bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning coarse-grained potentials of protein thermodynamics
Authors: Majewski Maciej , Pérez Adrià , Thölke Philipp , Doerr Stefan , Charron Nicholas E. , Giorgino Toni , Husic Brooke E. , Clementi Cecilia , Noé Frank , De Fabritiis Gianni 
Published: September 2023

AbstractA generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.
Propagation pathways of Indo-Pacific rainfall extremes are modulated by Pacific sea surface temperatures
Authors: Strnad Felix M. , Schlör Jakob , Geen Ruth , Boers Niklas , Goswami Bedartha 
Published: September 2023

AbstractIntraseasonal variation of rainfall extremes within boreal summer in the Indo-Pacific region is driven by the Boreal Summer Intraseasonal Oscillation (BSISO), a quasi-periodic north-eastward movement of convective precipitation from the Indian Ocean to the Western Pacific. Predicting the spatiotemporal location of the BSISO is essential for subseasonal prediction of rainfall extremes but still remains a major challenge due to insufficient understanding of its propagation pathway. Here, using unsupervised machine learning, we characterize how rainfall extremes travel within the region and reveal three distinct propagation modes: north-eastward, eastward-blocked, and quasi-stationary. We show that Pacific sea surface temperatures modulate BSISO propagation — with El Niño-like (La Niña-like) conditions favoring quasi-stationary (eastward-blocked) modes—by changing the background moist static energy via local overturning circulations. Finally, we demonstrate the potential for early warning of rainfall extremes in the region up to four weeks in advance.
Interlocking of co-opted developmental gene networks in Drosophila and the evolution of pre-adaptive novelty
Authors: Molina-Gil Sara , Sotillos Sol , Espinosa-Vázquez José Manuel , Almudi Isabel , Hombría James C.-G. 
Published: September 2023

AbstractThe re-use of genes in new organs forms the base of many evolutionary novelties. A well-characterised case is the recruitment of the posterior spiracle gene network to theDrosophilamale genitalia. Here we find that this network has also been co-opted to the testis mesoderm where is required for sperm liberation, providing an example of sequentially repeated developmental co-options. Associated to this co-option event, an evolutionary expression novelty appeared, the activation of the posterior segment determinant Engrailed to the anterior A8 segment controlled by common testis and spiracle regulatory elements. Enhancer deletion shows that A8 anterior Engrailed activation is not required for spiracle development but only necessary in the testis. Our study presents an example of pre-adaptive developmental novelty: the activation of the Engrailed transcription factor in the anterior compartment of the A8 segment where, despite having no specific function, opens the possibility of this developmental factor acquiring one. We propose that recently co-opted networks become interlocked, so that any change to the network because of its function in one organ, will be mirrored by other organs even if it provides no selective advantage to them.
Structural landscape of the respiratory syncytial virus nucleocapsids
Authors: Gonnin Lorène , Desfosses Ambroise , Bacia-Verloop Maria , Chevret Didier , Galloux Marie , Éléouët Jean-François , Gutsche Irina 
Published: September 2023

AbstractHuman Respiratory Syncytial Virus (HRSV) is a prevalent cause of severe respiratory infections in children and the elderly. The helical HRSV nucleocapsid is a template for the viral RNA synthesis and a scaffold for the virion assembly. This cryo-electron microscopy analysis reveals the non-canonical arrangement of the HRSV nucleocapsid helix, composed of 16 nucleoproteins per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from longitudinal interactions by the C-terminal arm of the HRSV nucleoprotein. We explore the polymorphism of the nucleocapsid-like assemblies, report five structures of the full-length particles and two alternative arrangements formed by a C-terminally truncated nucleoprotein mutant, and demonstrate the functional importance of the identified longitudinal interfaces. We put all these findings in the context of the HRSV RNA synthesis machinery and delineate the structural basis for its further investigation.
Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism
Authors: Ghanaeian Avrin , Majhi Sumita , McCafferty Caitlyn L. , Nami Babak , Black Corbin S. , Yang Shun Kai , Legal Thibault , Papoulas Ophelia , Janowska Martyna , Valente-Paterno Melissa , Marcotte Edward M. , Wloga Dorota , Bui Khanh Huy 
Published: September 2023

AbstractCilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein regulatory complex (N-DRC), which links adjacent doublet microtubules and regulates and coordinates the activity of outer doublet complexes. Despite its critical role in cilia motility, the assembly and molecular basis of the regulatory mechanism are poorly understood. Here, using cryo-electron microscopy in conjunction with biochemical cross-linking and integrative modeling, we localize 12 DRC subunits in the N-DRC structure of Tetrahymena thermophila. We also find that the CCDC96/113 complex is in close contact with the DRC9/10 in the linker region. In addition, we reveal that the N-DRC is associated with a network of coiled-coil proteins that most likely mediates N-DRC regulatory activity.
A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis
Authors: He Ting-Ting , Xu Yun-Fan , Li Xiang , Wang Xia , Li Jie-Yu , Ou-Yang Dan , Cheng Han-Sen , Li Hao-Yang , Qin Jia , Huang Yu , Wang Hai-Yan 
Published: September 2023

AbstractCircular RNAs have been extensively studied in eukaryotes, but their presence and/or biological functionality in bacteria are unclear. Here, we show that a regulatory noncoding RNA (DucS) exists in both linear and circular conformation in Bacillus altitudinis. The linear forms promote B. altitudinis tolerance to H2O2 stress, partly through increased translation of a stress-responsive gene, htrA. The 3′ end sequences of the linear forms are crucial for RNA circularization, and formation of circular forms can decrease the levels of the regulatory linear cognates. Bioinformatic analysis of available RNA-seq datasets from 30 bacterial species revealed multiple circular RNA candidates, distinct from DucS, for all the examined species. Experiments testing for the presence of selected circular RNA candidates in four species successfully validated 7 out of 9 candidates from B. altitudinis and 4 out of 5 candidates from Bacillus paralicheniformis; However, none of the candidates tested for Bacillus subtilis and Escherichia coli were detected. Our work identifies a dual-conformation regulatory RNA in B. altitutidinis, and indicates that circular RNAs exist in diverse bacteria. However, circularization of specific RNAs does not seem to be conserved across species, and the circularization mechanisms and biological functionality of the circular forms remain unclear.
Broad-high operating temperature range and enhanced energy storage performances in lead-free ferroelectrics
Authors: Zhao Weichen , Xu Diming , Li Da , Avdeev Max , Jing Hongmei , Xu Mengkang , Guo Yan , Shi Dier , Zhou Tao , Liu Wenfeng , Wang Dong , Zhou Di 
Published: September 2023

AbstractThe immense potential of lead-free dielectric capacitors in advanced electronic components and cutting-edge pulsed power systems has driven enormous investigations and evolutions heretofore. One of the significant challenges in lead-free dielectric ceramics for energy-storage applications is to optimize their comprehensive characteristics synergistically. Herein, guided by phase-field simulations along with rational composition-structure design, we conceive and fabricate lead-free Bi0.5Na0.5TiO3-Bi0.5K0.5TiO3-Sr(Sc0.5Nb0.5)O3 ternary solid-solution ceramics to establish an equitable system considering energy-storage performance, working temperature performance, and structural evolution. A giant Wrec of 9.22 J cm−3 and an ultra-high ƞ ~ 96.3% are realized in the BNKT-20SSN ceramic by the adopted repeated rolling processing method. The state-of-the-art temperature (Wrec ≈ 8.46 ± 0.35 J cm−3, ƞ ≈ 96.4 ± 1.4%, 25–160 °C) and frequency stability performances at 500 kV cm−1 are simultaneously achieved. This work demonstrates remarkable advances in the overall energy storage performance of lead-free bulk ceramics and inspires further attempts to achieve high-temperature energy storage properties.
Regulating electrostatic phenomena by cationic polymer binder for scalable high-areal-capacity Li battery electrodes
Authors: Kim Jung-Hui , Lee Kyung Min , Kim Ji Won , Kweon Seong Hyeon , Moon Hyun-Seok , Yim Taeeun , Kwak Sang Kyu , Lee Sang-Young 
Published: September 2023

AbstractDespite the enormous interest in high-areal-capacity Li battery electrodes, their structural instability and nonuniform charge transfer have plagued practical application. Herein, we present a cationic semi-interpenetrating polymer network (c-IPN) binder strategy, with a focus on the regulation of electrostatic phenomena in electrodes. Compared to conventional neutral linear binders, the c-IPN suppresses solvent-drying-induced crack evolution of electrodes and improves the dispersion state of electrode components owing to its surface charge-driven electrostatic repulsion and mechanical toughness. The c-IPN immobilizes anions of liquid electrolytes inside the electrodes via electrostatic attraction, thereby facilitating Li+ conduction and forming stable cathode–electrolyte interphases. Consequently, the c-IPN enables high-areal-capacity (up to 20 mAh cm–2) cathodes with decent cyclability (capacity retention after 100 cycles = 82%) using commercial slurry-cast electrode fabrication, while fully utilizing the theoretical specific capacity of LiNi0.8Co0.1Mn0.1O2. Further, coupling of the c-IPN cathodes with Li-metal anodes yields double-stacked pouch-type cells with high energy content at 25 °C (376 Wh kgcell−1/1043 Wh Lcell–1, estimated including packaging substances), demonstrating practical viability of the c-IPN binder for scalable high-areal-capacity electrodes.
Human skeletal muscle tissue chip autonomous payload reveals changes in fiber type and metabolic gene expression due to spaceflight
Authors: Parafati Maddalena , Giza Shelby , Shenoy Tushar S. , Mojica-Santiago Jorge A. , Hopf Meghan , Malany Legrand K. , Platt Don , Moore Isabel , Jacobs Zachary A. , Kuehl Paul , Rexroat Jason , Barnett Gentry , Schmidt Christine E. , McLamb William T. , Clements Twyman , Coen Paul M. , Malany Siobhan 
Published: September 2023

AbstractMicrophysiological systems provide the opportunity to model accelerated changes at the human tissue level in the extreme space environment. Spaceflight-induced muscle atrophy experienced by astronauts shares similar physiological changes to muscle wasting in older adults, known as sarcopenia. These shared attributes provide a rationale for investigating molecular changes in muscle cells exposed to spaceflight that may mimic the underlying pathophysiology of sarcopenia. We report the results from three-dimensional myobundles derived from muscle biopsies from young and older adults, integrated into an autonomous CubeLab™, and flown to the International Space Station (ISS) aboard SpaceX CRS-21 as part of the NIH/NASA funded Tissue Chips in Space program. Global transcriptomic RNA-Seq analyses comparing the myobundles in space and on the ground revealed downregulation of shared transcripts related to myoblast proliferation and muscle differentiation. The analyses also revealed downregulated differentially expressed gene pathways related to muscle metabolism unique to myobundles derived from the older cohort exposed to the space environment compared to ground controls. Gene classes related to inflammatory pathways were downregulated in flight samples cultured from the younger cohort compared to ground controls. Our muscle tissue chip platform provides an approach to studying the cell autonomous effects of spaceflight on muscle cell biology that may not be appreciated on the whole organ or organism level and sets the stage for continued data collection from muscle tissue chip experimentation in microgravity. We also report on the challenges and opportunities for conducting autonomous tissue-on-chip CubeLabTMpayloads on the ISS.
Sign language experience has little effect on face and biomotion perception in bimodal bilinguals
Authors: Lammert Jessica M. , Levine Alexandra T. , Koshkebaghi Dursa , Butler Blake E. 
Published: September 2023

AbstractSensory and language experience can affect brain organization and domain-general abilities. For example, D/deaf individuals show superior visual perception compared to hearing controls in several domains, including the perception of faces and peripheral motion. While these enhancements may result from sensory loss and subsequent neural plasticity, they may also reflect experience using a visual-manual language, like American Sign Language (ASL), where signers must process moving hand signs and facial cues simultaneously. In an effort to disentangle these concurrent sensory experiences, we examined how learning sign language influences visual abilities by comparing bimodal bilinguals (i.e., sign language users with typical hearing) and hearing non-signers. Bimodal bilinguals and hearing non-signers completed online psychophysical measures of face matching and biological motion discrimination. No significant group differences were observed across these two tasks, suggesting that sign language experience is insufficient to induce perceptual advantages in typical-hearing adults. However, ASL proficiency (but not years of experience or age of acquisition) was found to predict performance on the motion perception task among bimodal bilinguals. Overall, the results presented here highlight a need for more nuanced study of how linguistic environments, sensory experience, and cognitive functions impact broad perceptual processes and underlying neural correlates.
Clinical significance of MATN1-AS1 as ceRNA of Mir-200b in tissues and serum of patients with cervical cancer
Authors: He Lijie , Li Pu , Zhang Heping 
Published: September 2023

AbstractTo analyze the clinical significance of MATN1-AS1 as ceRNA of Mir-200b in the tissues and serum of cervical cancer patients. A total of 50 patients with cervical cancer admitted to our hospital from March 2018 to March 2019 were selected as the research objects. All patients underwent surgical resection of cancer tissues in our hospital, and cervical cancer tissues and adjacent tissues more than 2 cm away from the edge of cancer tissues were retained. Patients with cervical cancer were selected as the research group, and 50 patients with benign uterine lesions were selected as the control group. The expressions of MATN1-AS1 and Mir-200b in cervical cancer tissues and serum were detected by real-time PCR, and the correlation between MATN1-AS1 and Mir-200b was analyzed. The relationship between MATN1-AS1, Mir-200b and clinical features was analyzed, and the 3-year survival rate of cervical cancer patients was analyzed. Compared with adjacent tissues, the relative expression levels of MATN1-AS1 and Mir-200b in cancer tissues were significantly increased (P < 0.05). Compared with the control group, the relative expression levels of MATN1-AS1 and mir-200b in the study group were increased (P < 0.05). The expression levels of matn1-as1 and mir-200b were higher in poorly differentiated, tumor ≥ 4 cm, FIGO stage iii–iv, and lymph node metastasis patients (P < 0.05). Correlation analysis showed that MATN1-AS1 was positively correlated with Mir-200b (r = 0.625, P = 0.001). Compared with blank control group, the relative expression levels of MATN1-AS1 and Mir-200b in MATN1-AS1 silencing group were decreased (P < 0.05). The 3-year survival rate of 48 patients with cervical cancer was 66.67% (32/48). The survival rate of patients with high expression of MATN1-AS1 was lower than that of patients with low expression of MATN1-AS1, and the survival rate of patients with high expression of Mir-200b was lower than that of patients with low expression of Mir-200b (x2 = 4.251, 5.244, P = 0.011, 0.008). There is a potential binding point between MATN1-AS1 and Mir-200b. The expressions of MATN1-AS1 and Mir-200b are increased in the tissues and serum of cervical cancer patients, and they are positively correlated. Silencing of MATN1-AS1 in cervical cancer cell lines can reduce the expression of Mir-200b. Matn1-as1 can regulate the expression of Mir-200b and participate in the occurrence and development of cervical cancer.
ChatGPT in education: global reactions to AI innovations
Authors: Fütterer Tim , Fischer Christian , Alekseeva Anastasiia , Chen Xiaobin , Tate Tamara , Warschauer Mark , Gerjets Peter 
Published: September 2023

AbstractThe release and rapid diffusion of ChatGPT have caught the attention of educators worldwide. Some educators are enthusiastic about its potential to support learning. Others are concerned about how it might circumvent learning opportunities or contribute to misinformation. To better understand reactions about ChatGPT concerning education, we analyzed Twitter data (16,830,997 tweets from 5,541,457 users). Based on topic modeling and sentiment analysis, we provide an overview of global perceptions and reactions to ChatGPT regarding education. ChatGPT triggered a massive response on Twitter, with education being the most tweeted content topic. Topics ranged from specific (e.g., cheating) to broad (e.g., opportunities), which were discussed with mixed sentiment. We traced that authority decisions may influence public opinions. We discussed that the average reaction on Twitter (e.g., using ChatGPT to cheat in exams) differs from discussions in which education and teaching–learning researchers are likely to be more interested (e.g., ChatGPT as an intelligent learning partner). This study provides insights into people's reactions when new groundbreaking technology is released and implications for scientific and policy communication in rapidly changing circumstances.
Alteration of microbial composition in the skin and blood in vasculitis
Authors: Miyata Ryujin , Miyabe Chie , Oki Hiroya , Motooka Daisuke , Nakamura Shota , Miyabe Yoshishige , Takenaka Yuko , Fukuya Yasuko , Yudo Kazuo , Ishiguro Naoko 
Published: September 2023

AbstractVasculitis is a systemic autoimmune disease characterized by leukocyte infiltration into blood vessels. Various microorganisms have been associated with the pathogenesis of vasculitis; however, the causal microbial agents and underlying mechanisms are not fully understood, possibly because of the technical limitations of pathogen detection. In the present study, we characterized the microbiome profile of patients with cutaneous vasculitis using comprehensive metagenome shotgun sequencing. We found that the abundance of the SEN virus was increased in the affected skin and serum of patients with vasculitis compared to healthy donors. In particular, the abundance of SEN virus reads was increased in the sera of patients with cutaneous arteritis. Among the bacteria identified, Corynebacteriales was the most differentially associated with vasculitis. Linear discriminant analysis effect size also indicated differences in the microbial taxa between patients with vasculitis and healthy donors. These findings demonstrate that vasculitis is associated with considerable alteration of the microbiome in the blood and skin and suggest a role for the infectious trigger in vasculitis.
Risk of long COVID main symptoms after SARS-CoV-2 infection: a systematic review and meta-analysis
Authors: Marjenberg Zoe , Leng Sean , Tascini Carlo , Garg Megha , Misso Kate , El Guerche Seblain Clotilde , Shaikh Nabila 
Published: September 2023

AbstractThis review aimed to summarise the relative risk (RR) of the main symptoms of long COVID in people infected with SARS-CoV-2 compared to uninfected controls, as well as the difference in health-related quality of life (HRQoL) after infection. MEDLINE, EMBASE, PubMed, NLM-LitCovid, WHO-COVID-19, arXiv and Europe-PMC were searched up to 23rd March 2022. Studies reporting risk (four or more weeks after infection) of fatigue, shortness of breath, and cognitive dysfunction, as well as comparative HRQoL outcomes, were included. Pairwise random-effects meta-analyses were performed to pool risks of individual symptoms. Thirty-three studies were identified; twenty studies reporting symptom risks were included in the meta-analyses. Overall, infection with SARS-CoV-2 carried significantly higher risk of fatigue (RR 1.72, 95% confidence intervals [CIs] 1.41, 2.10), shortness of breath (RR 2.60, 95% CIs 1.96, 3.44), memory difficulties (RR 2.53, 95% CIs 1.30, 4.93), and concentration difficulties (RR 2.14, 95% CIs 1.25, 3.67). Quality of life findings were varied and comparisons between studies were challenging due to different HRQoL instruments used and study heterogeneity, although studies indicated that severe hospitalised COVID is associated with a significantly poorer HRQoL after infection. These risks are likely to constantly change as vaccines, reinfections, and new variants alter global immunity.