancy, partly caused by the higher prevalence of cardiovascular disease (CVD). This includes CV inflammation, rhythm disturbances, perfusion abnormalities (ischaemia/infarction), dysregulation of vasoreactivity, myocardial fibrosis, coagulation abnormalities, pulmonary hypertension, valvular disease, and side-effects of immunomodulatory therapy.

Currently, the evaluation of CV involvement in patients with ARDs is based on the assessment of cardiac symptoms, coupled with electrocardiography, blood testing, and echocardiography. However, CVD may not become overt until late in the course of the disease, thus potentially limiting the therapeutic window for intervention. More recently, cardiovascular magnetic resonance (CMR) has allowed for the early identification of pathophysiologic structural/functional alterations that take place before the onset of clinically overt CVD. CMR allows for detailed evaluation of biventricular function together with tissue characterization of vessels/myocardium in the same examination, yielding a reliable assessment of disease activity that might not be mirrored by blood biomarkers and other imaging modalities. Therefore, CMR provides diagnostic information that enables timely clinical decision-making and facilitates the tailoring of treatment to individual patients.

Here we review the role of CMR in the early and accurate diagnosis of CVD in patients with ARDs compared with other non-invasive imaging modalities. Furthermore, we present a consensus-based decision algorithm for when a CMR study could be considered in patients with ARDs, together with a standardized study protocol. Lastly, we discuss the clinical implications of findings from a CMR examination.
Impact of sex, race and socioeconomic status on survival after pulmonary thromboendarterectomy for chronic thromboembolic pulmonary hypertension
Authors: Su Austin Y , Vinogradsky Alice , Wang Amy S , Ning Yuming , Abrahams Elizabeth , Bacchetta Matthew , Kurlansky Paul , Rosenzweig Erika B , Takeda Koji
Published: July 2022

OBJECTIVES

Pulmonary thromboendarterectomy (PTE) is a definitive treatment for chronic thromboembolic pulmonary hypertension. Demographic-based disparities in PTE outcomes have not been well-studied.

METHODS

We reviewed all patients who underwent PTE for chronic thromboembolic pulmonary hypertension between 2009 and 2019 at our institution, tracking demographic information including self-identified race, preoperative characteristics and 2-year survival. Socioeconomic status was assessed using the zip code-linked Distressed Communities Index, a validated holistic measure of community well-being. Survival was estimated using Kaplan–Meier method and factors associated with mortality were estimated using Cox regression.

RESULTS

Of 235 PTE patients, 101 (42.9%) were white and 87 (37.0%) were black. White patients had a higher median age at surgery (57 vs 51 years, P = 0.035) and a lower degree of economic distress (33.6 vs 61.2 percentile, P < 0.001). Regarding sex, 106 (45.1%) patients were male and 129 (53.6%) were female. Male patients had a higher median age (59 vs 50 years, P = 0.004), greater rates of dyslipidaemia (34% vs 20.2%, P = 0.025), a lower ejection fraction (55% vs 57%, P = 0.046) and longer cross-clamp (77 vs 67.50 min, P = 0.004) and circulatory arrest times (42 vs 37.50 min, P = 0.007). No difference was observed in unadjusted 2-year survival after PTE between patients stratified by race and sex (P = 0.35). After adjustment for clinically relevant variables, neither socioeconomic status, sex nor race were associated with mortality in Cox proportional hazard analysis.

CONCLUSIONS

Sex, socioeconomic status and race were not associated with adverse outcomes after PTE in our single-centre experience.