bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MyoPulser field stimulator, a do it yourself programmable electronic pacemaker for contracting cells and tissues
Authors: Ott Christiane , Jung Tobias 
Published: February 2023

AbstractAfter providing the free software MYOCYTER that analyzes a large amount of data from videos of contracting cells, tissues or organs, we now present an “Arduino”-based programmable, customizable and cost-effective electronic pacemaker (“MyoPulser”) that triggers contraction by electric stimulation of the sample at arbitrary frequencies. In this work, construction, functions and application of the MyoPulser are explained in detail, the electronic pacemaker is also tested on isolated cardiomyocytes and HT22-cells to quantify biological effects of pacing. The device enables the user to select between different pulse types (monophasic, alternating, bi- and polyphasic) adjust the length of an applied pulse (1–200 ms), the gap between two consecutive pulses (20–2000 ms), application of irregular pulses with random length and gaps (simulation of arrhythmia) in a user-defined range, as well as manual pulsing, while extensive data are recorded for every single pulse during the experiment. Electrostimulation of isolated B6 cardiomyocytes showed very little deviation of the observed cellular contraction from the applied pulse settings of the device, while the carbon electrodes used proved to be biologically inert in long-term experiments. Due to the open source code and the expandable setup, the MyoPulser can be easily adapted to even highly specific requirements and together with the software MYOCYTER it represents a complete cardiomyophysiological measuring station.
Spatial and deep learning analyses of urban recovery from the impacts of COVID-19
Authors: Ma Shuang , Li Shuangjin , Zhang Junyi 
Published: February 2023

AbstractThis study investigates urban recovery from the COVID-19 pandemic by focusing on three main types of working, commercial, and night-life activities and associating them with land use and inherent socio-economic patterns as well as points of interests (POIs). Massive multi-source and multi-scale data include mobile phone signaling data (500 m × 500 m), aerial images (0.49 m × 0.49 m), night light satellite data (500 m × 500 m), land use data (street-block), and POIs data. Methods of convolutional neural network, guided gradient-weighted class activation mapping, bivariate local indicator of spatial association, Elbow and K-means are jointly applied. It is found that the recovery in central areas was slower than in suburbs, especially in terms of working and night-life activities, showing a donut-shaped spatial pattern. Residential areas with mixed land uses seem more resilient to the pandemic shock. More than 60% of open spaces are highly associated with recovery in areas with high-level pre-pandemic social-economic activities. POIs of sports and recreation are crucial to the recovery in all areas, while POIs of transportation and science/culture are also important to the recovery in many areas. Policy implications are discussed from perspectives of open spaces, public facilities, neighborhood units, spatial structures, and anchoring roles of POIs.
Effect of DFIG control parameters on small signal stability in power systems
Authors: Qi Liu , jiahui Wu , Haiyun Wang , Hua Zhang , Jian Yang 
Published: February 2023

AbstractThe doubly-fed induction generator (DFIG) with virtual inertia control and reactive damping control gives a renewable energy generation system inertia and damping characteristics similar to those of a thermal power plant, and the parameters of the control strategy have a direct impact on the small-signal stability of the system. This paper firstly introduces the operating characteristics and control strategies of DFIG-based damping control and virtual inertia control, establishes a small-signal model of the control-based DFIG integrated interconnected system, and investigates the effects of virtual inertia and reactive damping values on the small-signal stability of the system; then, the maximum damping ratio of the interval oscillation mode in small disturbance analysis is taken as the optimization objective, and the control parameters are the optimization variables. An optimization method of inertia and damping parameters is established for improving the small disturbance stability of the system. The results show that the optimization procedure could improve the damping ratio of the interval oscillation mode while ensuring the system frequency. The effects of virtual inertia and reactive damping values on the small signal stability of the system are investigated, and an optimal allocation model and method for virtual inertia used to improve the small disturbance stability of the system is proposed.
STR-based feature extraction and selection for genetic feature discovery in neurological disease genes
Authors: Dhaliwal Jasbir , Wagner John 
Published: February 2023

AbstractGene expression, often determined by single nucleotide polymorphisms, short repeated sequences known as short tandem repeats (STRs), structural variants, and environmental factors, provides means for an organism to produce gene products necessary to live. Variation in expression levels, sometimes known as enrichment patterns, has been associated with disease progression. Thus, the STR enrichment patterns have recently gained interest as potential genetic markers for disease progression. However, to the best of our knowledge, we are unaware of any study that evaluates and explores STRs, particularly trinucleotide sequences, as machine learning features for classifying neurological disease genes for the purpose of discovering genetic features. Thus, in this paper, we proposed a new metric and a novel feature extraction and selection algorithm based on statistically significant STR-based features and their respective enrichment patterns to create a statistically significant feature set. The proposed new metric has shown that the neurological disease family genes have a non-random AA, AT, TA, TG, and TT enrichment pattern. This is an important result, as it supports prior research that has established that certain trinucleotides, such as AAT, ATA, ATT, TAT, and TTA, are favored during protein misfolding. In contrast, trinucleotides, such as TAA, TAG, and TGA, are favored during premature termination codon mutations as they are stop codons. This suggests that the metric has the potential to identify patterns that may be genetic features in a sample of neurological genes. Moreover, the practical performance and high prediction results of the statistically significant STR-based feature set indicate that variations in STR enrichment patterns can distinguish neurological disease genes. In conclusion, the proposed approach may have the potential to discover differential genetic features for other diseases.
Numerical simulation of pneumatic throttle check valve using computational fluid dynamics (CFD)
Authors: Żyłka Marta , Marszałek Natalia , Żyłka Wojciech 
Published: February 2023

AbstractThe article presents a numerical CFD simulation of a throttle-check valve used in an innovative control system for two pneumatic drives. This type of control is used in an innovative rehabilitation device for lower limbs. In order to determine the boundary conditions, experimental tests were carried out. The throttle valves on the test stand were scaled and the air flow rate values were read for different valve opening heights. The purpose of this article is to present a CFD simulation of a pre-adjusted check valve throttle. Numerical simulation (CFD) makes it possible to study the flow phenomena inside a pneumatic throttle-check valve, with different sizes of flow gaps. The obtained results made it possible to determine the distribution of physical quantities of static pressure, the velocity of the medium flowing through the valve, or the vector velocity distribution. The throttle valve assembly has been scaled for a suitable degree of synchronization of the movement of the piston actuators independently of the different external loads acting on each of them. The authors investigated airflow phenomena for different valve opening heights. The simulation provided information on the occurrence of supersonic and subsonic flow velocities at specific valve opening heights.
Epigenetic alterations impede epithelial-mesenchymal transition by modulating centrosome amplification and Myc/RAS axis in triple negative breast cancer cells
Authors: Das Laxmidhar 
Published: February 2023

AbstractAlterations in centrosome proteins may result in centrosome abnormalities such as disorganized spindles and centrosome amplification, leading to aneuploidy and genomic instability. Centrosomes exhibit unique epigenetic properties in which structural or positional information is propagated through somatic lineage by non-genetic pathways. Excessive centrosome amplification in breast cancer is accompanied by efficient clustering and loss of E-cadherin, indicating an important adaptive mechanism of cancer. This study sought to elucidate the effect of epigenetic alterations on centrosome amplification, epithelial-mesenchymal transition (EMT) and apoptosis in triple negative human breast adenocarcinoma derived MDA-MB-231 cell line. The results obtained here show that siRNA mediated silencing of DNMT1 and specific inhibition of HDAC1 & HDAC2 by Tricostatin A (TSA) synergistically inhibit cell proliferation through modulation of centrosome proteins γ-tubulin, TUBGCP2 and pericentrin. In addition, induction of apoptosis was observed by downregulation of Bcl2, upregulation of Bax and activation of PARP cleavage. Inhibition of EMT was confirmed through upregulation of E-cadherin and downregulation of N-cadherin and vimentin. Similarly, downregulation of Myc, RAS and CDK2, which plays important roles in proliferation and survival, was observed. Nuclear protein analysis revealed downregulation in the nuclear translocation of E2F1, which regulates centrosome amplification and metastasis in breast cancer. In conclusion, this study confirmed the role of epigenetic regulators in centrosome amplification and suggests that inhibition of DNA methylation and histone deacetylation-mediated chromatin remodelling synergistically disrupt EMT through modulation of centrosome amplification and Myc/RAS axis to potentiate apoptosis and attenuate cell proliferation in triple negative breast cancer cells.
Examining associations between MDMA/ecstasy and classic psychedelic use and impairments in social functioning in a U.S. adult sample
Authors: Jones Grant , Lipson Joshua , Wang Erica 
Published: February 2023

AbstractImpairment in social functioning is a common source of morbidity across many mental health disorders, yet there is a dearth of effective and easily implemented interventions to support social functioning. MDMA/ecstasy and classic psychedelics (psilocybin, LSD, peyote, mescaline) represent two potential treatments for impairments in social functioning, as evidence suggests these compounds may be supportive for alleviating social difficulties. Using a nationally representative sample of U.S. adults from the National Survey on Drug Use and Health (2015–2019) (N = 214,505), we used survey-weighted multivariable ordinal and logistic regression to examine the associations between lifetime use of the aforementioned compounds and impairments in social functioning in the past year. Lifetime MDMA/ecstasy use was associated with lowered odds of three of our four social impairment outcomes: difficulty dealing with strangers (aOR 0.92), difficulty participating in social activities (aOR 0.90), and being prevented from participating in social activities (aOR 0.84). Lifetime mescaline use was also associated with lowered odds of difficulty dealing with strangers (aOR 0.85). All other substances either shared no relationship with impairments in social functioning or conferred increased odds of our outcomes. Future experimental studies can assess whether these relationships are causal.
Drilling and blasting designs for parallel hole cut and V-cut method in excavation of underground coal mine galleries
Authors: Yilmaz Ozgur 
Published: February 2023

AbstractThe Karadon mine, where field studies were carried out, is located in the north west of Turkey and is considered to be a highly gaseous coal mine. Explosives and ignition systems used in underground coal mines are determined by laws, statutes, regulations and strict rules. Restrictions arising from legal requirements, such as restrictions on charging and stemming lengths and blasting agents to be used, make the use of well-known tunnel blasting techniques difficult or sometimes not possible. In such cases, the designs made with the equations given in the literature must be revised and rearranged. The objective of this study is to recommend solutions to the blasting difficulties that are encountered in gaseous underground coal mines in which there are limitations arising from legal requirements. This study summarizes and analyses the blasting practices currently employed at Karadon mine along with their disadvantages. New blasting designs were then made using the methods suggested in the literature, and these designs were revised according to legal requirements. By keeping the charge concentration constant relative to its original value, the burden and spacing distances were adjusted. As a result of this study, it has been seen that rearrangement by keeping the charge concentration constant compared to its original value is an appropriate engineering solution.
Non-buoyant microplastic settling velocity varies with biofilm growth and ambient water salinity
Authors: Mendrik Freija , Fernández Roberto , Hackney Christopher R. , Waller Catherine , Parsons Daniel R. 
Published: February 2023

AbstractRivers are the major conveyor of plastics to the marine environment, but the mechanisms that impact microplastic (<5 mm) aquatic transport, and thus govern fate are largely unknown. This prevents progress in understanding microplastic dynamics and identifying zones of high accumulation, along with taking representative environmental samples and developing effective mitigation measures. Using a suite of settling experiments we show that non-buoyant microplastic settling is influenced by a combination of biofilm growth, water salinity and suspended clay concentrations typically seen across fluvial to marine environments. Results indicate that biofilms significantly increased settling velocity of three different polymer types of non-buoyant microplastics (fragments and fibres, size range 0.02–4.94 mm) by up to 130% and significant increases in settling velocity were observable within hours. Impacts were both polymer and shape specific and settling regimes differed according to both salinity and sediment concentrations. Our results further validate previous statements that existing transport formula are inadequate to capture microplastic settling and highlight the importance of considering the combination of these processes within the next generation of predictive frameworks. This will allow more robust predictions of transport, fate and impact of microplastic pollution within aquatic environments.
Free form deformation and symmetry constraint‐based multi‐modal brain image registration using generative adversarial nets
Authors: Zhu Xingxing , Ding Mingyue , Zhang Xuming 
Published: February 2023

AbstractMulti‐modal brain image registration has been widely applied to functional localisation, neurosurgery and computational anatomy. The existing registration methods based on the dense deformation fields involve too many parameters, which is not conducive to the exploration of correct spatial correspondence between the float and reference images. Meanwhile, the unidirectional registration may involve the deformation folding, which will result in the change of topology during registration. To address these issues, this work has presented an unsupervised image registration method using the free form deformation (FFD) and the symmetry constraint‐based generative adversarial networks (FSGAN). The FSGAN utilises the principle component analysis network‐based structural representations of the reference and float images as the inputs and uses the generator to learn the FFD model parameters, thereby producing two deformation fields. Meanwhile, the FSGAN uses two discriminators to decide whether the bilateral registration have been realised simultaneously. Besides, the symmetry constraint is utilised to construct the loss function, thereby avoiding the deformation folding. Experiments on BrainWeb, high grade gliomas, IXI and LPBA40 show that compared with state‐of‐the‐art methods, the FSGAN provides superior performance in terms of visual comparisons and such quantitative indexes as dice value, target registration error and computational efficiency.
Clival and Paraclival Lesions: A Pictorial Review
Authors: Palsetia Delnaz R. , Vijan Antariksh V. , Gala Foram B. , Sahu Amit C. , Patkar Deepak P. , A. Arpita Sahu 
Published: February 2023

AbstractThe clivus is a midline anatomical structure in the central skull base. It is affected by a wide range of non-neoplastic, benign and malignant pathologies, some of which typically affect the clivus because of its strategic location and embryological origins. Clival lesions may often be asymptomatic with occasional complaints like headache or cranial neuropathy in few. Cross-sectional imaging techniques, namely, computed tomographic scan and magnetic resonance imaging, thus, play a key role in approximating to the final diagnosis and estimating the disease extent. In this article, we highlight the important imaging features of various clival and paraclival pathologies to facilitate effective diagnosis, therapeutic planning, and management.
Ballet diplomacy: Political agency in the Japanese adaptation ofThe White-Haired Girl
Authors: Qi Lintao 
Published: February 2023

AbstractThis article presents a sociological study of the various agents involved in the production, circulation and reception of a 1955 Japanese ballet adapted from the Chinese Communist opera The White-Haired Girl (1945). The ballet served as an effective means of unofficial diplomacy between China and Japan, even prior to normalisation of bilateral relations between the two countries. Apart from the expected agents, such as translators and theatre practitioners, this case study also reveals the role of some extraordinary agents, including Chinese Communist leaders, such as Mao Zedong and Zhou Enlai, and senior Japanese political figures and institutions. Saturation with political agency renders the Japanese adaptation into a text consumed mostly by audiences from the source culture. The artistic life of the ballet, which was sustained by political needs, demonstrates how fundamental political factors are to research on translation in authoritarian contexts and amid geopolitical tensions.
Identification of metal ion-binding sites in RNA structures using deep learning method
Authors: Zhao Yanpeng , Wang Jingjing , Chang Fubin , Gong Weikang , Liu Yang , Li Chunhua 
Published: February 2023

AbstractMetal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA structures, it becomes possible to identify the metal ion-binding sites in RNA structures through in-silico methods. Here, we propose an approach called Metal3DRNA to identify the binding sites of the most common metal ions (Mg2+, Na+ and K+) in RNA structures by using a three-dimensional convolutional neural network model. The negative samples, screened out based on the analysis for binding surroundings of metal ions, are more like positive ones than the randomly selected ones, which are beneficial to a powerful predictor construction. The microenvironments of the spatial distributions of C, O, N and P atoms around a sample are extracted as features. Metal3DRNA shows a promising prediction power, generally surpassing the state-of-the-art methods FEATURE and MetalionRNA. Finally, utilizing the visualization method, we inspect the contributions of nucleotide atoms to the classification in several cases, which provides a visualization that helps to comprehend the model. The method will be helpful for RNA structure prediction and dynamics simulation study.Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/Metal3DRNA.
LAVAA: a lightweight association viewer across ailments
Authors: Fauman Eric B , Keppo Stella , Cerioli Nicola , Vyas Rupesh , Kurki Mitja , Daly Mark , Reeve Mary Pat 
Published: February 2023

AbstractMotivationBiobank scale genetic associations results over thousands of traits can be difficult to visualize and navigate.ResultsWe have created LAVAA, a visualization web-application to generate genetic volcano plots for simultaneously considering the P-value, effect size, case counts, trait class and fine-mapping posterior probability at a single-nucleotide polymorphism (SNP) across a range of traits from a large set of genome-wide association study. We find that user interaction with association results in LAVAA can enrich and enhance the biological interpretation of individual loci.Availability and implementationLAVAA is available as a stand-alone web service (https://geneviz.aalto.fi/LAVAA/) and will be available in future releases of the finngen.fi website starting with release 10 in late 2023.
Urinary matrix metalloproteinase-7 is a sensitive biomarker to evaluate renal tubular injury in patients with minimal change disease and focal segmental glomerulosclerosis
Authors: Yin Dan-yang , Hou Gai-ling , Yang Xiao-qing , Bi Liang-liang , Mei Xiao-feng , Bai Meng-ke , Zhou Li , Zhu Shan , Huang Yan-jie 
Published: February 2023

ABSTRACT

Objective
To explore the advantages of urinary matrix metalloproteinase-7 (MMP-7) in evaluating renal tubular injury in minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) patients compared with urinary cystatin C (CysC) and retinol-binding protein (RBP).

Methods
Serum and urine samples were collected from 20 healthy volunteers, and 40 MCD and 20 FSGS patients. Serum and urinary MMP-7 levels were measured by enzyme-linked immunosorbent assay. Urinary total protein, CysC and RBP levels were measured by automatic specific protein analyzer and compared with urinary creatinine level for calibration. The renal tissue serial sections were stained by MMP-7 immunohistochemistry and periodic acid–Schiff.

Results
Under light microscopy, MMP-7 granular weak positive expression was showed sporadically in the cytoplasm of a few renal tubular epithelial cells without obvious morphological changes in MCD patients, and MMP-7-positive expression was observed in the cytoplasm of some renal tubular epithelial cells in FSGS patients. There was no significant difference in serum MMP-7 level among the three groups. Compared with the control group, the urinary MMP-7 level in MCD patients was higher, but urinary CysC and RBP levels were not increased significantly. Compared with the control group and MCD patients, urinary MMP-7, CysC and RBP levels in FSGS patients were upregulated significantly.

Conclusions
Urinary MMP-7 could not only evaluate the mild renal tubular epithelial cells injury in MCD patients with massive proteinuria, but also evaluate the continuous renal tubular epithelial cells injury in FSGS patients.