bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic chain termination in bacterial pilus assembly
Authors: Giese Christoph , Puorger Chasper , Ignatov Oleksandr , Bečárová Zuzana , Weber Marco E. , Schärer Martin A. , Capitani Guido , Glockshuber Rudi 
Published: November 2023

AbstractAdhesive type 1 pili from uropathogenic Escherichia coli strains are filamentous, supramolecular protein complexes consisting of a short tip fibrillum and a long, helical rod formed by up to several thousand copies of the major pilus subunit FimA. Here, we reconstituted the entire type 1 pilus rod assembly reaction in vitro, using all constituent protein subunits in the presence of the assembly platform FimD, and identified the so-far uncharacterized subunit FimI as an irreversible assembly terminator. We provide a complete, quantitative model of pilus rod assembly kinetics based on the measured rate constants of FimD-catalyzed subunit incorporation. The model reliably predicts the length distribution of assembled pilus rods as a function of the ratio between FimI and the main pilus subunit FimA and is fully consistent with the length distribution of membrane-anchored pili assembled in vivo. The results show that the natural length distribution of adhesive pili formed via the chaperone-usher pathway results from a stochastic chain termination reaction. In addition, we demonstrate that FimI contributes to anchoring the pilus to the outer membrane and report the crystal structures of (i) FimI in complex with the assembly chaperone FimC, (ii) the FimI-FimC complex bound to the N-terminal domain of FimD, and (iii) a ternary complex between FimI, FimA and FimC that provides structural insights on pilus assembly termination and pilus anchoring by FimI.
Corrosion-resistant cobalt phosphide electrocatalysts for salinity tolerance hydrogen evolution
Authors: Xu Xinwu , Lu Yang , Shi Junqin , Hao Xiaoyu , Ma Zelin , Yang Ke , Zhang Tianyi , Li Chan , Zhang Dina , Huang Xiaolei , He Yibo 
Published: November 2023

AbstractSeawater electrolysis is a viable method for producing hydrogen on a large scale and low-cost. However, the catalyst activity during the seawater splitting process will dramatically degrade as salt concentrations increasing. Herein, CoP is discovered that could reject chloride ions far from catalyst in electrolyte based on molecular dynamic simulation. Thus, a binder-free electrode is designed and constructed by in-situ growth of homogeneous CoP on rGO nanosheets wrapped around the surface of Ti fiber felt for seawater splitting. As expected, the as-obtained CoP/rGO@Ti electrode exhibits good catalytic activity and stability in alkaline electrolyte. Especially, benefitting from the highly effective repulsive Cl− intrinsic characteristic of CoP, the catalyst maintains good catalytic performance with saturated salt concentration, and the overpotential increasing is less than 28 mV at 10 mA cm−2 from 0 M to saturated NaCl in electrolyte. Furthermore, the catalyst for seawater splitting performs superior corrosion-resistance with a low solubility of 0.04%. This work sheds fresh light into the development of efficient HER catalysts for salinity tolerance hydrogen evolution.
Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation
Authors: Mälarstig Anders , Grassmann Felix , Dahl Leo , Dimitriou Marios , McLeod Dianna , Gabrielson Marike , Smith-Byrne Karl , Thomas Cecilia E. , Huang Tzu-Hsuan , Forsberg Simon K. G. , Eriksson Per , Ulfstedt Mikael , Johansson Mattias , Sokolov Aleksandr V. , Schiöth Helgi B. , Hall Per , Schwenk Jochen M. , Czene Kamila , Hedman Åsa K. 
Published: November 2023

AbstractBiomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.
Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species
Authors: Hyun Jason C. , Monk Jonathan M. , Szubin Richard , Hefner Ying , Palsson Bernhard O. 
Published: November 2023

AbstractSurveillance programs for managing antimicrobial resistance (AMR) have yielded thousands of genomes suited for data-driven mechanism discovery. We present a workflow integrating pangenomics, gene annotation, and machine learning to identify AMR genes at scale. When applied to 12 species, 27,155 genomes, and 69 drugs, we 1) find AMR gene transfer mostly confined within related species, with 925 genes in multiple species but just eight in multiple phylogenetic classes, 2) demonstrate that discovery-oriented support vector machines outperform contemporary methods at recovering known AMR genes, recovering 263 genes compared to 145 by Pyseer, and 3) identify 142 AMR gene candidates. Validation of two candidates in E. coli BW25113 reveals cases of conditional resistance: ΔcycA confers ciprofloxacin resistance in minimal media with D-serine, and frdD V111D confers ampicillin resistance in the presence of ampC by modifying the overlapping promoter. We expect this approach to be adaptable to other species and phenotypes.
In vivo imaging of mitochondrial DNA mutations using an integrated nano Cas12a sensor
Authors: Li Yanan , Wu Yonghua , Xu Ru , Guo Jialing , Quan Fenglei , Zhang Yongyuan , Huang Di , Pei Yiran , Gao Hua , Liu Wei , Liu Junjie , Zhang Zhenzhong , Deng Ruijie , Shi Jinjin , Zhang Kaixiang 
Published: November 2023

AbstractMutations in mitochondrial DNA (mtDNA) play critical roles in many human diseases. In vivo visualization of cells bearing mtDNA mutations is important for resolving the complexity of these diseases, which remains challenging. Here we develop an integrated nano Cas12a sensor (InCasor) and show its utility for efficient imaging of mtDNA mutations in live cells and tumor-bearing mouse models. We co-deliver Cas12a/crRNA, fluorophore-quencher reporters and Mg2+ into mitochondria. This process enables the activation of Cas12a’s trans-cleavage by targeting mtDNA, which efficiently cleave reporters to generate fluorescent signals for robustly sensing and reporting single-nucleotide variations (SNVs) in cells. Since engineered crRNA significantly increase Cas12a’s sensitivity to mismatches in mtDNA, we can identify tumor tissue and metastases by visualizing cells with mutant mtDNAs in vivo using InCasor. This CRISPR imaging nanoprobe holds potential for applications in mtDNA mutation-related basic research, diagnostics and gene therapies.
Real-time correction of channel-bed roughness and water level in river network hydrodynamic modeling for accurate forecasting
Authors: Chen Yifan , Cao Feifeng , Cheng Weiping , Liu Bin , Yu Pubing 
Published: November 2023

AbstractThe accuracy and reliability of hydrodynamic models are sensitive to both hydraulic state variables and model parameters, particularly the bed roughness, while their simultaneous real-time corrections and corresponding effects still need to be well-established and understood. This paper presents a real-time data assimilation model that corrects channel-bed roughness and water level in a river network hydrodynamic model, ensuring its accuracy and reliability. Experiments and parameter analysis evaluated the effect of initial roughness and observation noise level on model performance. Correcting both roughness and water level improved filtering time and forecasting accuracy by up to 63% and 80%, respectively, compared to methods only correcting water level. The filtering time was reduced by 44–63%, and the water level forecasting RMSE decreased by up to 80%. Both models experienced increased filtering time and forecasting error as observation noise increased, but the proposed model had a lower increase. With accurate hydraulic state measurement (e.g., 0.005 m error), the model achieved negligible water level forecasting error after 7 h of data assimilation. The model's accuracy depended on the initial channel-bed roughness, and the algorithm enables real-time roughness correction, making it useful for flood forecasting.
A study on table tennis landing point detection algorithm based on spatial domain information
Authors: Ning Tao , Wang Changcheng , Fu Meng , Duan Xiaodong 
Published: November 2023

AbstractTo address the limitations of computer vision-assisted table tennis ball detection, which heavily relies on vision acquisition equipment and exhibits slow processing speed, we propose a real-time calculation method for determining the landing point of table tennis balls. This novel approach is based on spatial domain information and reduces the dependency on vision acquisition equipment. This method incorporates several steps: employing dynamic color thresholding to determine the centroid coordinates of all objects in the video frames, utilizing target area thresholding and spatial Euclidean distance to eliminate interference balls and noise, optimizing the total number of video frames through keyframe extraction to reduce the number of operations for object recognition and landing point detection, and employing the four-frame difference slope method and polygonal area determination to detect the landing point and area of the target object, thereby obtaining precise coordinates and their corresponding areas. Experimental results on the above method on the Jetson Nano development board show that the dynamic color thresholding method achieves a detection speed of 45.3 fps. The keyframe extraction method correctly identifies the landing point frames with an accuracy rate exceeding 93.3%. In terms of drop point detection, the proposed method achieves 78.5% overall accuracy in detecting table tennis ball drop points while ensuring real-time detection. These experiments validate that the proposed method has the ability to detect table tennis ball drop points in real time and accurately in low frame rate vision acquisition devices and real environments.
Investigation on the origin of hot electrons in laser plasma interaction at shock ignition intensities
Authors: Cristoforetti G. , Baffigi F. , Batani D. , Dudzak R. , Fedosejevs R. , Filippov E. D. , Gajdos P. , Juha L. , Khan M. , Koester P. , Krus M. , Mancelli D. , Martynenko A. S. , Nicolai Ph. , Pikuz S. A. , Renner O. , Tentori A. , Volpe L. , Woolsey N. , Zeraouli G. , Gizzi L. A. 
Published: November 2023

AbstractShock Ignition is a two-step scheme to reach Inertial Confinement Fusion, where the precompressed fuel capsule is ignited by a strong shock driven by a laser pulse at an intensity in the order of $$10^{16}$$

10
16

W/cm$$^2$$

2

. In this report we describe the results of an experiment carried out at PALS laser facility designed to investigate the origin of hot electrons in laser-plasma interaction at intensities and plasma temperatures expected for Shock Ignition. A detailed time- and spectrally-resolved characterization of Stimulated Raman Scattering and Two Plasmon Decay instabilities, as well as of the generated hot electrons, suggest that Stimulated Raman Scattering is the dominant source of hot electrons via the damping of daughter plasma waves. The temperature dependence of laser plasma instabilities was also investigated, enabled by the use of different ablator materials, suggesting that Two Plasmon Decay is damped at earlier times for higher plasma temperatures, accompanied by an earlier ignition of SRS. The identification of the predominant hot electron source and the effect of plasma temperature on laser plasma interaction, here investigated, are extremely useful for developing the mitigation strategies for reducing the impact of hot electrons on the fuel ignition.
Assessment of interactive acoustic deterrent devices set on trammel nets to reduce dolphin–fishery interactions in the Northern Tyrrhenian Sea
Authors: Ceciarini Ilaria , Franchi Enrica , Capanni Francesca , Consales Guia , Minoia Lorenzo , Ancora Stefania , D’Agostino Antonella , Lucchetti Alessandro , Li Veli Daniel , Marsili Letizia 
Published: November 2023

AbstractDolphin–fishery interaction is a worldwide issue affecting dolphins through bycatch and fishers through catch or gear damages. Concerning the Mediterranean Sea, problematic interactions mainly occur between common bottlenose dolphin and small-scale fisheries. Acoustic Deterrent Devices such as pingers, are one of the most widespread measures used in attempts to face this issue. Therefore, the efficiency of interactive pingers (DiD01) in protecting the trammel nets from dolphin interactions was assessed in the Northern Tyrrhenian Sea. From March to October 2021, a total of 139 fishing trials using nets with pingers (TEST) and without pingers (CTRL), respectivelyn = 97 andn = 42, were carried out. Non-parametric statistic of the Catch per Unit Effort, comparing control and test nets, was not significantly different (p > 0.05) using catches weights (CPUEW) while it was significant (p < 0.01) considering the number of individuals (CPUEN). Moreover, richness and relative abundance of species resulted statistically higher in test nets (p < 0.05). This finding suggests that the absence of dolphin in the neighbourhood of fishing areas thanks to the use of pingers increases the diversity of target species. Catch damages caused by dolphins were statistically higher in nets without pinger than in nets with pinger (p < 0.05). No dolphin bycatch was recorded during fishing operations.
Biophysical properties of NaV1.5 channels from atrial-like and ventricular-like cardiomyocytes derived from human induced pluripotent stem cells
Authors: Chapotte-Baldacci Charles-Albert , Pierre Marion , Djemai Mohammed , Pouliot Valérie , Chahine Mohamed 
Published: November 2023

AbstractGenerating atrial-like cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) is crucial for modeling and treating atrial-related diseases, such as atrial arrythmias including atrial fibrillations. However, it is essential to obtain a comprehensive understanding of the electrophysiological properties of these cells. The objective of the present study was to investigate the molecular, electrical, and biophysical properties of several ion channels, especially NaV1.5 channels, in atrial hiPSC cardiomyocytes. Atrial cardiomyocytes were obtained by the differentiation of hiPSCs treated with retinoic acid (RA). The quality of the atrial specification was assessed by qPCR, immunocytofluorescence, and western blotting. The electrophysiological properties of action potentials (APs), Ca2+ dynamics, K+ and Na+ currents were investigated using patch-clamp and optical mapping approaches. We evaluated mRNA transcript and protein expressions to show that atrial cardiomyocytes expressed higher atrial- and sinoatrial-specific markers (MYL7, CACNA1D) and lower ventricular-specific markers (MYL2, CACNA1C, GJA1) than ventricular cardiomyocytes. The amplitude, duration, and steady-state phase of APs in atrial cardiomyocytes decreased, and had a shape similar to that of mature atrial cardiomyocytes. Interestingly, NaV1.5 channels in atrial cardiomyocytes exhibited lower mRNA transcripts and protein expression, which could explain the lower current densities recorded by patch-clamp. Moreover, Na+ currents exhibited differences in activation and inactivation parameters. These differences could be explained by an increase in SCN2B regulatory subunit expression and a decrease in SCN1B and SCN4B regulatory subunit expressions. Our results show that a RA treatment made it possible to obtain atrial cardiomyocytes and investigate differences in NaV1.5 channel properties between ventricular- and atrial-like cells.
Influence of individual quadriceps and hamstrings muscle architecture and quality on knee adduction and flexion moment in gait
Authors: Jeong Jiyoung , Choi Dai-Hyuk , Shin Choongsoo S. 
Published: November 2023

AbstractThe purpose of this study was to investigate the relationship between muscular parameters of quadriceps/hamstrings and knee joint kinetics in gait. Muscle architecture (thickness, pennation angle, and fascicle length), and quality (echo intensity) of individual quadriceps and hamstrings of 30 healthy participants (16 males and 14 females) was measured using ultrasound. Peak knee flexion moment (KFM), KFM impulse, peak knee adduction moment (KAM), and KAM impulse during walking were obtained at preferred speed. Pearson’s correlation coefficient and multiple regression analyses were performed at significance level of 0.05, and Cohen’s f2 values were calculated to examine the effect sizes of multiple regression. The hamstring-to-quadriceps muscle thickness ratio (r = 0.373) and semitendinosus echo intensity (r =  − 0.371) were predictors of first peak KFM (R2 = 0.294, P = 0.009, f2 = 0.42), whereas only vastus medialis (VM) echo intensity was a significant predictor of second peak KFM (r = 0.517, R2 = 0.267, P = 0.003, f2 = 0.36). Only the VM thickness was the predictor of first (r = 0.504, R2 = 0.254, P = 0.005, f2 = 0.34) and second peak KAM (r = 0.581, R2 = 0.337, P = 0.001, f2 = 0.51), and KAM impulse (r = 0.693, R2 = 0.480, P < 0.001, f2 = 0.92). In conclusion, the greater hamstring-to-quadriceps muscle thickness ratio and the muscle architecture and quality of medial quadriceps/hamstring play an important role in KFM and KAM, and may have implications in knee osteoarthritis.
Study on instability mechanism of soft rock roadway and pressure-relief bolt-grouting support technology
Authors: Yang Tuo , Liu Jianzhuang , Luo Jianqiao , Shen Yupeng , Fu Peng 
Published: November 2023

AbstractAiming at the engineering problem of roadway deformation and instability of swelling soft rock widely existed in Kailuan mining area, the mineral composition and microstructure of such soft rock were obtained by conducting scanning electron microscopy, X-ray diffraction experiments, uniaxial and conventional triaxial tests, and the law of softening and expanding of such soft rock and the failure mechanism of surrounding rock were identified. The combined support scheme of multi-level anchor bolt, bottom corner pressure relief and fractional grouting is proposed. The roadway supporting parameters are adjusted and optimized by FLAC3D numerical simulation, and three supporting methods of multi-layer anchor bolt, bottom corner pressure relief and fractional grouting are determined and their parameters are optimized. The study results show that: the total amount of clay minerals is 53–75%, pores, fissures, nanoscale and micron layer gaps are developed, providing a penetrating channel for water infiltration to soften the surrounding rock; the three-level anchor pressure-relief and grouting support technology can control the sinking amount of the roof within 170 mm, the bottom drum amount within 210 mm, the bolts of each level is evenly distributed in tension, and the maximum stress and bottom drum displacement in the pressure relief area are significantly reduced; the pressure-relief groove promotes the development of bottom corner cracks, accelerates the secondary distribution of peripheral stress, and weakens the effect of high stress on the shallow area. Using time or displacement as the index, optimizing the grouting time, filling the primary and excavation cracks, blocking the expansion and softening effect of water on the rock mass, realizing the dynamic unity of structural yielding pressure and surrounding rock modification, has guiding significance for the support control of soft rock roadway.
Application of 3D scanner to measure physical size and improvement of hip brace manufacturing technology in severe cerebral palsy patients
Authors: Kim Jung-Min , Lim Jiwoon , Choi Sun-Young , Rhim Sung-Han , Beom Jaewon , Ryu Ju Seok 
Published: November 2023

AbstractThis prospective pilot study aimed to develop a personalized hip brace for treating hip subluxation in children with cerebral palsy. Nineteen children, aged 1–15, with severe cerebral palsy participated in the study. Customized hip braces were created based on 3D scanner measurements and worn for 7 days. The primary outcome, Hip Migration Index (MI), and secondary outcomes, including range of motion (ROM) in the hip and knee joints, pain intensity, satisfaction, discomfort scores, CPCHILD, and wearability test, were assessed. The MI and ROM were assessed at screening and at Visit 1 (when the new hip brace was first worn), while other indicators were evaluated at screening, Visit 1, and Visit 2 (7 days after wearing the new hip brace). The study demonstrated significant improvements in the MI for the right hip, left hip, and both sides. However, there were no statistically significant differences in hip and knee joint ROM. Other indicators showed significant changes between screening, Visit 1, and Visit 2. The study suggests that customized hip braces effectively achieved immediate correction, positively impacting the quality of life and satisfaction in children with cerebral palsy. Furthermore, the hip braces have the potential to enhance compliance and prevent hip subluxation.Clinical Trial Registration number: NCT05388422
Diffusion controlled electrochemical analysis of MoS2 and MOF derived metal oxide–carbon hybrids for high performance supercapacitors
Authors: Shrivastav Vishal , Mansi  , Dubey Prashant , Shrivastav Vaishali , Kaur Ashwinder , Hołdyński Marcin , Krawczyńska Agnieszka , Tiwari Umesh K. , Deep Akash , Nogala Wojciech , Sundriyal Shashank 
Published: November 2023

AbstractIn the context of emerging electric devices, the demand for advanced energy storage materials has intensified. These materials must encompass both surface and diffusion-driven charge storage mechanisms. While diffusion-driven reactions offer high capacitance by utilizing the bulk of the material, their effectiveness diminishes at higher discharge rates. Conversely, surface-controlled reactions provide rapid charge/discharge rates and high power density. To strike a balance between these attributes, we devised a tri-composite material, TiO2/Carbon/MoS2 (T10/MoS2). This innovative design features a highly porous carbon core for efficient diffusion and redox-active MoS2 nanosheets on the surface. Leveraging these characteristics, the T10/MoS2 composite exhibited impressive specific capacitance (436 F/g at 5 mV/s), with a significant contribution from the diffusion-controlled process (82%). Furthermore, our symmetrical device achieved a notable energy density of ~ 50 Wh/kg at a power density of 1.3 kW/kg. This concept holds promise for extending the approach to other Metal–Organic Framework (MOF) structures, enabling enhanced diffusion-controlled processes in energy storage applications.