bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yield of genetic association signals from genomes, exomes and imputation in the UK Biobank
Authors: Gaynor Sheila M. , Joseph Tyler , Bai Xiaodong , Zou Yuxin , Boutkov Boris , Maxwell Evan K. , Delaneau Olivier , Hofmeister Robin J. , Krasheninina Olga , Balasubramanian Suganthi , Marcketta Anthony , Backman Joshua ,   Regeneron Genetics Center, Reid Jeffrey G. , Overton John D. , Lotta Luca A. , Marchini Jonathan , Salerno William J. , Baras Aris , Abecasis Goncalo R. , Thornton Timothy A. 
Published: September 2024

AbstractWhole-genome sequencing (WGS), whole-exome sequencing (WES) and array genotyping with imputation (IMP) are common strategies for assessing genetic variation and its association with medically relevant phenotypes. To date, there has been no systematic empirical assessment of the yield of these approaches when applied to hundreds of thousands of samples to enable the discovery of complex trait genetic signals. Using data for 100 complex traits from 149,195 individuals in the UK Biobank, we systematically compare the relative yield of these strategies in genetic association studies. We find that WGS and WES combined with arrays and imputation (WES + IMP) have the largest association yield. Although WGS results in an approximately fivefold increase in the total number of assayed variants over WES + IMP, the number of detected signals differed by only 1% for both single-variant and gene-based association analyses. Given that WES + IMP typically results in savings of lab and computational time and resources expended per sample, we evaluate the potential benefits of applying WES + IMP to larger samples. When we extend our WES + IMP analyses to 468,169 UK Biobank individuals, we observe an approximately fourfold increase in association signals with the threefold increase in sample size. We conclude that prioritizing WES + IMP and large sample sizes rather than contemporary short-read WGS alternatives will maximize the number of discoveries in genetic association studies.
Phylogenetic position of the pigeon mite, Ornithonyssus sylviarum, with amplification of its immunogenetic biomarkers in Egypt
Authors: Salem Mai A. , Taha Noha Madbouly , El-Bahy Mohamed M. , Ramadan Reem M. 
Published: September 2024

AbstractOrnithonyssus sylviarum (O. sylviarum) is an obligatory, blood-sucking ectoparasite widely distributed among poultry and other mammals, causing significant economic losses. This study represented the first report of molecular genotypic identification of O. sylviarum from pigeons, Columba livia domestica, in Egypt. PCR and sequencing of the 28S rRNA gene were conducted. The resulting mite sequences were subjected to BLAST analysis, revealing 90–100% similarity to O. sylviarum in all tested samples. The sequences were deposited in GenBank under the accession numbers PP049086 and PP033720. A phylogenetic tree was constructed to compare the obtained species with related species worldwide. Additionally, infected pigeons showed increased expression of IL-1, IL-10, IFN-γ, and TGF-β3 genes and elevated serum levels of stress biomarkers. The increased level of these cytokines indicates there was a disturbance in the immune status of the infected host with parasite compared with control healthy ones. This increases the susceptibility to infection with other pathogens.
Exploring the impacts of high-speed rail on technology-intensive manufacturing: the case of the Yangtze River Delta region, 2007–2016
Authors: Ma Xiuxin , Van Rompaey Anton , Qiang Will W. , Derudder Ben 
Published: September 2024

AbstractHigh-speed rail (HSR) may influence economic activities that rely heavily on innovation by facilitating skilled labour, face-to-face interactions, and knowledge spillovers. This study explores how HSR development affects the spatial distribution of technology-intensive manufacturing (TIM) in the Yangtze River Delta (YRD), China. Using a panel dataset including 24 cities for the period 2007–2016 and employing the output of communications equipment, computers, and other electronic equipment (CCOE) as a proxy for TIM’s economic productivity at the city level, we apply the staggered difference-in-differences (DID) and spatial Durbin model (SDM) to measure the impacts of HSR’s initial opening and connectivity on CCOE development and capture the spatial spillover effects of HSR connectivity. Our findings indicate that the initial opening of HSR and HSR connectivity are negatively associated with CCOE productivity in both DID and SDM. Additionally, the reduction of CCOE is more pronounced in cities with larger populations and higher levels of economy. Moreover, HSR has a more significant effect on CCOE than other manufacturing sectors. However, the spillover effects remain insignificant, indicating HSR’s limited impact on CCOE development in adjacent cities within the YRD.
EXCRETE workflow enables deep proteomics of the microbial extracellular environment
Authors: Russo David A. , Oliinyk Denys , Pohnert Georg , Meier Florian , Zedler Julie A. Z. 
Published: September 2024

AbstractExtracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85% of all potentially secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the predicted cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and suggest that multiple functions of the secretome are conserved across freshwater, marine, and terrestrial species.
Combining systems and synthetic biology for in vivo enzymology
Authors: Castaño-Cerezo Sara , Chamas Alexandre , Kulyk Hanna , Treitz Christian , Bellvert Floriant , Tholey Andreas , Galéote Virginie , Camarasa Carole , Heux Stéphanie , Garcia-Alles Luis F , Millard Pierre , Truan Gilles 
Published: September 2024

AbstractEnzymatic parameters are classically determined in vitro, under conditions that are far from those encountered in cells, casting doubt on their physiological relevance. We developed a generic approach combining tools from synthetic and systems biology to measure enzymatic parameters in vivo. In the context of a synthetic carotenoid pathway in Saccharomyces cerevisiae, we focused on a phytoene synthase and three phytoene desaturases, which are difficult to study in vitro. We designed, built, and analyzed a collection of yeast strains mimicking substantial variations in substrate concentration by strategically manipulating the expression of geranyl-geranyl pyrophosphate (GGPP) synthase. We successfully determined in vivo Michaelis-Menten parameters (KM, Vmax, and kcat) for GGPP-converting phytoene synthase from absolute metabolomics, fluxomics and proteomics data, highlighting differences between in vivo and in vitro parameters. Leveraging the versatility of the same set of strains, we then extracted enzymatic parameters for two of the three phytoene desaturases. Our approach demonstrates the feasibility of assessing enzymatic parameters directly in vivo, providing a novel perspective on the kinetic characteristics of enzymes in real cellular conditions.
SUMOylation of protein phosphatase 5 regulates phosphatase activity and substrate release
Authors: Sager Rebecca A , Backe Sarah J , Dunn Diana M , Heritz Jennifer A , Ahanin Elham , Dushukyan Natela , Panaretou Barry , Bratslavsky Gennady , Woodford Mark R , Bourboulia Dimitra , Mollapour Mehdi 
Published: September 2024

AbstractThe serine/threonine protein phosphatase 5 (PP5) regulates hormone and stress-induced signaling networks. Unlike other phosphoprotein phosphatases, PP5 contains both regulatory and catalytic domains and is further regulated through post-translational modifications (PTMs). Here we identify that SUMOylation of K430 in the catalytic domain of PP5 regulates phosphatase activity. Additionally, phosphorylation of PP5-T362 is pre-requisite for SUMOylation, suggesting the ordered addition of PTMs regulates PP5 function in cells. Using the glucocorticoid receptor, a well known substrate for PP5, we demonstrate that SUMOylation results in substrate release from PP5. We harness this information to create a non-SUMOylatable K430R mutant as a ‘substrate trap’ and globally identified novel PP5 substrate candidates. Lastly, we generated a consensus dephosphorylation motif using known substrates, and verified its presence in the new candidate substrates. This study unravels the impact of cross talk of SUMOylation and phosphorylation on PP5 phosphatase activity and substrate release in cells.
RIG-I is an intracellular checkpoint that limits CD8+ T-cell antitumour immunity
Authors: Duan Xiaobing , Hu Jiali , Zhang Yuncong , Zhao Xiaoguang , Yang Mingqi , Sun Taoping , Liu Siya , Chen Xin , Feng Juan , Li Wenting , Yang Ze , Zhang Yitian , Lin Xiaowen , Liu Dingjie , Meng Ya , Yang Guang , Lin Qiuping , Zhang Guihai , Lei Haihong , Yi Zhengsheng , Liu Yanyan , Liang Xiaobing , Wu Yujuan , Diao Wenqing , Li Zesong , Liang Haihai , Zhan Meixiao , Sun Hong-Wei , Li Xian-Yang , Lu Ligong 
Published: September 2024

AbstractRetinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor involved in innate immunity, but its role in adaptive immunity, specifically in the context of CD8+ T-cell antitumour immunity, remains unclear. Here, we demonstrate that RIG-I is upregulated in tumour-infiltrating CD8+ T cells, where it functions as an intracellular checkpoint to negatively regulate CD8+ T-cell function and limit antitumour immunity. Mechanistically, the upregulation of RIG-I in CD8+ T cells is induced by activated T cells, and directly inhibits the AKT/glycolysis signalling pathway. In addition, knocking out RIG-I enhances the efficacy of adoptively transferred T cells against solid tumours, and inhibiting RIG-I enhances the response to PD-1 blockade. Overall, our study identifies RIG-I as an intracellular checkpoint and a potential target for alleviating inhibitory constraints on T cells in cancer immunotherapy, either alone or in combination with an immune checkpoint inhibitor.
Forensic Science
Authors: Shaw Ian , Sandiford Anna 
Published: September 2024

Forensic science is often important in criminal cases, so criminal justice professionals, including lawyers and forensic scene investigators, must have a basic understanding of what is often complex science. This book explains the science underpinning forensic techniques to give those who engage with forensic science professionally, but who are not primarily scientists, a level of understanding that will enable them to use forensic science data effectively. In addition, the book places the use of forensic data in the context of criminal cases to assess the reliability and usefulness of forensic data in court.
Succinctly presented, this book covers all the facets of forensic science for students who are hoping to become police officers, lawyers or other members of the criminal justice system. As forensic investigations have advanced, e.g. in DNA profiling, computer modelling and behavioural sciences, so has the need for an increase in the level of scientific knowledge. The author understands the challenges this brings and has written the book to explain complex information in an accessible and undemanding style. Using international case studies, this book will bring forensic science to life and include aspects of the author's personal journey.
Differences Between French and English in the Use of Suprasegmental Cues for the Short-Term Recall of Word Lists
Authors: Lew Emilia C. , Sares Anastasia , Gilbert Annie C. , Zhang Yue , Lehmann Alexandre , Deroche Mickael 
Published: September 2024

Purpose:
Greater recognition of the impact of hearing loss on cognitive functions has led speech/hearing clinics to focus more on auditory memory outcomes. Typically evaluated by scoring participants' recall on a list of unrelated words after they have heard the list read out loud, this method implies pitch and timing variations across words. Here, we questioned whether these variations could impact performance differentially in one language or another.

Method:
In a series of online studies evaluating auditory short-term memory in normally hearing adults, we examined how pitch patterns (Experiment 1), timing patterns (Experiment 2), and interactions between the two (Experiment 3) affected free recall of words, cued recall of forgotten words, and mental demand. Note that visual memory was never directly tested; written words were only used after auditory encoding in the cued recall part. Studies were administered in both French and English, always conducted with native listeners.

Result:
Confirming prior work, grouping mechanisms facilitated free recall, but not cued recall (the latter being only affected by longer presentation time) or ratings of mental demand. Critically, grouping by pitch provided more benefit for French than for English listeners, while grouping by time was equally beneficial in both languages.

Conclusion:
Pitch is more useful to French- than to English-speaking listeners for encoding spoken words in short-term memory, perhaps due to the syllable-based versus stress-based rhythms inherent to each language.

Supplemental Material:

https://doi.org/10.23641/asha.27048328
Hyperspectral imagery quality assessment and band reconstruction using the prophet model
Authors: Ma Ping , Ren Jinchang , Gao Zhi , Li Yinhe , Chen Rongjun 
Published: September 2024

AbstractIn Hyperspectral Imaging (HSI), the detrimental influence of noise and distortions on data quality is profound, which has severely affected the following‐on analytics and decision‐making such as land mapping. This study presents an innovative framework for assessing HSI band quality and reconstructing the low‐quality bands, based on the Prophet model. By introducing a comprehensive quality metric to start, the authors approach factors in both spatial and spectral characteristics across local and global scales. This metric effectively captures the intricate noise and distortions inherent in the HSI data. Subsequently, the authors employ the Prophet model to forecast information within the low‐quality bands, leveraging insights from neighbouring high‐quality bands. To validate the effectiveness of the authors’ proposed model, extensive experiments on three publicly available uncorrected datasets are conducted. In a head‐to‐head comparison, the framework against six state‐of‐the‐art band reconstruction algorithms including three spectral methods, two spatial‐spectral methods and one deep learning method is benchmarked. The authors’ experiments also delve into strategies for band selection based on quality metrics and the quality evaluation of the reconstructed bands. In addition, the authors assess the classification accuracy utilising these reconstructed bands. In various experiments, the results consistently affirm the efficacy of the authors’ method in HSI quality assessment and band reconstruction. Notably, the authors’ approach obviates the need for manually prefiltering of noisy bands. This comprehensive framework holds promise in addressing HSI data quality concerns whilst enhancing the overall utility of HSI.
Multiple‐nodes based cooperative jamming detection for reactive follower jamming in ISAC
Authors: Li Cheng , Shi Yuxin , Lu Xinjin , Wang Junjie , Zhu Yonggang , Xiao Ming 
Published: September 2024

AbstractAccurate jamming detection is a prerequisite and important support for efficient anti‐jamming communication in integrated sensing and communications. In recent years, the reactive follower jamming, characterized by the high jamming efficiency and the difficulty of detection, is seen as the main opponent for frequency hopping spread spectrum communication, which poses a threat to the reliability of wireless communication. Based on the background, a multiple‐nodes based cooperative jamming detection scheme is proposed for accurately detecting the reactive follower jamming. Specifically, the secondary nodes send the average energy of the suspected attacked symbols to the primary user as the uplink data in each detection period, and then the detection result is provided by the detection threshold. The optimal detection threshold is derived for the primary user according to the uplink data and channel conditions. In addition, the theoretical probability of detection under the optimal threshold is derived, and the complexity of the scheme is analysed. Simulation results show that the proposed multiple‐nodes based cooperative jamming detection scheme for reactive follower jamming can effectively improve the probability of detection.
New trends on noise reduction for power grid by acoustic metamaterials
Authors: Li Xing , Huang Weichun , Yu Yonghua , Pan Xinrong , Shen Xiaohai , Chen Jinglun , Qiu Junjie , Wang Jiawei , Zou Linyang , Qian Siwen , Nie Jingkai , Lu Ming‐Hui , Chen Yan‐Feng 
Published: September 2024

AbstractLightweight low‐frequency acoustic materials have become an important direction in the development of acoustic protection materials for power grid facilities and equipment. However, conventional acoustic materials cannot simultaneously meet the special requirements of low frequency, frequency‐selective, lightweight, and fire‐proofing for noise reduction of power grid facilities and equipment. Acoustic metamaterials have extraordinary acoustic properties, such as low‐frequency sound absorption and sound insulation that breaks the mass law. They mainly rely on microstructure design rather than the inherent properties of raw materials to achieve macroscopic extraordinary performance and are expected to meet the above requirements. The authors introduced the physical mechanisms and latest developments of different acoustic metamaterials for sound absorption, sound and vibration control, and briefly described the latest design methods based on artificial intelligence technologies. The potential application of acoustic metamaterials is discussed for noise reduction of power grid facilities and equipment.
A data mining‐based interruptible load contract model for the modern power system
Authors: Hui Zou , Jun Yang , Qi Meng 
Published: September 2024

AbstractTo devise more scientifically rational interruptible load contracts, this paper introduces a novel model for interruptible load contracts within modern electric power systems, grounded in data mining techniques. Initially, user characteristics are clustered using data mining technology to determine the optimal number of clusters. Building on this, the potential for different users to participate in interruptible load programs is analysed based on daily load ratios, yielding various user‐type parameters. Furthermore, the paper develops an interruptible load contract model that incorporates load response capabilities, enhancing the traditional interruptible load contract model based on principal‐agent theory through considerations of user type parameters and maximum interruptible load limits. The objective function, aimed at maximizing the profits of the electric company, is solved, and lastly, through the use of real data, a case study analysis focusing on commercial users with the strongest load response capabilities is conducted. The results affirm the efficacy of the proposed model.
Deep handwritten diagram segmentation
Authors: Pravalpruk Buntita , Dailey Matthew N. 
Published: September 2024

AbstractHandwriting is a natural way to communicate and exchange ideas, but converting handwritten diagrams to application‐specific digital formats requires skill and time. Automatic handwritten document conversion can save time, but diagrams and text require different recognition engines. Since accurate segmentation of handwritten diagrams can improve the accuracy of later diagram recognition steps, the authors propose to solve the problem of segmentation of text and non‐text elements of handwritten diagrams using deep semantic segmentation. The model, DeepDP is a flexible U‐net style architecture that can be tuned in complexity to a level appropriate for a particular dataset and diagram type. Experiments on a public hand‐drawn flowchart dataset and a business process diagram dataset show excellent performance, with a per pixel accuracy of 98.6% on the public flowchart datasets and improvement over the 99.3% text stroke accuracy and 96.6% non‐text stroke accuracy obtained by state of the art methods that use online stroke information. On the smaller offline business process diagram dataset, the method obtains a per‐pixel accuracy of 96.9%.
A novel and easy‐to‐implement modulation scheme for reducing modulation complexity in modular multilevel converter
Authors: Wang Zichen , Liu Zhijie , Li Ke‐Jun , Dou Jinxin , Guo Zhonglin , Ge Xiaoxue 
Published: September 2024

AbstractModulation strategy plays a key role in the operation of modular multilevel converters (MMC). Although many studies have been carried out on its optimization in MMC, the limitations of hardware implementation are seldom considered. This paper presents a novel and easy‐to‐implement modulation strategy that simplifies both hardware design and application. From the analysis in this paper, the widely‐used modulation methods have the problems of pulse width modulation (PWM) signal feedback and complex carrier configuration in hardware implementation. By setting up a flexible insertion and removal submodule and proposing a capacitor voltage balance algorithm based on duty ratio allocation, the proposed modulation method can allow for the separate design of the Algorithm Unit and the PWM Unit in the hardware, which solves the problem of PWM feedback and reduces the hardware requirement of the trigger system. Moreover, the proposed method can broaden the selection range of processor chips. Finally, a downscaled MMC prototype is built; the proposed method is verified by both simulation and experiment.