bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translocated Legionella pneumophila small RNAs mimic eukaryotic microRNAs targeting the host immune response
Authors: Sahr Tobias , Escoll Pedro , Rusniok Christophe , Bui Sheryl , Pehau-Arnaudet Gérard , Lavieu Gregory , Buchrieser Carmen 
Published: February 2022

AbstractLegionella pneumophila is an intracellular bacterial pathogen that can cause a severe form of pneumonia in humans, a phenotype evolved through interactions with aquatic protozoa in the environment. Here, we show that L. pneumophila uses extracellular vesicles to translocate bacterial small RNAs (sRNAs) into host cells that act on host defence signalling pathways. The bacterial sRNA RsmY binds to the UTR of ddx58 (RIG-I encoding gene) and cRel, while tRNA-Phe binds ddx58 and irak1 collectively reducing expression of RIG-I, IRAK1 and cRel, with subsequent downregulation of IFN-β. Thus, RsmY and tRNA-Phe are bacterial trans-kingdom regulatory RNAs downregulating selected sensor and regulator proteins of the host cell innate immune response. This miRNA-like regulation of the expression of key sensors and regulators of immunity is a feature of L. pneumophila host-pathogen communication and likely represents a general mechanism employed by bacteria that interact with eukaryotic hosts.
Signatures of TOP1 transcription-associated mutagenesis in cancer and germline
Authors: Reijns Martin A. M. , Parry David A. , Williams Thomas C. , Nadeu Ferran , Hindshaw Rebecca L. , Rios Szwed Diana O. , Nicholson Michael D. , Carroll Paula , Boyle Shelagh , Royo Romina , Cornish Alex J. , Xiang Hang , Ridout Kate ,   The Genomics England Research Consortium, Ambrose John C. , Arumugam Prabhu , Bevers Roel , Bleda Marta , Boardman-Pretty Freya , Boustred Christopher R. , Brittain Helen , Caulfield Mark J. , Chan Georgia C. , Elgar Greg , Fowler Tom , Giess Adam , Hamblin Angela , Henderson Shirley , Hubbard Tim J. P. , Jackson Rob , Jones Louise J. , Kasperaviciute Dalia , Kayikci Melis , Kousathanas Athanasios , Lahnstein Lea , Leigh Sarah E. A. , Leong Ivonne U. S. , Lopez Javier F. , Maleady-Crowe Fiona , McEntagart Meriel , Minneci Federico , Moutsianas Loukas , Mueller Michael , Murugaesu Nirupa , Need Anna C. , O’Donovan Peter , Odhams Chris A. , Patch Christine , Pereira Mariana Buongermino , Perez-Gil Daniel , Pullinger John , Rahim Tahrima , Rendon Augusto , Rogers Tim , Savage Kevin , Sawant Kushmita , Scott Richard H. , Siddiq Afshan , Sieghart Alexander , Smith Samuel C. , Sosinsky Alona , Stuckey Alexander , Tanguy Mélanie , Taylor Tavares Ana Lisa , Thomas Ellen R. A. , Thompson Simon R. , Tucci Arianna , Welland Matthew J. , Williams Eleanor , Witkowska Katarzyna , Wood Suzanne M. ,   Colorectal Cancer Domain UK 100,000 Genomes Project, Chubb Daniel , Cornish Alex , Kinnersley Ben , Houlston Richard , Wedge David , Gruber Andreas , Frangou Anna , Cross William , Graham Trevor , Sottoriva Andrea , Caravagna Gulio , Lopez-Bigas Nuria , Arnedo-Pac Claudia , Church David , Culliford Richard , Thorn Steve , Quirke Phil , Wood Henry , Tomlinson Ian , Noyvert Boris , Schuh Anna , Aden Konrad , Palles Claire , Campo Elias , Stankovic Tatjana , Taylor Martin S. , Jackson Andrew P. 
Published: February 2022

AbstractThe mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4—a cancer insertion–deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions —is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome.
Design and optimization of high temperature optocouplers as galvanic isolation
Authors: Sabbar Abbas , Madhusoodhanan Syam , Tran Huong , Dong Binzhong , Wang Jiangbo , Mantooth Alan , Yu Shui-Qing , Chen Zhong 
Published: February 2022

AbstractThe commercial InGaN-based (blue and green) and AlGaInP-based (red) multiple quantum well (MQW) lighting emitting diodes (LEDs) were studied in a wide range of temperatures up to 800 K for their light emission and detection (i.e., LEDs operated under reverse bias as photodiodes (PDs)) characteristics. The results indicate the feasibility of integrating a pair of selected LEDs to fabricate high temperature (HT) optocouplers, which can be utilized as galvanic isolation to replace the bulky isolation transforms in the high-density power modules. A detailed study on LEDs and PDs were performed. The external quantum efficiency (EQE) of the LED and PDs were calculated. Higher relative external quantum efficiency (EQE) and lower efficiency droops with temperatures are obtained from the blue and green LEDs for display compared with the blue one for lighting and red LED for display. The blue for lighting and red for display devices show superior responsivity, specific detectivity (D*), and EQE compared with blue and green for display when operated as PDs. The results suggest that red LED devices for display can be used to optimize HT optocouplers due to the highest wavelength overlapping compared with others.
The superior photocatalytic performance and DFT insights of S-scheme CuO@TiO2 heterojunction composites for simultaneous degradation of organics
Authors: Hamad Hesham , Elsenety Mohamed M. , Sadik Wagih , El-Demerdash Abdel-Ghaffar , Nashed Adel , Mostafa Amr , Elyamny Shaimaa 
Published: February 2022

AbstractThe necessity to resolve the issue of rapid charge carrier recombination for boosting photocatalytic performance is a vigorous and challenging research field. To address this, the construction of a binary system of step-scheme (S-scheme) CuO@TiO2 heterostructure composite has been demonstrated through a facile solid-state route. The remarkably enhanced photocatalytic performance of CuO@TiO2, compared with single TiO2, which can consequence in the more efficient separation of photoinduced charge carriers, reduced the band gap of TiO2, improved the electrical transport performance, and improved the lifetimes, thus donating it with the much more powerful oxidation and reduction capability. A photocatalytic mechanism was proposed to explain the boosted photocatalytic performance of CuO@TiO2 on a complete analysis of physicochemical, DFT calculations, and electrochemical properties. In addition, this work focused on the investigation of the stability and recyclability of CuO@TiO2 in terms of efficiency and its physical origin using XRD, BET, and XPS. It is found that the removal efficiency diminishes 4.5% upon five recycling runs. The current study not only promoted our knowledge of the binary system of S-scheme CuO@TiO2 heterojunction composite photocatalyst but also shed new light on the design of heterostructure photocatalysts with high-performance and high stability.
Parametric investigation of an injection-jet self-powered Fontan circulation
Authors: Prather Ray , Das Arka , Farias Michael , Divo Eduardo , Kassab Alain , DeCampli William 
Published: February 2022

AbstractApproximately $$1/2500$$

1
/
2500

babies are born with only one functioning ventricle and the Fontan is the third and, ideally final staged palliative operation for these patients. This altered circulation is prone to failure with survival rates below $$50\%$$

50
%

into adulthood. Chronically elevated inferior vena cava (IVC) pressure is implicated as one cause of the mortality and morbidity in this population. An injection jet shunt (IJS) drawing blood-flow directly from the aortic arch to significantly lower IVC pressure is proposed. A computer-generated 3D model of a 2–4 year old patient with a fenestrated Fontan and a cardiac output of 2.3 L/min was generated. The detailed 3D pulsatile hemodynamics are resolved in a zero-dimensional lumped parameter network tightly-coupled to a 3D computational fluid dynamics model accounting for non-Newtonian blood rheology and resolving turbulence using large eddy simulation. IVC pressure and systemic oxygen saturation were tracked for various IJS-assisted Fontan configurations, altering design parameters such as shunt and fenestration diameters and locations. A baseline “failing” Fontan with a 4 mm fenestration was tuned to have an elevated IVC pressure (+ 17.8 mmHg). Enlargement of the fenestration to 8 mm resulted in a 3 mmHg IVC pressure drop but an unacceptable reduction in systemic oxygen saturation below 80%. Addition of an IJS with a 2 mm nozzle and minor volume load to the ventricle improved the IVC pressure drop to 3.2 mmHg while increasing systemic oxygen saturation above 80%. The salutary effects of the IJS to effectively lower IVC pressure while retaining acceptable levels of oxygen saturation are successfully demonstrated.
Nonlinear frequency analysis of COVID-19 spread in Tokyo using empirical mode decomposition
Authors: Dong Ran , Ni Shaowen , Ikuno Soichiro 
Published: February 2022

AbstractEmpirical mode decomposition (EMD) was adopted to decompose daily COVID-19 infections in Tokyo from February 28, 2020, to July 12, 2021. Daily COVID-19 infections were nonlinearly decomposed into several monochromatic waves, intrinsic mode functions (IMFs), corresponding to their periodic meanings from high frequency to low frequency. High-frequency IMFs represent variabilities of random factors and variations in the number of daily PCR and antigen inspections, which can be nonlinearly denoised using EMD. Compared with a moving average and Fourier transform, EMD provides better performance in denoising and analyzing COVID-19 spread. After variabilities of daily inspections were weekly denoised by EMD, one low-frequency IMF reveals that the average period of external influences (public health and social measures) to stop COVID-19 spread was 19 days, corresponding to the measures response duration based on the incubation period. By monitoring this nonlinear wave, public health and social measures for stopping COVID-19 spread can be evaluated and visualized quantitatively in the instantaneous frequency domain. Moreover, another low-frequency IMF revealed that the period of the COVID-19 outbreak and retreat was 57 days on average. This nonlinear wave can be used as a reference for setting the timeframe for state of emergency declarations. Thus, decomposing daily infections in the instantaneous frequency domain using EMD represents a useful tool to improve public health and social measures for stopping COVID-19 spread.
Morphological and molecular diversity patterns of the genus Tropodiaptomus Kiefer, 1932 (Copepoda, Calanoida, Diaptomidae) in Thailand
Authors: Saetang Thanida , Marrone Federico , Vecchioni Luca , Maiphae Supiyanit 
Published: February 2022

AbstractTropodiaptomusis one of the most specious genera in the family Diaptomidae, but it is often rare in terms of distribution and abundance. Moreover,Tropodiaptomusspecies show a noteworthy variability in some of the morphological characters considered of prime importance in diaptomid taxonomy, and the presence of cryptic or pseudocryptic species is likely. Thus, through a geographically-wide sampling in Thailand, we aimed to investigate the local diversity of the genus and to compare the morphological and molecular diversity pattern based on mitochondrial and nuclear genes sequences. DNA taxonomy was also implemented in order to check whether theTropodiaptomuslineages were independent species according to the “evolutionary genetic species concept”. SixTropodiaptomusmorphospecies were found, three of which are putative species new to Science pending a formal description. The finding of such a high incidence of undescribed species stresses the existence of a significant “Linnean shortfall” affecting Thai diaptomids. The molecular results showed that most of the studied species could be identified consistently with their morphology-based taxonomy. However,Tropodiaptomus vicinusandT. cf.lanaonusshowed a high level of genetic diversity, suggesting that traditional morphological techniques might be inadequate for correctly assessing their taxonomical status.
The effects of super spreading events and movement control measures on the COVID-19 pandemic in Malaysia
Authors: Herng Lai Chee , Singh Sarbhan , Sundram Bala Murali , Zamri Ahmed Syahmi Syafiq Md , Vei Tan Cia , Aris Tahir , Ibrahim Hishamshah , Abdullah Noor Hisham , Dass Sarat Chandra , Gill Balvinder Singh 
Published: February 2022

AbstractThis paper aims to develop an automated web application to generate validated daily effective reproduction numbers (Rt) which can be used to examine the effects of super-spreading events due to mass gatherings and the effectiveness of the various Movement Control Order (MCO) stringency levels on the outbreak progression of COVID-19 in Malaysia. The effective reproduction number, Rt, was estimated by adopting and modifying an Rt estimation algorithm using a validated distribution mean of 3.96 and standard deviation of 4.75 with a seven-day sliding window. The Rt values generated were validated using thea moving window SEIR model with a negative binomial likelihood fitted using methods from the Bayesian inferential framework. A Pearson’s correlation between the Rt values estimated by the algorithm and the SEIR model was r = 0.70, p < 0.001 and r = 0.81, p < 0.001 during the validation period The Rt increased to reach the highest values at 3.40 (95% CI 1.47, 6.14) and 1.72 (95% CI 1.54, 1.90) due to the Sri Petaling and Sabah electoral process during the second and third waves of COVID-19 respectively. The MCOs was able to reduce the Rt values by 63.2 to 77.1% and 37.0 to 47.0% during the second and third waves of COVID-19, respectively. Mass gathering events were one of the important drivers of the COVID-19 outbreak in Malaysia. However, COVID-19 transmission can be fuelled by noncompliance to Standard Operating Procedure, population mobility, ventilation and environmental factors.
Strong laser polarization control of coherent phonon excitation in van der Waals material Fe3GeTe2
Authors: Gong Yu , Hu Ming , Harris Nico , Yang Zhonghua , Xie Ti , Teklu Alem , Kuthirummal Narayanan , koenemann Jacob , Xu Xianghan , Cheong Sang-Wook , McLoud Will , Gong Cheng 
Published: February 2022

AbstractOptical manipulation of coherent phonon frequency in two-dimensional (2D) materials could advance the development of ultrafast phononics in atomic-thin platforms. However, conventional approaches for such control are limited to doping, strain, structural or thermal engineering. Here, we report the experimental observation of strong laser-polarization control of coherent phonon frequency through time-resolved pump-probe spectroscopic study of van der Waals (vdW) materials Fe3GeTe2. When the polarization of the pumping laser with tilted incidence is swept between in-plane and out-of-plane orientations, the frequencies of excited phonons can be monotonically tuned by as large as 3% (~100 GHz). Our first-principles calculations suggest the strong planar and vertical inter-atomic interaction asymmetry in layered materials accounts for the observed polarization-dependent phonon frequencies, as in-plane/out-of-plane polarization modifies the restoring force of the lattice vibration differently. Our work provides insightful understanding of the coherent phonon dynamics in layered vdW materials and opens up new avenues to optically manipulating coherent phonons.
Inter-individual variability amplified through breeding reveals control of reward-related action strategies by Melanocortin-4 Receptor in the dorsomedial striatum
Authors: Allen Aylet T. , Heaton Elizabeth C. , Shapiro Lauren P. , Butkovich Laura M. , Yount Sophie T. , Davies Rachel A. , Li Dan C. , Swanson Andrew M. , Gourley Shannon L. 
Published: February 2022

AbstractIn day-to-day life, we often must choose between pursuing familiar behaviors or adjusting behaviors when new strategies might be more fruitful. The dorsomedial striatum (DMS) is indispensable for arbitrating between old and new action strategies. To uncover molecular mechanisms, we trained mice to generate nose poke responses for food, then uncoupled the predictive relationship between one action and its outcome. We then bred the mice that failed to rapidly modify responding. This breeding created offspring with the same tendencies, failing to inhibit behaviors that were not reinforced. These mice had less post-synaptic density protein 95 in the DMS. Also, densities of the melanocortin-4 receptor (MC4R), a high-affinity receptor for α-melanocyte-stimulating hormone, predicted individuals’ response strategies. Specifically, high MC4R levels were associated with poor response inhibition. We next found that reducing Mc4r in the DMS in otherwise typical mice expedited response inhibition, allowing mice to modify behavior when rewards were unavailable or lost value. This process required inputs from the orbitofrontal cortex, a brain region canonically associated with response strategy switching. Thus, MC4R in the DMS appears to propel reward-seeking behavior, even when it is not fruitful, while moderating MC4R presence increases the capacity of mice to inhibit such behaviors.
Multimerin-1 and cancer: a review
Authors: Posner Mareike G. 
Published: February 2022

Abstract
Multimerin-1 (MMRN1) is a platelet protein with a role in haemostasis and coagulation. It is also present in endothelial cells (ECs) and the extracellular matrix (ECM), where it may be involved in cell adhesion, but its molecular functions and protein–protein interactions in these cellular locations have not been studied in detail yet. In recent years, MMRN1 has been identified as a differentially expressed gene (DEG) in various cancers and it has been proposed as a possible cancer biomarker. Some evidence suggest that MMRN1 expression is regulated by methylation, protein interactions, and non-coding RNAs (ncRNAs) in different cancers. This raises the questions if a functional role of MMRN1 is being targeted during cancer development, and if MMRN1’s differential expression pattern correlates with cancer progression. As a result, it is timely to review the current state of what is known about MMRN1 to help inform future research into MMRN1’s molecular mechanisms in cancer.
Model predictive control of switching continuous‐time systems with stochastic jumps: Application to an electric current source
Authors: Vargas Alessandro N. , Ishihara João Y. , Caruntu Constantin F. , Zhang Lixian , Djanan Armand A. Nanha 
Published: February 2022

AbstractThis paper proposes an extension of the model predictive control framework for switching continuous‐time linear systems. The switching times follow a stochastic process with limited statistical information. At each switching time, the controller knows the system state, but it is blind with respect to the switching continuous‐time subsystems. In this setting, the paper's main contribution is to show how to compute the model predictive control gain. The paper also illustrates the implications of our approach for applications. The approach was used in practice to control an electric current source that supplied a switching load. The experimental data support the usefulness of our approach.
Dynamic event‐triggered control for leader‐following consensus of multiagent systems with the estimator
Authors: Hu Shunwei , Qiu Jianlong , Chen Xiangyong , Zhao Feng , Jiang Xiaowei 
Published: February 2022

AbstractIn this paper, the leader‐following consensus problem of general linear multi‐agent systems with distributed dynamic event‐triggered control is studied. A distributed controller with estimated states is designed and a dynamic event‐triggered communication protocol with an auxiliary variable is proposed for each agent to update its triggering threshold. Under this control strategy, the systems only need the states in triggering instants as a result of the utilisation of estimated states. The existence of a dynamic threshold guarantees fewer triggering times, in contrast to the conventional static one. Meanwhile, the estimator is designed between the triggering instants to reduce the state shift, the next state of each agent depends on the local information of itself and its neighbours rather than global information. Then, the multi‐agent systems can achieve consensus without Zeno behaviour. Finally, a simulation example is offered to verify the effectiveness and feasibility of the proposed approach.
Visual perception and local features for foreground‐background segmentation
Authors: Peng Tong , He Kun , Su Yao , Hui Ziwei 
Published: February 2022

AbstractThe traditional foreground‐background segmentation models mainly depend on the low‐level features of the image, while ignoring the visual effect. Combining visual perception and local features, a top‐down segmentation model is proposed. This model regards foreground‐background segmentation as a reasoning problem based on visual perception, and calculates the association between two‐pixel blocks through Kullback–Leibler divergence, which solves the ill‐posed problem of traditional single‐pixel recognition. Meanwhile, local features are used to optimize the overall segmentation results in detail and improve the segmentation accuracy. The experimental results on the CMU‐Cornell iCoseg database and the BSDS500 database show that visual perception and local features can help improve the segmentation performance to a certain extent.
Probabilistic context integration‐based aircraft behaviour intention classification at airport ramps
Authors: Lee Soomok , Seo Seung‐Woo 
Published: February 2022

AbstractSelf‐driving baggage tractors driving on airport ramps/aprons present new trends that promote better airport operation procedures and proliferate the aviation market. Airport ramps have unique mobility requirements when it comes to layout, population, demand, and patterns. Estimating aircraft movement is highly crucial and must be required because of safety reasons and airport operations rules. The movement of aircraft at the airport ramp is not dynamic but relatively static and slow. However, it is more complicated in estimating attributes. Even though the aircraft is parked and stationary, all operational vehicles should be cautious on aircraft pushing in or out from the parking stand. However, this is never dealt with in any research since aircraft detection observed at the airport ramp is not suggested in previous research. In this paper, a context‐aware fusion‐based method for aircraft intention detection at airport ramps is proposed. A parallel extraction of behavioural features from the aircraft and situational context detection from other adjacent objects are suggested. Using the proposed method, aircraft can be detected and aircraft movement context can be estimated. The feasibility of this algorithm is demonstrated based on the fluent dataset obtained at Cincinnati Airport.