bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of brewing waste in the technology of synthetic polymers
Authors: Sannikova N Yu , Baturina E V , Vlasova L A , Rudyka E A , Nikulin S S , Ponomareva E Yu
Published: July 2022

At present, much attention is paid to the production of synthetic polymers. The production of rubbers by emulsion polymerization is of particular interest. Sodium chloride, currently used as a coagulating agent, has a high consumption of up to 200 kg / t of rubber and increases environmental pollution. In the presented work, for the first time, the possibility of using dispersed systems of brewing waste (yeast) to reduce the aggregate stability is considered. The use of waste material in the technology of extracting rubber from latex makes it possible to exclude sodium chloride from the technological cycle. The use of a system based on a protein coagulant makes it possible to achieve complete separation of rubber from latex at a waste consumption of 10-15 kg / t of rubber. The best results were achieved when yeast pre-acidified with sulfuric acid was used in this process, which leads to charging the nitrogen atom of the protein component. It was noted that the best temperature regime for the process of rubber extraction from latex is 1-20 ° C. An increase in temperature to 60 ° C leads to an increase in the consumption of coagulant by 5 kg / t of rubber. According to all the main physical and mechanical indicators, rubbers isolated by this technology meet the requirements.
Modification of ultrasonic machining of polyolefinic, starch-containing composite materials in the process of extrusion
Authors: Tveritnikova I S , Kirsh I A , Beznaeva O V
Published: July 2022

Nowadays the problem of polymeric and bio-degradable materials producing aimed at the load decrease of the environment is paid more and more attention. The development and study of such materials are the main research priorities. In the field of polymeric and biodegradable materials producing the research of biocomposites on the basis of natural and synthetic polymers is made. A lot of attention is paid to questions of composition modification for the activation of the polymer matrix destruction. The aim of the study was to examine the effect of ultrasonic machining on the properties of polyolefinic starch-containing compositions and to get compositions with the accelerated period of biodestruction. The following materials were chosen for the research: polyethylene, polypropylene and starch as a filler. As the result of the performed research the following conclusions can be done: 1) the increase of the starch loading brings to the decrease of the physical and mechanical properties; 2) the effect of the ultrasonic machining on polymeric compositions increases deformative and strength properties, and helps to accelerate the process of destruction.
Selection of a system for automatic control of the sterilization process of canned food in an industrial autoclave
Authors: Mokrushin S A , Nazoikin E A , Zabenkova N A , Blagoveschenskiy V G , Terekhin A R , Galkin N S
Published: July 2022

The article proposes an automatic control system that meets the technical criteria of the technological process of sterilization of canned food in an industrial autoclave. The proposed algorithm of operation and the developed structure of the automatic process control system implement modern automatic control laws and take into account the mutual influence of control coordinates. A two-circuit four-channel temperature and pressure regulator in the autoclave has been developed, which reduces the volume of defective products and saves energy resources, due to a more accurate correction of the mutual influence of control circuits. The regulator is the basis for creating an automatic control system that allows compensating for disturbing effects associated with changes in technological parameters. The proposed control device can be used to improve existing and create new automatic control systems for sterilization installations. The reliability of the study was proved by means of simulation modeling and comparison of the results with experiments on the operating equipment of the cannery.
Mathematical model of the extrusion process of grain crops during non-isothermal flow of crop melting to the temperature at the beginning of the Maillard reaction
Authors: Ostrikov A N , Vasilenko V N , Frolova L N , Kochkin I B , Eremin I D
Published: July 2022

To describe the non-isothermal flow of grain crops melt in the extruder, the equations of motion, the equation of continuity, the equation of energy (heat balance), and the rheological equation were chosen as initial equations. To solve the model, the following assumptions were made. The flow of a moving viscous medium is assumed to be laminar and steady. The forces of inertia and gravity are so small compared to the forces of friction and pressure that they can be neglected. A viscous medium (melt) is an incompressible liquid characterized by constant thermal conductivity and thermal diffusivity. The change in thermal conductivity in the longitudinal direction was neglected due to the fact that convective heat transfer in the direction of flow is higher than the heat transfer by thermal conductivity. Heat transfer in the direction perpendicular to flow of the melt occurs only due to thermal conductivity. To solve the system of equations taking into account convective heat transfer, a numerical finite difference method was used, according to which the considered area (extruder channel) is divided into computational cells using a grid. The grid consisted of rectangular cells with a constant step between nodes, which exactly lie on the boundaries of the integration region. In this case, the differential equations were transformed into difference equations by replacing the derivatives at a point with finite differences along the cell boundaries. As a result, a mathematical model of non-isothermal melt flow in the extruder channel was obtained. To solve a mathematical model of the grain crops extrusion process with a non-isothermal flow of their melts, a program in the programming language C++ was compiled. A non-isothermal mathematical model of the grain crops extrusion process at temperatures at the beginning of the Maillard reaction, i.e., up to 120-125 °C, was obtained, which makes it possible to reveal the nature of the temperature change along the length of the extruder. Comparative analysis of the results of the numerical solution and experimental data showed good convergence: the standard deviation did not exceed 12.7%.
Study of the production process of extruded feed and evaluation of the quality of the resulting product using software methods
Authors: Kovaleva E N , Safonova Yu A , Lemeshkin A V , Agaeva N Yu , Machtakov S G , Shchetilina I P
Published: July 2022

Enterprises for the production of food products are mainly aimed at obtaining a product with the best quality. To obtain the final product with the specified quality indicators, it is necessary to control the process that ensures its production. Therefore, in the present it is relevant to talk about quality management, which includes not only the control indicators of the finished product, but also the establishment of parameters that determine the technological process. The production of co-extruded feed mixtures is innovative. The distinctive feature of these feed mixtures is their increased nutritional value due to the use of non-traditional types of raw materials. It is possible to evaluate the quality of the mixtures obtained not only by conducting laboratory experiments, but also in an empirical way, using mathematical modeling methods and their software implementation. Thus, the relevance of the topic is dictated by the need to improve the evaluation systems of technological processes based on the mathematical apparatus and programming methods.
Development and research of a digital control system for juice consumption after the diffusion apparatus in sugar production
Authors: Alekseev M V , Kudryashov V S , Gavrilov A N , Ivanov A V , Kozenko I A , Sukhanova N V
Published: July 2022

The article is devoted to solving the problem of stabilizing the flow rate of diffusion juice at the outlet from the buffer tank under conditions of an unstable hydrodynamic mode of operation of the diffusion apparatus in sugar production. The existing system does not provide effective stabilization of the juice consumption in case of significant fluctuations in the level and situations arise when the buffer tank is empty or overflowed. A digital control system is proposed that improves the dynamic accuracy of juice flow stabilization due to digital correction according to the integral law of setting the flow regulator according to filtered (smoothed) level values and including proportional, differential components in the correction algorithm when the level leaves the “smooth” control area. The effectiveness of the digital control system is confirmed by mathematical modeling in various modes.
Improving the effectiveness of preliminary heat treatment (blanching) of cartilage fish of the Northern Basin
Authors: Zhikhoruk A , Golubeva O , Malaeva A
Published: July 2022

Blanching is the process of preliminary heat treatment (PHT) of raw materials or semi-finished products before canning using various methods, which serves to inactivate unfavorable enzymes, improve organoleptic properties of the product produced and increase its storage period. Modern trend to rationalization of raw material processing requires the search for new methods of more efficient use of natural resources. Existing traditional blanching technology is well developed, but has a number of significant drawbacks. The article presents the methodology of experimental research focused on combined blanching, delivers the overview results of the most rational temperature of pre-heat treatment (combined blanching - water-steam), the effect of the steam generator capacity on the loss of raw materials mass and PHT is assessed. The article analyzes the advantages and disadvantages of blanching with water and steam separately. The use of both methods in one technological process made it possible to mitigate the disadvantages of each method individually. While improving the method of combined blanching, a mathematical model was obtained, allowing to perform the prediction calculation of rational modes of PHT of thorny skate, to produce a product with the necessary final characteristics. Based on the results of improving the method of combined blanching, with sequential use of water and steam, a continuous PHT tunnel-type unit was designed. It was decided to issue the patent on this utility model. The use of combined methods allows reducing the impact of disadvantages of each method applied. The technology of using combined blanching will make it possible to process the underutilized water biological resources of the northern seas, broaden the product range and reduce the price of the product for the consumer.
High-frequency acoustic cavitation in the technology of producing milk and dairy products
Authors: Kanina K A , Krasulya O N , Zhizhin N A
Published: July 2022

The article tells us about the issue of the influence of high-frequency acoustic cavitation on the quality characteristics of raw milk and white cheese produced with its use. It is shown that with the duration of milk processing for 30 minutes and the impact power of 45 kHz, the number of bacteria of the Escherichia coli group decreases by 40% and native calcium is preserved, which is subsequently necessary for the formation of a high-quality cheese layer. The effect of high-frequency acoustic cavitation on the components of milk, such as fat and protein, has been studied. It is established that during the initial period of exposure to high-frequency cavitation, there is a crushing of fat particles - homogenization with subsequent agglomeration, and then the release of free (destabilized) fat. It is worth noting that acoustic cavitation does not have a negative effect on the protein component of milk. Thus, whey proteins, which are most susceptible to denaturation (precipitation) during heat treatment, remain in the native state during cavitation exposure. The authors concluded that high-frequency acoustic exposure is technologically feasible in the production of high-protein products, in particular, in the production of white cheese. The results of histological analysis indicate that calcium in this type of processing in cheese has a structured appearance and larger associations in size compared to cheese obtained from unprocessed milk, which has a positive effect on the quality of the protein matrix of the product.
Theoretical and experimental determination of number of impacts required for caryopsis destruction
Authors: Voronin V V , Smyshlyaev A A , Orobinsky V I , Vorokhobin A V , Chekhunov O A , Merchalov S V
Published: July 2022

The article presents theoretical and experimental studies to determine the number of impacts to destroy the caryopsis. To substantiate the number of shock impacts, the Rebinder’s equation for determining the work on grinding was taken as the basis for theoretical studies. The transformation and development of the Rebinder’s equation enabled to theoretically obtain expressions for determining the amount of work required for guaranteed destruction of the caryopsis when a single impact was applied. An equation for determining the work of a particle destruction during a multiple number of impacts was also obtained. Its transformation enabled to obtain a function and implement a theoretical nomogram. The performed theoretical analysis of the obtained nomogram enabled to consider the energy costs when determining the required number of impacts for guaranteed caryopsis destruction at certain voltages. To validate the theoretical studies, the experiments on breaking down whole grains of wheat and barley were carried out. To conduct the experiments, an experimental setup to perform a series of experiments was developed. As a result of experimental studies, the value of the limiting stresses, at which no grain destruction is observed with any number of impacts, was determined. The magnitude of the stress for a single impact for guaranteed destruction of the caryopsis was determined. The main result of the experiments is the determination of the number of impacts for the destruction of barley and wheat kernels with minimal energy consumption.
Substantiation for variables technological modes convective and microwave drying of apples
Authors: Kalashnikov G V , Litvinov E V , Bunin E S , Makeev S V
Published: July 2022

The processes of dehydration and transformation of dry matter of apples are experimentally studied on the basis of differential thermal and thermogravimetric analysis. The kinetics of the process of apple thermolysis was investigated on the basis of differential thermal and thermogravimetric analysis. The thermoanalytical curves obtained by the method of non-isothermal kinetics were based on the experimental dependences of the change in the mass of the TGA sample, the rate of temperature change DTA, and the rate of change in the DTG mass. Differential thermal analysis was used to determine the thermal effect of the dehydration reaction. For apples in the temperature range of (376 ... 475) K, an endothermic effect is noted with an increase in temperature to (473 ... 495) K, a significant destruction of substances is noted. On the basis of the performed theoretical and experimental studies, it is proposed to use variable thermal effects during convective and microwave drying, as well as variable hydrodynamic regimes of a layer of dispersed material in the production of rapidly recovered dried apples.
Temporal electric field of a helium plasma jet by electric field induced second harmonic (E-FISH) method
Authors: LI Xu , JIN Shaohui , SONG Ke , NIE Lanlan , LIU Dawei , LU Xinpei
Published: July 2022

Electric field is an important parameter of plasma, which is related to electron temperature, electron density, excited species density, and so on. In this work, the electric field of an atmospheric pressure plasma jet is diagnosed by the electric field induced second harmonic (E-FISH) method, and the time-resolved electric field under different conditions is investigated. When positive pulse voltage is applied, the electric field has a peak of about 25 kV cm−1 at the rising edge of the voltage pulse. A dark channel is left behind the plasma bullet and the electric field in the dark channel is about 5 kV cm−1. On the other hand, when negative pulse voltage is applied, the electric field has a peak of −16 kV cm−1 when the negative voltage is increased to −8 kV. A relatively bright channel is left behind the plasma head and the electric field in this relatively bright channel is about −6 kV cm−1. When the pulse rising time increases from 60 to 200 ns, the peak electric field at both the rising edge and the falling edge of the voltage decreases significantly. When 0.5% of oxygen is added to the main working gas helium, the peak electric field at the rising edge is only about 15 kV cm−1. On the other hand, when 0.5% nitrogen is added, the peak electric field increases especially at the falling edge of the voltage pulse, where it increases reversely from −12 to −16 kV cm−1 (the minus sign only represents the direction of electric field).
Preparation and application of lignin nanoparticles: a review
Authors: Zhu Baoping , Xu Yang , Xu Huanfei
Published: July 2022

Lignin is a natural renewable biopolymer with abundant reserves and great potential. As a by-product of the pulp and paper industry, the world can produce 150 billion tons of it every year, but it has not been effectively utilized. It was found that disordered and complex lignin can be converted into ordered and homogeneous nanoparticles by self-assembly, solvent exchange and acid precipitation. Lignin nanoparticles (LNPs) have the advantages of high stability, high activity, good biocompatibility and biodegradability, as well as improved structural and size control, antioxidant activity and other properties. LNPs have great potential for application not only as a natural alternative to traditional petroleum derivatives, biopharmaceutical carriers, but also in hydrogels. In recent years, the research of LNPs has received a lot of attention. It is hoped that more economical, environmentally friendly and high yielding methods for the synthesis of LNPs will be investigated in the future. This paper reviews the preparation methods of LNPs and their applications in various fields.
General formulation of Coulomb explosion dynamics of highly symmetric charge distributions
Authors: Zandi Omid , van der Veen Renske M
Published: July 2022

We present a theoretical approach to study the dynamics of spherical, cylindrical and ellipsoidal charge distributions under their self-Coulomb field and a stochastic force due to collisions and random motions of charged particles. The approach is based on finding the current density of the charge distribution from the charge-current continuity equation and determining the drift velocities of the particles. The latter can be used either to derive the Lagrangian of the system, or to write Newton’s equation of motion with the Lorentz force. We develop a kinetic theory to include the stochastic force due to random motions of electrons in our model. To demonstrate the efficacy of our method, we apply it to various charge distributions and compare our results to N-body simulations. We show that our method reproduces the well-known emittance term in the envelope equation of uniform spherical and cylindrical charge distributions with correct coefficients. We use our model for the gravitational collapse of an ideal gas as well as the cyclotron dynamics of a cylindrical charge distribution in a uniform magnetic field and propose a method to measure the emittance of electron beams.
Coordinately regulated transcription factors EIN3/EIL1 and MYCs in ethylene and jasmonate signaling interact with the same domain of MED25
Authors: Liu Ruiqi , Niimi Hikaru , Ueda Minoru , Takaoka Yousuke
Published: July 2022

Ethylene (ET) and jasmonate (JA) are plant hormones that act synergistically to regulate plant development and defense against necrotrophic fungi infections, and antagonistically in response to wounds and apical hook formation. Previous studies revealed that the coordination of these responses is due to dynamic protein-protein interactions (PPI) between their master transcription factors (TFs) EIN3/EIL1 and MYC in ET and JA signaling, respectively. In addition, both TFs are activated via interactions with the same transcriptional mediator MED25, which upregulates downstream gene expression. Herein, we analyzed the PPI between EIN3/EIL1 and MED25, and as with the PPI between MYC3 and MED25, found that the short binding domain of MED25 (CMIDM) is also responsible for the interaction with EIN3/EIL1 − a finding which suggests that both TFs compete for binding with MED25. These results further inform our understanding of the coordination between the ET and JA regulatory systems.
Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies
Authors: Zhuang Yongwen , Wolford Brooke N , Nam Kisung , Bi Wenjian , Zhou Wei , Willer Cristen J , Mukherjee Bhramar , Lee Seunggeun
Published: July 2022

Motivation

In the genome-wide association analysis of population-based biobanks, most diseases have low prevalence, which results in low detection power. One approach to tackle the problem is using family disease history, yet existing methods are unable to address type I error inflation induced by increased correlation of phenotypes among closely related samples, as well as unbalanced phenotypic distribution.

Results

We propose a new method for genetic association test with family disease history, mixed-model-based Test with Adjusted Phenotype and Empirical saddlepoint approximation, which controls for increased phenotype correlation by adopting a two-variance-component mixed model, accounts for case–control imbalance by using empirical saddlepoint approximation, and is flexible to incorporate any existing adjusted phenotypes, such as phenotypes from the LT-FH method. We show through simulation studies and analysis of UK Biobank data of white British samples and the Korean Genome and Epidemiology Study of Korean samples that the proposed method is robust and yields better calibration compared to existing methods while gaining power for detection of variant–phenotype associations.

Availability and implementation

The summary statistics and code generated in this study are available at https://github.com/styvon/TAPE.

Supplementary information

Supplementary data are available at Bioinformatics online.
MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis
Authors: Zheng Jun-Jie , Wang Po-Wen , Huang Tzu-Wen , Yang Yao-Jong , Chiu Hua-Sheng , Sumazin Pavel , Chen Ting-Wen
Published: July 2022

Motivation

Microbiota analyses have important implications for health and science. These analyses make use of 16S/18S rRNA gene sequencing to identify taxa and predict species diversity. However, most available tools for analyzing microbiota data require adept programming skills and in-depth statistical knowledge for proper implementation. While long-read amplicon sequencing can lead to more accurate taxa predictions and is quickly becoming more common, practitioners have no easily accessible tools with which to perform their analyses.

Results

We present MOCHI, a GUI tool for microbiota amplicon sequencing analysis. MOCHI preprocesses sequences, assigns taxonomy, identifies different abundant species and predicts species diversity and function. It takes either taxonomic count table or FASTQ of partial 16S/18S rRNA or full-length 16S rRNA gene as input. It performs analyses in real time and visualizes data in both tabular and graphical formats.

Availability and implementation

MOCHI can be installed to run locally or accessed as a web tool at https://mochi.life.nctu.edu.tw.

Supplementary information

Supplementary data are available at Bioinformatics online.
BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task
Authors: Mahbub Maria , Srinivasan Sudarshan , Begoli Edmon , Peterson Gregory D
Published: July 2022

Motivation

Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model’s performance.

Results

We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets—BioASQ-7b, BioASQ-8b and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets.

Availability and implementation

BioADAPT-MRC is freely available as an open-source project at https://github.com/mmahbub/BioADAPT-MRC.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models
Authors: Pradelli Franco , Minervini Giovanni , Tosatto Silvio C E
Published: July 2022

Mathematical models are effective in studying cancer development at different scales from metabolism to tissue. Phase Field Models (PFMs) have been shown to reproduce accurately cancer growth and other related phenomena, including expression of relevant molecules, extracellular matrix remodeling and angiogenesis. However, implementations of such models are rarely published, reducing access to these techniques. To reduce this gap, we developed Mocafe, a modular open-source Python package that implements some of the most important PFMs reported in the literature. Mocafe is designed to handle both PFMs purely based on differential equations and hybrid agent-based PFMs. Moreover, Mocafe is meant to be extensible, allowing the inclusion of new models in future releases.

Availability and implementation

Mocafe is a Python package based on FEniCS, a popular computing platform for solving partial differential equations. The source code, extensive documentation and demos are provided on GitHub at URL: https://github.com/BioComputingUP/mocafe. Moreover, we uploaded on Zenodo an archive of the package, which is available at https://doi.org/10.5281/zenodo.6366052.
Overcoming selection bias in synthetic lethality prediction
Authors: Seale Colm , Tepeli Yasin , Gonçalves Joana P
Published: July 2022

Motivation

Synthetic lethality (SL) between two genes occurs when simultaneous loss of function leads to cell death. This holds great promise for developing anti-cancer therapeutics that target synthetic lethal pairs of endogenously disrupted genes. Identifying novel SL relationships through exhaustive experimental screens is challenging, due to the vast number of candidate pairs. Computational SL prediction is therefore sought to identify promising SL gene pairs for further experimentation. However, current SL prediction methods lack consideration for generalizability in the presence of selection bias in SL data.

Results

We show that SL data exhibit considerable gene selection bias. Our experiments designed to assess the robustness of SL prediction reveal that models driven by the topology of known SL interactions (e.g. graph, matrix factorization) are especially sensitive to selection bias. We introduce selection bias-resilient synthetic lethality (SBSL) prediction using regularized logistic regression or random forests. Each gene pair is described by 27 molecular features derived from cancer cell line, cancer patient tissue and healthy donor tissue samples. SBSL models are built and tested using approximately 8000 experimentally derived SL pairs across breast, colon, lung and ovarian cancers. Compared to other SL prediction methods, SBSL showed higher predictive performance, better generalizability and robustness to selection bias. Gene dependency, quantifying the essentiality of a gene for cell survival, contributed most to SBSL predictions. Random forests were superior to linear models in the absence of dependency features, highlighting the relevance of mutual exclusivity of somatic mutations, co-expression in healthy tissue and differential expression in tumour samples.

Availability and implementation

https://github.com/joanagoncalveslab/sbsl

Supplementary information

Supplementary data are available at Bioinformatics online.
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments
Authors: Ansaloni Federico , Gualandi Nicolò , Esposito Mauro , Gustincich Stefano , Sanges Remo
Published: July 2022

Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts.

Availability and implementation

The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331).

Supplementary information

Supplementary data are available at Bioinformatics online.
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning
Authors: Dănăilă Vlad-Rareş , Buiu Cătălin
Published: July 2022

Motivation

Knowing the sensitivity of a viral strain versus a monoclonal antibody is of interest for HIV vaccine development and therapy. The HIV strains vary in their resistance to antibodies, and the accurate prediction of virus-antibody sensitivity can be used to find potent antibody combinations that broadly neutralize multiple and diverse HIV strains. Sensitivity prediction can be combined with other methods such as generative algorithms to design novel antibodies in silico or with feature selection to uncover the sites of interest in the sequence. However, these tools are limited in the absence of in silico accurate prediction methods.

Results

Our method leverages the CATNAP dataset, probably the most comprehensive collection of HIV-antibodies assays, and predicts the antibody-virus sensitivity in the form of binary classification. The methods proposed by others focus primarily on analyzing the virus sequences. However, our article demonstrates the advantages gained by modeling the antibody-virus sensitivity as a function of both virus and antibody sequences. The input is formed by the virus envelope and the antibody variable region aminoacid sequences. No structural features are required, which makes our system very practical, given that sequence data is more common than structures. We compare with two other state-of-the-art methods that leverage the same dataset and use sequence data only. Our approach, based on neuronal networks and transfer learning, measures increased predictive performance as measured on a set of 31 specific broadly neutralizing antibodies.

Availability and implementation

https://github.com/vlad-danaila/deep_hiv_ab_pred/tree/fc-att-fix
Decreased junctional adhesion molecule 3 expression induces reactive oxygen species production and apoptosis in trophoblasts
Authors: Chen Chie-Pein , Wang Liang-Kai , Chen Chen-Yu , Chen Chia-Yu , Kuo Yi-Hsiu , Wu Yi-Hsin
Published: July 2022

Junctional adhesion molecule 3 (JAM3) is involved in epithelial cell junction, cell polarity, and motility. The molecular mechanisms underlying the role of JAM3 in placental dysfunction remain unclear. We hypothesized that JAM3 expression regulates trophoblast fusion, differentiation, proliferation, and apoptosis. Our results revealed that JAM3 was expressed in the cytotrophoblasts and syncytiotrophoblasts of first-trimester and term placental villi. JAM3 expression in cell–cell junctions decreased with the formation of syncytiotrophoblasts. Using trophoblasts as an in vitro model, we observed that forskolin and JAM3 knockdown significantly reduced JAM3 expression and increased syncytium formation. JAM3 knockdown additionally inhibited trophoblast proliferation and increased the number of trophoblasts in the sub-G1 and G2/M phases, indicating cell-cycle disturbance and apoptosis. Cell-cycle arrest was associated with the engagement of checkpoint kinase 2-cell division cycle 25C-cyclin-dependent kinase 1/cyclin B1 signaling. Increased expression of BIM, NOXA, XAF1, cytochrome c, and cleaved caspase-3 further indicated trophoblast apoptosis. Overexpression of JAM3 or recombinant JAM3 protein enhanced trophoblast adhesion and migration, which were inhibited by JAM3 knockdown. JAM3 knockdown induced reactive oxygen species and syncytin 2 expression in trophoblasts. Furthermore, H2O2-induced oxidative stress reduced JAM3 expression in trophoblasts and cell culture supernatants. H2O2 simultaneously induced trophoblast apoptosis. JAM3 expression was significantly decreased in the plasmas and placentas of patients with early-onset severe preeclampsia. Thus, our results show that JAM3 may not only be a structural component of trophoblast cell junctions but also regulates trophoblast fusion, differentiation, proliferation, apoptosis, and motility. Dysregulated trophoblast JAM3 expression is crucial in preeclampsia development.
Lithium treatment promotes the activation of primordial follicles through PI3K/Akt signaling
Authors: Li Biao , Wang Weiyong , Huang Yingying , Han Lincheng , Li Jia , Zheng Nana , Wu Zhanying , Zhang Xiaodan , Li Xuelan , Deng Ling , Lin Min , Chen Xin , Zhang Meijia
Published: July 2022

In mammals, dormant primordial follicles represent the ovarian reserve throughout reproductive life. In vitro activation of dormant primordial follicles has been used to treat patients with premature ovarian insufficiency (POI). However, there remains a lack of effective strategies to stimulate follicle activation in vivo. In this study, we used an in vitro ovarian culture system and intraperitoneal injection to study the effect of lithium treatment on primordial follicle activation. Lithium increased the number of growing follicles in cultured mouse ovaries and promoted pre-granulosa cell proliferation. Furthermore, lithium significantly increased the levels of phosphorylated protein kinase B (Akt) and the number of oocytes with forkhead Box O3a (FOXO3a) nuclear export. Inhibition of the phosphatidylinositol 3 kinase (PI3K)/Akt pathway by LY294002 reversed lithium-promoted mouse primordial follicle activation. These results suggest that lithium promotes mouse primordial follicle activation by the PI3K/Akt signaling. Lithium also promoted primordial follicle activation and increased the levels of p-Akt in mouse ovaries in vivo and in human ovarian tissue cultured in vitro. Taken together, lithium promotes primordial follicle activation in mice and humans by the PI3K/Akt signaling. Lithium might be a potential oral drug for treating infertility in POI patients with residual dormant primordial follicles.
Inhibition of SHMT2 mRNA translation increases embryonic mortality in sheep
Authors: Sah Nirvay , Stenhouse Claire , Halloran Katherine M , Moses Robyn M , Seo Heewon , Burghardt Robert C , Johnson Gregory A , Wu Guoyao , Bazer Fuller W
Published: July 2022

The one-carbon metabolism (OCM) pathway provides purines and thymidine for synthesis of nucleic acids required for cell division, and S-adenosyl methionine for polyamine and creatine syntheses and the epigenetic regulation of gene expression. This study aimed to determine if serine hydroxymethyltransferase 2 (SHMT2), a key enzyme in the OCM pathway, is critical for ovine trophectoderm (oTr) cell function and conceptus development by inhibiting translation of SHMT2 mRNA using a morpholino antisense oligonucleotide (MAO). In vitro treatment of oTr cells with MAO-SHMT2 decreased expression of SHMT2 protein, which was accompanied by reduced proliferation (P = 0.053) and migration (P < 0.05) of those cells. Intrauterine injection of MAO-SHMT2 in ewes on Day 11 post-breeding tended to decrease the overall pregnancy rate (on Days 16 and 18) compared with MAO-control (3/10 vs. 7/10, P = 0.07). The three viable conceptuses (n = 2 on Day 16 and n = 1 on Day 18) recovered from MAO-SHMT2 ewes had only partial inhibition of SHMT2 mRNA translation. Conceptuses from the three pregnant MAO-SHMT2 ewes had similar levels of expression of mRNAs and proteins involved in OCM as compared with conceptuses from MAO-control ewes. These results indicate that knockdown of SHMT2 protein reduces proliferation and migration of oTr cells (in vitro) to decrease elongation of blastocysts from spherical to elongated forms. These in vitro effects suggest that increased embryonic deaths in ewes treated with MAO-SHMT2 are the result of decreased SHMT2-mediated trophectoderm cell proliferation and migration supporting a role for the OCM pathway in survival and development of ovine conceptuses.
Use of solar PV inverters during night-time for voltage regulation and stability of the utility grid
Authors: Tharuka Lulbadda Kushan , Hemapala Udayanga
Published: July 2022

Photovoltaic (PV) inverters are vital components for future smart grids. Although the popularity of PV-generator installations is high, their effective performance remains low. Certain inverters are designed to operate in volt-ampere reactive (VAR) mode during the night. Yet, this approach is ineffective due to the consumption of active power from the grid (as internal losses) and the regulation necessity of the direct-current (DC) bus. This paper will demonstrate the operation of a PV inverter in reactive power-injection mode when solar energy is unavailable. The primary focus is on the design of the inverter controller with respect to the synchronous rotating frame control method. The proposed novel method enables an inverter to inject the required level of reactive power to regulate the voltage levels of the utility grid within specified limits. In the process, the inverter does not absorb active power from the grid for its internal operation. The presented model has the ability to inject ≤2 kVAR of reactive power at zero power factor without absorbing active power from the grid. Simulation and hardware models of the inverter were developed and tested for different reactive loads in which the hardware model represented the real-world application. The reactive power injection of the two models ran at zero power factor and produced the expected outcomes for their corresponding independent reactive loads. Henceforth, it was evident that the proposed method can enhance the efficiency of an inverter and ensure the stability of the utility grid to which it is connected.
Effects of Refugee Inflow on the Voting Behavior of Natives: Application of Mobile Phone Data
Authors: Usta Emine Kübra
Published: July 2022

This paper investigates the effects of refugee inflow on the voting behavior of natives. I employ a difference in differences strategy to identify the voter reaction against the sudden inflow of Syrian refugees to Turkey and use unique data provided by Turk Telecom to proxy natives’ refugee exposure. Data coming from mobile phone usage track the mobility of refugees throughout the year and enables the construction of refugee exposure measures across small geographical areas. I show a small drop in the government party vote share that announced an ‘open door’ policy for refugees. Furthermore, there is evidence for the reaction heterogeneity based on the socio-economic development levels of refugee-hosting areas. While there is a null response in ethnically Kurdish and economically lagging East, a negative reaction is concentrated in socioeconomically more developed areas. Then, exploring the effects in rural and urban areas reveals an interesting divide in the refugee exposure patterns of hosting areas. While in rural areas, natives react against the refugee presence, in urban areas, they react when the mobility (visibility) increases. Anecdotal evidence might help to put findings in context. Manipulating the concerns of voters on Syrians’ receiving citizenship and demographic change might be regarded as two main strategies used by opposition parties. These strategies help convince the secular and conservative-nationalist voters in socioeconomically developed areas. (JEL codes: J01, J08, and J15)
Insolvency Law and Policy in Times of COVID-19 and Beyond: Academic Roundtable Proceedings
Authors: Wan Wai Yee , Yan Xin
Published: July 2022

The Centre for Chinese and Comparative Law and Asian Business Law Institute jointly organised an academic roundtable entitled ‘Insolvency Law and Policy in Times of COVID-19 and Beyond’ on 29 March 2022. The event brought together judges, scholars, experts and professionals from world-leading universities and institutions. This note sets out a summary of the proceedings held at the academic roundtable.
Long COVID and the cardiovascular system—elucidating causes and cellular mechanisms in order to develop targeted diagnostic and therapeutic strategies: a joint Scientific Statement of the ESC Working Groups on Cellular Biology of the Heart and Myocardial and Pericardial Diseases
Authors: Gyöngyösi Mariann , Alcaide Pilar , Asselbergs Folkert W , Brundel Bianca J J M , Camici Giovanni G , Martins Paula da Costa , Ferdinandy Péter , Fontana Marianna , Girao Henrique , Gnecchi Massimiliano , Gollmann-Tepeköylü Can , Kleinbongard Petra , Krieg Thomas , Madonna Rosalinda , Paillard Melanie , Pantazis Antonis , Perrino Cinzia , Pesce Maurizio , Schiattarella Gabriele G , Sluijter Joost P G , Steffens Sabine , Tschöpe Carsten , Van Linthout Sophie , Davidson Sean M
Published: July 2022

Long COVID has become a world-wide, non-communicable epidemic, caused by long-lasting multiorgan symptoms that endure for weeks or months after SARS-CoV-2 infection has already subsided. This scientific document aims to provide insight into the possible causes and therapeutic options available for the cardiovascular manifestations of long COVID. In addition to chronic fatigue, which is a common symptom of long COVID, patients may present with chest pain, ECG abnormalities, postural orthostatic tachycardia, or newly developed supraventricular or ventricular arrhythmias. Imaging of the heart and vessels has provided evidence of chronic, post-infectious perimyocarditis with consequent left or right ventricular failure, arterial wall inflammation, or microthrombosis in certain patient populations. Better understanding of the underlying cellular and molecular mechanisms of long COVID will aid in the development of effective treatment strategies for its cardiovascular manifestations. A number of mechanisms have been proposed, including those involving direct effects on the myocardium, microthrombotic damage to vessels or endothelium, or persistent inflammation. Unfortunately, existing circulating biomarkers, coagulation, and inflammatory markers, are not highly predictive for either the presence or outcome of long COVID when measured 3 months after SARS-CoV-2 infection. Further studies are needed to understand underlying mechanisms, identify specific biomarkers, and guide future preventive strategies or treatments to address long COVID and its cardiovascular sequelae.
Improving explainability of deep neural network-based electrocardiogram interpretation using variational auto-encoders
Authors: van de Leur Rutger R , Bos Max N , Taha Karim , Sammani Arjan , Yeung Ming Wai , van Duijvenboden Stefan , Lambiase Pier D , Hassink Rutger J , van der Harst Pim , Doevendans Pieter A , Gupta Deepak K , van Es René
Published: July 2022

Aims

Deep neural networks (DNNs) perform excellently in interpreting electrocardiograms (ECGs), both for conventional ECG interpretation and for novel applications such as detection of reduced ejection fraction (EF). Despite these promising developments, implementation is hampered by the lack of trustworthy techniques to explain the algorithms to clinicians. Especially, currently employed heatmap-based methods have shown to be inaccurate.

Methods and results

We present a novel pipeline consisting of a variational auto-encoder (VAE) to learn the underlying factors of variation of the median beat ECG morphology (the FactorECG), which are subsequently used in common and interpretable prediction models. As the ECG factors can be made explainable by generating and visualizing ECGs on both the model and individual level, the pipeline provides improved explainability over heatmap-based methods. By training on a database with 1.1 million ECGs, the VAE can compress the ECG into 21 generative ECG factors, most of which are associated with physiologically valid underlying processes. Performance of the explainable pipeline was similar to ‘black box’ DNNs in conventional ECG interpretation [area under the receiver operating curve (AUROC) 0.94 vs. 0.96], detection of reduced EF (AUROC 0.90 vs. 0.91), and prediction of 1-year mortality (AUROC 0.76 vs. 0.75). Contrary to the ‘black box’ DNNs, our pipeline provided explainability on which morphological ECG changes were important for prediction. Results were confirmed in a population-based external validation dataset.

Conclusions

Future studies on DNNs for ECGs should employ pipelines that are explainable to facilitate clinical implementation by gaining confidence in artificial intelligence and making it possible to identify biased models.