bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiotherapy remodels the tumor microenvironment for enhancing immunotherapeutic sensitivity
Authors: Liu Senbo , Wang Wenkang , Hu Shengyun , Jia Bin , Tuo Baojing , Sun Haifeng , Wang Qiming , Liu Yang , Sun Zhenqiang 
Published: October 2023

AbstractCancer immunotherapy has transformed traditional treatments, with immune checkpoint blockade being particularly prominent. However, immunotherapy has minimal benefit for patients in most types of cancer and is largely ineffective in some cancers (such as pancreatic cancer and glioma). A synergistic anti-tumor response may be produced through the combined application with traditional tumor treatment methods. Radiotherapy (RT) not only kills tumor cells but also triggers the pro-inflammatory molecules’ release and immune cell infiltration, which remodel the tumor microenvironment (TME). Therefore, the combination of RT and immunotherapy is expected to achieve improved efficacy. In this review, we summarize the effects of RT on cellular components of the TME, including T cell receptor repertoires, different T cell subsets, metabolism, tumor-associated macrophages and other myeloid cells (dendritic cells, myeloid-derived suppressor cells, neutrophils and eosinophils). Meanwhile, non-cellular components such as lactate and extracellular vesicles are also elaborated. In addition, we discuss the impact of different RT modalities on tumor immunity and issues related to the clinical practice of combination therapy.
The risk of withdrawal from hypertension treatment in coastal areas after the Great East Japan Earthquake: the TMM CommCohort Study
Authors: Hatanaka Rieko , Nakaya Naoki , Kogure Mana , Nakaya Kumi , Chiba Ippei , Kanno Ikumi , Hashimoto Hideaki , Nakamura Tomohiro , Nochioka Kotaro , Obara Taku , Hamanaka Yohei , Sugawara Junichi , Kobayashi Tomoko , Uruno Akira , Kodama Eiichi N. , Fuse Nobuo , Kuriyama Shinichi , Hozawa Atsushi 
Published: October 2023

AbstractThis study aimed to examine whether risk of withdrawal from HTTx was higher in coastal areas that were severely damaged by tsunami than in inland areas. We conducted a cross-sectional study of 9218 participants aged ≥20 years in Miyagi, Japan. The odds ratios (ORs) and confidence interval (CI) for withdrawal from HTTx in coastal and inland groups were compared using multivariate logistic regression analysis, adjusting for potential confounders. In total, 194 of 5860 and 146 of 3358 participants in the inland and coastal groups, respectively, withdrew from HTTx treatment. OR (95%CI) of withdrawal from HTTx in the coastal group was 1.46 (1.14–1.86) compared to the inland group. According to housing damage, ORs (95% CI) in the no damage, partially destroyed, and more than half destroyed coastal groups compared with the no damage inland group were 1.62 (1.04–2.50), 1.69 (1.17–2.45), and 1.08 (0.71–1.65), respectively. In conclusion, the risk of HTTx withdrawal for participants whose homes in coastal areas were relatively less damaged was significantly higher compared with those in inland areas, while the risk of HTTx withdrawal for participants whose homes were more than half destroyed was not. Post-disaster administrative support for disaster victims is considered vital for continuation of their treatment.
Terahertz radiation by quantum interference of excitons in a one-dimensional Mott insulator
Authors: Miyamoto Tatsuya , Kondo Akihiro , Inaba Takeshi , Morimoto Takeshi , You Shijia , Okamoto Hiroshi 
Published: October 2023

AbstractNearly monocyclic terahertz waves are used for investigating elementary excitations and for controlling electronic states in solids. They are usually generated via second-order optical nonlinearity by injecting a femtosecond laser pulse into a nonlinear optical crystal. In this framework, however, it is difficult to control phase and frequency of terahertz waves. Here, we show that in a one-dimensional Mott insulator of a nickel-bromine chain compound a terahertz wave is generated with high efficiency via strong electron modulations due to quantum interference between odd-parity and even-parity excitons produced by two-color femtosecond pulses. Using this method, one can control all of the phase, frequency, and amplitude of terahertz waves by adjusting the creation-time difference of two excitons with attosecond accuracy. This approach enables to evaluate the phase-relaxation time of excitons under strong electron correlations in Mott insulators. Moreover, phase- and frequency-controlled terahertz pulses are beneficial for coherent electronic-state controls with nearly monocyclic terahertz waves.
High-Q lasing via all-dielectric Bloch-surface-wave platform
Authors: Lee Yang-Chun , Ho Ya-Lun , Lin Bo-Wei , Chen Mu-Hsin , Xing Di , Daiguji Hirofumi , Delaunay Jean-Jacques 
Published: October 2023

AbstractControlling the propagation and emission of light via Bloch surface waves (BSWs) has held promise in the field of on-chip nanophotonics. BSW-based optical devices are being widely investigated to develop on-chip integration systems. However, a coherent light source that is based on the stimulated emission of a BSW mode has yet to be developed. Here, we demonstrate lasers based on a guided BSW mode sustained by a gain-medium guiding structure microfabricated on the top of a BSW platform. A long-range propagation length of the BSW mode and a high-quality lasing emission of the BSW mode are achieved. The BSW lasers possess a lasing threshold of 6.7 μJ/mm2 and a very narrow linewidth reaching a full width at half maximum as small as 0.019 nm. Moreover, the proposed lasing scheme exhibits high sensitivity to environmental changes suggesting the applicability of the proposed BSW lasers in ultra-sensitive devices.
Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies
Authors: Karna Deepak , Mano Eriko , Ji Jiahao , Kawamata Ibuki , Suzuki Yuki , Mao Hanbin 
Published: October 2023

AbstractThe intrinsic complexity of many mesoscale (10–100 nm) cellular machineries makes it challenging to elucidate their topological arrangement and transition dynamics. Here, we exploit DNA origami nanospring as a model system to demonstrate that tens of piconewton linear force can modulate higher-order conformation dynamics of mesoscale molecular assemblies. By switching between two chemical structures (i.e., duplex and tetraplex DNA) in the junctions of adjacent origami modules, the corresponding stretching or compressing chemo-mechanical stress reversibly flips the backbone orientations of the DNA nanosprings. Both coarse-grained molecular dynamics simulations and atomic force microscopy measurements reveal that such a backbone conformational switch does not alter the right-handed chirality of the nanospring helix. This result suggests that mesoscale helical handedness may be governed by the torque, rather than the achiral orientation, of nanospring backbones. It offers a topology-based caging/uncaging concept to present chemicals in response to environmental cues in solution.
Structure of the transcription open complex of distinct σI factors
Authors: Li Jie , Zhang Haonan , Li Dongyu , Liu Ya-Jun , Bayer Edward A. , Cui Qiu , Feng Yingang , Zhu Ping 
Published: October 2023

AbstractBacterial σI factors of the σ70-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σI paralogues in some cellulolytic bacteria have been shown to be responsible for the regulation of the cellulosome, a multienzyme complex that mediates efficient cellulose degradation. Here, we report two structures at 3.0 Å and 3.3 Å of two transcription open complexes formed by two σI factors, SigI1 and SigI6, respectively, from the thermophilic, cellulolytic bacterium, Clostridium thermocellum. These structures reveal a unique, hitherto-unknown recognition mode of bacterial transcriptional promoters, both with respect to domain organization and binding to promoter DNA. The key characteristics that determine the specificities of the σI paralogues were further revealed by comparison of the two structures. Consequently, the σI factors represent a distinct set of the σ70-family σ factors, thus highlighting the diversity of bacterial transcription.
Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication
Authors: Chakraborty Chaitali , Nissen Itzel , Vincent Craig A. , Hägglund Anna-Carin , Hörnblad Andreas , Remeseiro Silvia 
Published: October 2023

AbstractChromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regulatory landscape of glioblastoma, the most aggressive primary brain tumour. Our data reveals profound rewiring of promoter-enhancer interactions, chromatin accessibility and redistribution of histone marks in glioblastoma. This leads to loss of long-range regulatory interactions and overall activation of promoters, which orchestrate changes in the expression of genes associated to glutamatergic synapses, axon guidance, axonogenesis and chromatin remodelling. SMAD3 and PITX1 emerge as major transcription factors controlling genes related to synapse organization and axon guidance. Inhibition of SMAD3 and neuronal activity stimulation cooperate to promote proliferation of glioblastoma cells in co-culture with glutamatergic neurons, and in mice bearing patient-derived xenografts. Our findings provide mechanistic insight into the regulatory networks that mediate neurogliomal synaptic communication.
Hyperbranched polymer functionalized flexible perovskite solar cells with mechanical robustness and reduced lead leakage
Authors: Li Zhihao , Jia Chunmei , Wan Zhi , Xue Jiayi , Cao Junchao , Zhang Meng , Li Can , Shen Jianghua , Zhang Chao , Li Zhen 
Published: October 2023

AbstractPerovskite solar cells (PSCs) are multilayer structures. The interface between electron transport layer and perovskite is the mechanical weakest point in flexible PSCs due to its low fracture energy. Herein, we develop a highly adhesive polyamide-amine-based hyperbranched polymers to reinforce the interface. The interface fracture energy is improved from 1.08 to 2.13 J·m−2 by the hyperbranched polymers with adhesive groups and dynamic hydrogen bond networks. The polymer functionalized perovskite solar cells achieve superior power conversion efficiencies of 25.05% and 23.86% for rigid and flexible devices, respectively. Furthermore, the hyperbranched polymer contains abundant intramolecular cavities that can capture Pb2+. Pb leakage after solar cell damage is effectively suppressed. Our findings provide insights on designing adhesive interface layers towards high-efficiency, mechanical-stable and environment-friendly flexible perovskite solar cells.
A systematic study of key elements underlying molecular property prediction
Authors: Deng Jianyuan , Yang Zhibo , Wang Hehe , Ojima Iwao , Samaras Dimitris , Wang Fusheng 
Published: October 2023

AbstractArtificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property prediction remain largely unexplored, which impedes further advancements in this field. Herein, we conduct an extensive evaluation of representative models using various representations on the MoleculeNet datasets, a suite of opioids-related datasets and two additional activity datasets from the literature. To investigate the predictive power in low-data and high-data space, a series of descriptors datasets of varying sizes are also assembled to evaluate the models. In total, we have trained 62,820 models, including 50,220 models on fixed representations, 4200 models on SMILES sequences and 8400 models on molecular graphs. Based on extensive experimentation and rigorous comparison, we show that representation learning models exhibit limited performance in molecular property prediction in most datasets. Besides, multiple key elements underlying molecular property prediction can affect the evaluation results. Furthermore, we show that activity cliffs can significantly impact model prediction. Finally, we explore into potential causes why representation learning models can fail and show that dataset size is essential for representation learning models to excel.
Overcrowding induces fast colloidal solitons in a slowly rotating potential landscape
Authors: Cereceda-López Eric , Antonov Alexander P. , Ryabov Artem , Maass Philipp , Tierno Pietro 
Published: October 2023

AbstractCollective particle transport across periodic energy landscapes is ubiquitously present in many condensed matter systems spanning from vortices in high-temperature superconductors, frictional atomic sliding, driven skyrmions to biological and active matter. Here we report the emergence of fast solitons propagating against a rotating optical landscape. These experimentally observed solitons are stable cluster waves that originate from a coordinated particle exchange process which occurs when the number of trapped microparticles exceeds the number of potential wells. The size and speed of individual solitons rapidly increase with the particle diameter as predicted by theory and confirmed by numerical simulations. We show that when several solitons coexist, an effective repulsive interaction can stabilize their propagation along the periodic potential. Our experiments demonstrate a generic mechanism for cluster-mediated transport with potential applications to condensed matter systems on different length scales.
Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility
Authors: Dorn Georg , Gmeiner Christoph , de Vries Tebbe , Dedic Emil , Novakovic Mihajlo , Damberger Fred F. , Maris Christophe , Finol Esteban , Sarnowski Chris P. , Kohlbrecher Joachim , Welsh Timothy J. , Bolisetty Sreenath , Mezzenga Raffaele , Aebersold Ruedi , Leitner Alexander , Yulikov Maxim , Jeschke Gunnar , Allain Frédéric H.-T. 
Published: October 2023

AbstractRNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
Moisture control of tropical cyclones in high-resolution simulations of paleoclimate and future climate
Authors: Raavi Pavan Harika , Chu Jung-Eun , Timmermann Axel , Lee Sun-Seon , Walsh Kevin J. E. 
Published: October 2023

AbstractThe intensity of tropical cyclones (TCs) is expected to increase in response to greenhouse warming. However, how future climate change will affect TC frequencies and tracks is still under debate. Here, to further elucidate the underlying sensitivities and mechanisms, we study TCs response to different past and future climate forcings. Using a high-resolution TC-resolving global Earth system model with 1/4° atmosphere and 1/10° ocean resolution, we conducted a series of paleo-time-slice and future greenhouse warming simulations targeting the last interglacial (Marine Isotope Stage (MIS) 5e, 125 ka), glacial sub-stage MIS5d (115 ka), present-day (PD), and CO2 doubling (2×CO2) conditions. Our analysis reveals that precessional forcing created an interhemispheric difference in simulated TC densities, whereas future CO2 forcing impacts both hemispheres in the same direction. In both cases, we find that TC genesis frequency, density, and intensity are primarily controlled by changes in tropospheric thermal and moisture structure, exhibiting a clear reduction in TC genesis density in warmer hemispheres.
PPTC7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy
Authors: Niemi Natalie M. , Serrano Lia R. , Muehlbauer Laura K. , Balnis Catherine E. , Wei Lianjie , Smith Andrew J. , Kozul Keri-Lyn , Forny Merima , Connor Olivia M. , Rashan Edrees H. , Shishkova Evgenia , Schueler Kathryn L. , Keller Mark P. , Attie Alan D. , Friedman Jonathan R. , Pagan Julia K. , Coon Joshua J. , Pagliarini David J. 
Published: October 2023

AbstractPPTC7 is a resident mitochondrial phosphatase essential for maintaining proper mitochondrial content and function. Newborn mice lacking Pptc7 exhibit aberrant mitochondrial protein phosphorylation, suffer from a range of metabolic defects, and fail to survive beyond one day after birth. Using an inducible knockout model, we reveal that loss of Pptc7 in adult mice causes marked reduction in mitochondrial mass and metabolic capacity with elevated hepatic triglyceride accumulation. Pptc7 knockout animals exhibit increased expression of the mitophagy receptors BNIP3 and NIX, and Pptc7-/- mouse embryonic fibroblasts (MEFs) display a major increase in mitophagy that is reversed upon deletion of these receptors. Our phosphoproteomics analyses reveal a common set of elevated phosphosites between perinatal tissues, adult liver, and MEFs, including multiple sites on BNIP3 and NIX, and our molecular studies demonstrate that PPTC7 can directly interact with and dephosphorylate these proteins. These data suggest that Pptc7 deletion causes mitochondrial dysfunction via dysregulation of several metabolic pathways and that PPTC7 may directly regulate mitophagy receptor function or stability. Overall, our work reveals a significant role for PPTC7 in the mitophagic response and furthers the growing notion that management of mitochondrial protein phosphorylation is essential for ensuring proper organelle content and function.
Structural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410
Authors: Remm Sille , De Vecchis Dario , Schöppe Jendrik , Hutter Cedric A. J. , Gonda Imre , Hohl Michael , Newstead Simon , Schäfer Lars V. , Seeger Markus A. 
Published: October 2023

AbstractMycobacterium tuberculosis is protected from antibiotic therapy by a multi-layered hydrophobic cell envelope. Major facilitator superfamily (MFS) transporter Rv1410 and the periplasmic lipoprotein LprG are involved in transport of triacylglycerides (TAGs) that seal the mycomembrane. Here, we report a 2.7 Å structure of a mycobacterial Rv1410 homologue, which adopts an outward-facing conformation and exhibits unusual transmembrane helix 11 and 12 extensions that protrude ~20 Å into the periplasm. A small, very hydrophobic cavity suitable for lipid transport is constricted by a functionally important ion-lock likely involved in proton coupling. Combining mutational analyses and MD simulations, we propose that TAGs are extracted from the core of the inner membrane into the central cavity via lateral clefts present in the inward-facing conformation. The functional role of the periplasmic helix extensions is to channel the extracted TAG into the lipid binding pocket of LprG.
Developmental atlas of phase-amplitude coupling between physiologic high-frequency oscillations and slow waves
Authors: Sakakura Kazuki , Kuroda Naoto , Sonoda Masaki , Mitsuhashi Takumi , Firestone Ethan , Luat Aimee F. , Marupudi Neena I. , Sood Sandeep , Asano Eishi 
Published: October 2023

AbstractWe investigated the developmental changes in high-frequency oscillation (HFO) and Modulation Index (MI) – the coupling measure between HFO and slow-wave phase. We generated normative brain atlases, using subdural EEG signals from 8251 nonepileptic electrode sites in 114 patients (ages 1.0–41.5 years) who achieved seizure control following resective epilepsy surgery. We observed a higher MI in the occipital lobe across all ages, and occipital MI increased notably during early childhood. The cortical areas exhibiting MI co-growth were connected via the vertical occipital fasciculi and posterior callosal fibers. While occipital HFO rate showed no significant age-association, the temporal, frontal, and parietal lobes exhibited an age-inversed HFO rate. Assessment of 1006 seizure onset sites revealed that z-score normalized MI and HFO rate were higher at seizure onset versus nonepileptic electrode sites. We have publicly shared our intracranial EEG data to enable investigators to validate MI and HFO-centric presurgical evaluations to identify the epileptogenic zone.
Species-specific metabolic reprogramming in human and mouse microglia during inflammatory pathway induction
Authors: Sabogal-Guáqueta Angélica María , Marmolejo-Garza Alejandro , Trombetta-Lima Marina , Oun Asmaa , Hunneman Jasmijn , Chen Tingting , Koistinaho Jari , Lehtonen Sarka , Kortholt Arjan , Wolters Justina C. , Bakker Barbara M. , Eggen Bart J. L. , Boddeke Erik , Dolga Amalia 
Published: October 2023

AbstractMetabolic reprogramming is a hallmark of the immune cells in response to inflammatory stimuli. This metabolic process involves a switch from oxidative phosphorylation (OXPHOS) to glycolysis or alterations in other metabolic pathways. However, most of the experimental findings have been acquired in murine immune cells, and little is known about the metabolic reprogramming of human microglia. In this study, we investigate the transcriptomic, proteomic, and metabolic profiles of mouse and iPSC-derived human microglia challenged with the TLR4 agonist LPS. We demonstrate that both species display a metabolic shift and an overall increased glycolytic gene signature in response to LPS treatment. The metabolic reprogramming is characterized by the upregulation of hexokinases in mouse microglia and phosphofructokinases in human microglia. This study provides a direct comparison of metabolism between mouse and human microglia, highlighting the species-specific pathways involved in immunometabolism and the importance of considering these differences in translational research.