bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of PNPase activity in Enterococcus faecalis 14 increases the stability of EntDD14 bacteriocin transcripts
Authors: Ladjouzi Rabia , Lucau-Danila Anca , López Paloma , Drider Djamel 
Published: December 2023

AbstractA mutant deficient in polynucleotide phosphorylase (PNPase) activity was previously constructed in Enterococcus faecalis 14; a strain producing a leaderless two-peptide enterocin DD14 (EntDD14). Here, we examined the impact of the absence of PNPase on the expression and synthesis of EntDD14, at the transcriptional and functional levels. As result, EntDD14 synthesis augmented in line with the growth curve, reaching a two- to fourfold increase in the ΔpnpA mutant compared to the E. faecalis 14 wild-type strain (WT). EntDD14 synthesis has reached its highest level after 9 h of growth in both strains. Notably, high expression level of the ddABCDEFGHIJ cluster was registered in ΔpnpA mutant. Transcriptional and in silico analyses support the existence of ddAB and ddCDEFGHIJ independent transcripts, and analysis of the fate of ddAB and ddCDEFGHIJ mRNAs indicated that the differences in mRNA levels and the high EntDD14 activity are likely due to a better stability of the two transcripts in the ΔpnpA mutant, which should result in a higher translation efficiency of the ddAB EntDD14 structural genes and their other protein determinants. Consequently, this study shows a potential link between the mRNA stability and EntDD14 synthesis, secretion and immunity in a genetic background lacking PNPase.
Development of new magnetic nanocomposite designed by reduced graphene oxide aerogel and HKUST-1, and its catalytic application in the synthesis of polyhydroquinoline and 1,8-dioxo-decahydroacridine derivatives
Authors: Farzaneh Naghmeh , Radinekiyan Fateme , Naimi-Jamal Mohammad Reza , Dekamin Mohammad G. 
Published: December 2023

AbstractIn this study, new magnetic reduced graphene oxide aerogel/HKUST-1 nanocomposite was designed and synthesized given the transformation of graphene oxide sheets to three-dimensional reduced graphene oxide aerogel, the in-situ magnetization of aerogel substrate, and the in-situ formation of HKUST-1 particles. Apart from characterizing the chemistry and structure of the designed magnetic nanocomposite (FT-IR, EDX, ICP, FE-SEM, DLS, XRD, VSM, and TG analyses), its catalytic performance was evaluated in the one-pot synthesis of biologically active 1,8-dioxo-decahydroacridine and polyhydroquinoline derivatives. The combination of magnetized reduced graphene oxide aerogel and HKUST-1 in the form of a new heterogeneous magnetic nanocatalyst was accompanied by a high synergetic catalytic effect in the symmetric and unsymmetrical Hantzsch condensation reactions. Compared to previous research studies, the pharmaceutical 1,8-dioxo-decahydroacridine and polyhydroquinoline derivatives can be synthesized using a partial amount of this nanocatalyst with a high percentage of yields in a short reaction time.
Development of nanosecond spike pulse power supply for electrochemical micromachining
Authors: Zhao Chuanjun , Zou Qingzhi , Ren Xiaoguang , Xu Lizhong 
Published: December 2023

AbstractThe use of pulse voltage can greatly improve the precision of electrochemical microfabrication, and the narrower the pulse width of the applied pulse voltage signal, the higher the machining precision. However, the commonly used chopper circuit topology of pulse power supplies is limited by the maximum switching frequency of the field-effect transistor. To address this problem, this paper proposes a nanosecond pulse electrochemical micromachining power supply based on a differential circuit. The power supply uses the STM32F103C8T6 microcontroller as the control core to output high-performance rectangular waves through a DDS device. After differential, rectification, filtering, and power amplification processing, stable, frequency, amplitude, and pulse width adjustable spike pulse voltage signals are obtained. By establishing a system mathematical model and optimizing the time constant of the differential circuit, theoretically, the sub-nanosecond pulse width can be obtained. Prototype performance tests show that the power supply has a maximum frequency of 20 MHz, a minimum pulse width of 1.8 ns, and a maximum peak voltage of 10 V. By using this power supply for microhole electrochemical machining experiments, nanometer-level machining precision has been achieved.
Stochastic forecasting of variable small data as a basis for analyzing an early stage of a cyber epidemic
Authors: Kovtun Viacheslav , Grochla Krzysztof , Kharchenko Vyacheslav , Haq Mohd Anul , Semenov Andriy 
Published: December 2023

AbstractSecurity Information and Event Management (SIEM) technologies play an important role in the architecture of modern cyber protection tools. One of the main scenarios for the use of SIEM is the detection of attacks on protected information infrastructure. Consorting that ISO 27001, NIST SP 800-61, and NIST SP 800-83 standards objectively do not keep up with the evolution of cyber threats, research aimed at forecasting the development of cyber epidemics is relevant. The article proposes a stochastic concept of describing variable small data on the Shannon entropy basis. The core of the concept is the description of small data by linear differential equations with stochastic characteristic parameters. The practical value of the proposed concept is embodied in the method of forecasting the development of a cyber epidemic at an early stage (in conditions of a lack of empirical information). In the context of the research object, the stochastic characteristic parameters of the model are the generation rate, the death rate, and the independent coefficient of variability of the measurement of the initial parameter of the research object. Analytical expressions for estimating the probability distribution densities of these characteristic parameters are proposed. It is assumed that these stochastic parameters of the model are imposed on the intervals, which allows for manipulation of the nature and type of the corresponding functions of the probability distribution densities. The task of finding optimal functions of the probability distribution densities of the characteristic parameters of the model with maximum entropy is formulated. The proposed method allows for generating sets of trajectories of values of characteristic parameters with optimal functions of the probability distribution densities. The example demonstrates both the flexibility and reliability of the proposed concept and method in comparison with the concepts of forecasting numerical series implemented in the base of Matlab functions.
Cross-sensitivity analysis of land use transition and ecological service values in rare earth mining areas in southern China
Authors: Zhu Chenhui , Chen Yonglin , Wan Zhiwei , Chen Zebin , Lin Jianping , Chen Peiru , Sun Weiwei , Yuan Hao , Zhang Yunping 
Published: December 2023

AbstractExploring the cross-sensitivity between land use transformation and ecological service values in rare earth mining areas is of great significance for the development of ecological protection and restoration in rare earth mining areas. To study the impact of land use changes on ecosystem service functions in rare earth mining areas, firstly, the land use change trends in the study area from 2009 to 2019 were analyzed using the land transfer matrix; then the distribution of ecosystem service values and the flow direction of ecosystem service values in the study area were measured based on the ecosystem service value equivalents; a spatial autocorrelation analysis was done on the ecosystem service values to explore their spatial distribution patterns; and finally, the cross-sensitivity coefficient was used to quantitatively assess the extent and direction of the impact of land use change on ecosystem service values. The results show that the land use types in the study area are mainly forest land and farmland, with woodland accounting for the highest proportion of the study area. The ESV changes in the study area are consistent with the trend of land use transformation, with the overall increase and decrease being comparable, and the decrease in ESV is mainly concentrated in the areas with a large increase in mining land and construction land; during the study period, the study area was significantly reduced with low—low cluster areas and the ecological environment was improved; from 2009 to 2014, the ecological sensitivity coefficient is more variable, and is more sensitive to the net conversion between water and desert, from 2014 to 2019, the ecological sensitivity coefficient is less variable, and the most sensitive is the net conversion between cultivated land and water. The study area should be reasonably developed for rare earth resources and the ecological environment around the mining area should be reasonably protected to build an ecological security pattern.
Towards interpretable speech biomarkers: exploring MFCCs
Authors: Tracey Brian , Volfson Dmitri , Glass James , Haulcy R’mani , Kostrzebski Melissa , Adams Jamie , Kangarloo Tairmae , Brodtmann Amy , Dorsey E. Ray , Vogel Adam 
Published: December 2023

AbstractWhile speech biomarkers of disease have attracted increased interest in recent years, a challenge is that features derived from signal processing or machine learning approaches may lack clinical interpretability. As an example, Mel frequency cepstral coefficients (MFCCs) have been identified in several studies as a useful marker of disease, but are regarded as uninterpretable. Here we explore correlations between MFCC coefficients and more interpretable speech biomarkers. In particular we quantify the MFCC2 endpoint, which can be interpreted as a weighted ratio of low- to high-frequency energy, a concept which has been previously linked to disease-induced voice changes. By exploring MFCC2 in several datasets, we show how its sensitivity to disease can be increased by adjusting computation parameters.
Anaerobic threshold using sweat lactate sensor under hypoxia
Authors: Okawara Hiroki , Iwasawa Yuji , Sawada Tomonori , Sugai Kazuhisa , Daigo Kyohei , Seki Yuta , Ichihara Genki , Nakashima Daisuke , Sano Motoaki , Nakamura Masaya , Sato Kazuki , Fukuda Keiichi , Katsumata Yoshinori 
Published: December 2023

AbstractWe aimed to investigate the reliability and validity of sweat lactate threshold (sLT) measurement based on the real-time monitoring of the transition in sweat lactate levels (sLA) under hypoxic exercise. In this cross-sectional study, 20 healthy participants who underwent exercise tests using respiratory gas analysis under hypoxia (fraction of inspired oxygen [FiO2], 15.4 ± 0.8%) in addition to normoxia (FiO2, 20.9%) were included; we simultaneously monitored sLA transition using a wearable lactate sensor. The initial significant elevation in sLA over the baseline was defined as sLT. Under hypoxia, real-time dynamic changes in sLA were successfully visualized, including a rapid, continual rise until volitionary exhaustion and a progressive reduction in the recovery phase. High intra- and inter-evaluator reliability was demonstrated for sLT’s repeat determinations (0.782 [0.607–0.898] and 0.933 [0.841–0.973]) as intraclass correlation coefficients [95% confidence interval]. sLT correlated with ventilatory threshold (VT) (r = 0.70, p < 0.01). A strong agreement was found in the Bland–Altman plot (mean difference/mean average time: − 15.5/550.8 s) under hypoxia. Our wearable device enabled continuous and real-time lactate assessment in sweat under hypoxic conditions in healthy participants with high reliability and validity, providing additional information to detect anaerobic thresholds in hypoxic conditions.
Accessible and reliable neurometric testing in humans using a smartphone platform
Authors: Boele H. J. , Jung C. , Sherry S. , Roggeveen L. E. M. , Dijkhuizen S. , Öhman J. , Abraham E. , Uvarov A. , Boele C. P. , Gultig K. , Rasmussen A. , Vinueza-Veloz M. F. , Medina J. F. , Koekkoek S. K. E. , De Zeeuw C. I. , Wang S. S. -H. 
Published: December 2023

AbstractTests of human brain circuit function typically require fixed equipment in lab environments. We have developed a smartphone-based platform for neurometric testing. This platform, which uses AI models like computer vision, is optimized for at-home use and produces reproducible, robust results on a battery of tests, including eyeblink conditioning, prepulse inhibition of acoustic startle response, and startle habituation. This approach provides a scalable, universal resource for quantitative assays of central nervous system function.
Effects of endothelial nitric oxide synthase on mouse arteriovenous fistula hemodynamics
Authors: Baltazar Shelly , Northrup Hannah , Chang Joshua , Somarathna Maheshika , Isayeva Waldrop Tatyana , Lee Timmy , Shiu Yan-Ting 
Published: December 2023

AbstractNewly created arteriovenous fistulas (AVFs) often fail to mature for dialysis use due to disturbed blood flow at and near the AVF anastomosis. The disturbed flow inhibits the endothelial nitric oxide synthase (NOS3) pathway, thus decreasing the production of nitric oxide, a vasodilator. Previously, our group reported that NOS3 expression levels affect AVF lumen size in a mouse model. In this study, we performed MRI-based computational fluid dynamics simulations to investigate the hemodynamical parameters (velocity, wall shear stress (WSS), and vorticity) in a mouse AVF model at day 7 and day 21 post-AVF creation using three NOS3 strains: overexpression (OE), knockout (KO), and wild-type (WT) control. This study is the first to reveal hemodynamics over time in mouse AVFs, consider spatial heterogeneity along the vein, and reveal the effect of NOS3 on the natural history of mouse AVF hemodynamics. From day 7 to day 21, OE has smoother streamlines and had significantly lower vorticity and WSS than WT and KO, suggesting that WSS was attempting to return to pre-surgery baseline, respectively. Our results conclude that the overexpression of NOS3 leads to desired optimal hemodynamics during AVF remodeling. Future studies can investigate enhancing the NOS3 pathway to improve AVF development.
Solvent-activated 3D-printed electrodes and their electroanalytical potential
Authors: Kwaczyński Karolina , Szymaniec Olga , Bobrowska Diana M. , Poltorak Lukasz 
Published: December 2023

AbstractThis work is a comprehensive study describing the optimization of the solvent-activated carbon-based 3D printed electrodes. Three different conductive filaments were used for the preparation of 3D-printed electrodes. Electrodes treatment with organic solvents, electrochemical characterization, and finally electroanalytical application was performed in a dedicated polyamide-based cell also created using 3D printing. We have investigated the effect of the used solvent (acetone, dichloromethane, dichloroethane, acetonitrile, and tetrahydrofuran), time of activation (from immersion up to 3600 s), and the type of commercially available filament (three different options were studied, each being a formulation of a polylactic acid and conductive carbon material). We have obtained and analysed a significant amount of collected data which cover the solvent-activated carbon-based electrodes surface wettability, microscopic insights into the surface topography analysed with scanning electron microscopy and atomic force microscopy, and finally voltammetric evaluation of the obtained carbon electrodes electrochemical response. All data are tabulated, discussed, and compared to finally provide the superior activation procedure. The electroanalytical performance of the chosen electrode is discussed based on the voltammetric detection of ferrocenemethanol.
Annual trends of ophthalmic surgeries in Japan’s super-aged society, 2014–2020: a national claims database study
Authors: Wada Saori , Miyake Masahiro , Hata Masayuki , Kido Ai , Kamei Takuro , Akada Masahiro , Hiragi Shusuke , Tamura Hiroshi , Tsujikawa Akitaka 
Published: December 2023

AbstractThis study aimed to analyze the trends and factors influencing the number of ophthalmic surgeries in Japan using the open data from the National Database of Health Insurance Claims and Specific Health Checkups of Japan published by the Ministry of Health, Labour and Welfare. We calculated the number of cataract, glaucoma, and vitreoretinal surgeries, categorized by sex, age, and surgical type, for the fiscal years (FY) 2014 to 2020. The number of cataract surgeries remained stable at approximately 1.45 million cases from FY 2014 to 2018, increased to nearly 1.6 million cases in FY 2019, and decreased to 1.45 million cases in FY 2020. Among glaucoma surgeries, surgical treatments were increased 1.8 times over 7 years, from 33,000 to 60,000 cases. Laser treatment remained steady at around 55,000 cases from FY 2014 to 2017 and then increased to approximately 60,000 cases. The number of vitreoretinal surgeries was increased 1.2 times from FY 2014 to 2019, from 120,000 to 140,000, and decreased to 130,000 by FY 2020. Trends in ophthalmic surgeries over the past 7 years may be influenced by population aging, minimally invasive surgery, and the coronavirus disease pandemic. These findings have implications on surgical decision-making and resource allocation.
Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes
Authors: Ngom Serigne Inssa , Maski Soufiane , Rached Bahia , Chouati Taha , Oliveira Correia Lydie , Juste Catherine , Meylheuc Thierry , Henrissat Bernard , El Fahime Elmostafa , Amar Mohamed , Béra-Maillet Christel 
Published: December 2023

AbstractBacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation
Authors: Hejret Vaclav , Varadarajan Nandan Mysore , Klimentova Eva , Gresova Katarina , Giassa Ilektra-Chara , Vanacova Stepanka , Alexiou Panagiotis 
Published: December 2023

AbstractArgonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA ‘guide’ sequences, and identifies its targets primarily via a ‘seed’ mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 ‘guide’–’target’ interactions remains elusive. Our study employs two experimental methods—AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA ‘guide’ and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 ‘guides’ derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each ‘guide’ class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its ‘guide’ repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/.
Intraocular pressure-lowering effects of ripasudil on open-angle glaucoma in eyes with high myopia and pathological myopia
Authors: Yoshida Takeshi , Yoshimoto Sota , Nomura Takuhei , Ito Taiju , Ohno Motohisa , Yasuda Shintaro , Shiotani Yuto , Ohno-Matsui Kyoko 
Published: December 2023

AbstractThe aim is to study the intraocular pressure (IOP)-lowering effects of additional administration of ripasudil in open-angle glaucoma (OAG) patients including high myopia (HM) and pathological myopia (PM). Study design is retrospective cohort study. We assessed the changes in the mean IOP between the HM eyes (axial length ≧ 26.5 mm 33 eyes) and the non-HM eyes (axial length < 26.5 mm 29 eyes) at 4 and 12 weeks from baseline. We also assessed the IOP changes between the PM eyes (21 eyes) and the non-PM eyes (41 eyes). The significant IOP reduction by the ripasudil administration was observed at 4 weeks in the non-HM eyes and at 12 weeks in HM and non-HM eyes. And the IOP reduction in the HM eyes was significantly less than the non-HM eyes at 4 and 12 weeks. IOP reduction by ripasudil had statistically significant association with the baseline IOP and presence of PM. Furthermore, significant IOP reduction by the ripasudil administration was observed at 4 and 12 weeks in the non-PM eyes, but not in the PM eyes. The additional administration of ripasudil was effective in the HM eyes, but less than non-HM eyes. And the PM may negatively contribute to reducing the IOP by ripasudil.
Flagellar dynamics reveal fluctuations and kinetic limit in the Escherichia coli chemotaxis network
Authors: Bano Roshni , Mears Patrick , Golding Ido , Chemla Yann R. 
Published: December 2023

AbstractThe Escherichia coli chemotaxis network, by which bacteria modulate their random run/tumble swimming pattern to navigate their environment, must cope with unavoidable number fluctuations (“noise”) in its molecular constituents like other signaling networks. The probability of clockwise (CW) flagellar rotation, or CW bias, is a measure of the chemotaxis network’s output, and its temporal fluctuations provide a proxy for network noise. Here we quantify fluctuations in the chemotaxis signaling network from the switching statistics of flagella, observed using time-resolved fluorescence microscopy of individual optically trapped E. coli cells. This approach allows noise to be quantified across the dynamic range of the network. Large CW bias fluctuations are revealed at steady state, which may play a critical role in driving flagellar switching and cell tumbling. When the network is stimulated chemically to higher activity, fluctuations dramatically decrease. A stochastic theoretical model, inspired by work on gene expression noise, points to CheY activation occurring in bursts, driving CW bias fluctuations. This model also shows that an intrinsic kinetic ceiling on network activity places an upper limit on activated CheY and CW bias, which when encountered suppresses network fluctuations. This limit may also prevent cells from tumbling unproductively in steep gradients.