bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deacetylated MDH1 and IDH1 aggravates PANoptosis in acute liver failure through endoplasmic reticulum stress signaling
Authors: Shi Chunxia , Wang Yukun , Guo Jin , Zhang Danmei , Zhang Yanqiong , Gong Zuojiong 
Published: June 2024

AbstractAcute liver failure (ALF) is a disease with a high mortality rate and poor prognosis, whose pathogenesis is not fully understood. PANoptosis is a recently proposed mode of cell death characterized by pyroptosis, apoptosis, and necroptosis, but it cannot be explained by any of them alone. This study aims to explore the role of PANoptosis in ALF and the impact and mechanism of deacetylated malate dehydrogenase 1 (MDH1) and isocitrate dehydrogenase 1 (IDH1) on PANoptosis. Our results found that, compared with the control group, the cell viability in the lipopolysaccharide (LPS)/D-galactosamine (D-Gal) group decreased, lactate dehydrogenase (LDH) release increased, cell death increased, and the levels of PANoptosis-related molecules RIPK1, GSDMD, caspase-3, MLKL, IL-18, IL-1β increased, indicating that PANoptosis increased during ALF. Deacetylated MDH1 at K118 and IDH1 at K93 increased the expression of PANoptosis-related molecules RIPK1, GSDMD, caspase-3, MLKL, IL-18, and IL-1β in vivo and in vitro. The deacetylation weakened the inhibitory effect of histone deacetylase (HDAC) inhibitor ACY1215 on PANoptosis-related molecules, suggesting that deacetylated MDH1 at K118 and IDH1 at K93 aggravated PANoptosis during ALF. Deacetylated MDH1 at K118 and IDH1 at K93 also promoted the expression of endoplasmic reticulum stress-related molecules BIP, ATF6, XBP1, and CHOP in vivo and in vitro. The use of endoplasmic reticulum stress inhibitor 4-PBA weakened the promotion effect of deacetylated MDH1 K118 and IDH1 K93 on PANoptosis. The results suggested that deacetylated MDH1 at K118 and IDH1 at K93 may aggravate PANoptosis in ALF through endoplasmic reticulum stress signaling. In conclusion, deacetylated MDH1 and IDH1 may aggravate PANoptosis in ALF, and the mechanism may act through endoplasmic reticulum stress signaling.
Quantum coherence and interference of a single moiré exciton in nano-fabricated twisted monolayer semiconductor heterobilayers
Authors: Wang Haonan , Kim Heejun , Dong Duanfei , Shinokita Keisuke , Watanabe Kenji , Taniguchi Takashi , Matsuda Kazunari 
Published: June 2024

AbstractThe moiré potential serves as a periodic quantum confinement for optically generated excitons, creating spatially ordered zero-dimensional quantum systems. However, a broad emission spectrum resulting from inhomogeneity among moiré potentials hinders the investigation of their intrinsic properties. In this study, we demonstrated a method for the optical observation of quantum coherence and interference of a single moiré exciton in a twisted semiconducting heterobilayer beyond the diffraction limit of light. We observed a single and sharp photoluminescence peak from a single moiré exciton following nanofabrication. Our findings revealed the extended duration of quantum coherence in a single moiré exciton, persisting beyond 10 ps, and an accelerated decoherence process with increasing temperature and excitation power density. Moreover, quantum interference experiments revealed the coupling between moiré excitons in different moiré potential minima. The observed quantum coherence and interference of moiré exciton will facilitate potential applications of moiré quantum systems in quantum technologies.
Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state
Authors: Jaiswal Vishal Kumar , Aranda Ruiz Daniel , Petropoulos Vasilis , Kabaciński Piotr , Montorsi Francesco , Uboldi Lorenzo , Ugolini Simone , Mukamel Shaul , Cerullo Giulio , Garavelli Marco , Santoro Fabrizio , Nenov Artur 
Published: June 2024

AbstractExcitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54±11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.
Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates
Authors: Cheng Zhuo , He Bei-Bei , Lei Kangfan , Gao Ying , Shi Yuqi , Zhong Zheng , Liu Hongyan , Liu Runze , Zhang Haili , Wu Song , Zhang Wenxuan , Tang Xiaoyu , Li Yong-Xin 
Published: June 2024

AbstractAntimicrobial resistance remains a significant global threat, driving up mortality rates worldwide. Ribosomally synthesized and post-translationally modified peptides have emerged as a promising source of novel peptide antibiotics due to their diverse chemical structures. Here, we report the discovery of new aminovinyl-(methyl)cysteine (Avi(Me)Cys)-containing peptide antibiotics through a synergistic approach combining biosynthetic rule-based omics mining and heterologous expression. We first bioinformatically identify 1172 RiPP biosynthetic gene clusters (BGCs) responsible for Avi(Me)Cys-containing peptides formation from a vast pool of over 50,000 bacterial genomes. Subsequently, we successfully establish the connection between three identified BGCs and the biosynthesis of five peptide antibiotics via biosynthetic rule-guided metabolic analysis. Notably, we discover a class V lanthipeptide, massatide A, which displays excellent activity against gram-positive pathogens, including drug-resistant clinical isolates like linezolid-resistantS. aureusand methicillin-resistantS. aureus, with a minimum inhibitory concentration of 0.25 μg/mL. The remarkable performance of massatide A in an animal infection model, coupled with a relatively low risk of resistance and favorable safety profile, positions it as a promising candidate for antibiotic development. Our study highlights the potential of Avi(Me)Cys-containing peptides in expanding the arsenal of antibiotics against multi-drug-resistant bacteria, offering promising drug leads in the ongoing battle against infectious diseases.
Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals
Authors: Kong Deqiang , Zhou Yang , Wei Yu , Wang Xinyi , Huang Qin , Gao Xianyun , Wan Hang , Liu Mengyao , Kang Liping , Yu Guiling , Yin Jianli , Guan Ningzi , Ye Haifeng 
Published: June 2024

AbstractSynthetic biology applications require finely tuned gene expression, often mediated by synthetic transcription factors (sTFs) compatible with the human genome and transcriptional regulation mechanisms. While various DNA-binding and activation domains have been developed for different applications, advanced artificially controllable sTFs with improved regulatory capabilities are required for increasingly sophisticated applications. Here, in mammalian cells and mice, we validate the transactivator function and homo-/heterodimerization activity of the plant-derived phytochrome chaperone proteins, FHY1 and FHL. Our results demonstrate that FHY1/FHL form a photosensing transcriptional regulation complex (PTRC) through interaction with the phytochrome, ΔPhyA, that can toggle between active and inactive states through exposure to red or far-red light, respectively. Exploiting this capability, we develop a light-switchable platform that allows for orthogonal, modular, and tunable control of gene transcription, and incorporate it into a PTRC-controlled CRISPRa system (PTRCdcas) to modulate endogenous gene expression. We then integrate the PTRC with small molecule- or blue light-inducible regulatory modules to construct a variety of highly tunable systems that allow rapid and reversible control of transcriptional regulation in vitro and in vivo. Validation and deployment of these plant-derived phytochrome chaperone proteins in a PTRC platform have produced a versatile, powerful tool for advanced research and biomedical engineering applications.
Group-theoretic error mitigation enabled by classical shadows and symmetries
Authors: Zhao Andrew , Miyake Akimasa 
Published: June 2024

AbstractEstimating expectation values is a key subroutine in quantum algorithms. Near-term implementations face two major challenges: a limited number of samples required to learn a large collection of observables, and the accumulation of errors in devices without quantum error correction. To address these challenges simultaneously, we develop a quantum error-mitigation strategy called symmetry-adjusted classical shadows, by adjusting classical-shadow tomography according to how symmetries are corrupted by device errors. As a concrete example, we highlight global U(1) symmetry, which manifests in fermions as particle number and in spins as total magnetization, and illustrate their group-theoretic unification with respective classical-shadow protocols. We establish rigorous sampling bounds under readout errors obeying minimal assumptions, and perform numerical experiments with a more comprehensive model of gate-level errors derived from existing quantum processors. Our results reveal symmetry-adjusted classical shadows as a low-cost strategy to mitigate errors from noisy quantum experiments in the ubiquitous presence of symmetry.
Chlorophyll a in lakes and streams of the United States (2005–2022)
Authors: Spaulding Sarah A. , Platt Lindsay R. C. , Murphy Jennifer C. , Covert Alex , Harvey Judson W. 
Published: June 2024

AbstractThe concentration of chlorophyll a in phytoplankton and periphyton represents the amount of algal biomass. We compiled an 18-year record (2005–2022) of pigment data from water bodies across the United States (US) to support efforts to develop process-based, machine learning, and remote sensing models for prediction of harmful algal blooms (HABs). To our knowledge, this dataset of nearly 84,000 sites and over 1,374,000 pigment measurements is the largest compilation of harmonized discrete, laboratory-extracted chlorophyll data for the US. These data were compiled from the Water Quality Portal (WQP) and previously unpublished U.S. Geological Survey’s National Water Quality Laboratory (NWQL) data. Data were harmonized for reporting units, pigment type, duplicate values, collection depth, site name, negative values, and some extreme values. Across the country, data show great variation by state in sampling frequency, distribution, and methods. Uses for such data include the calibration of models, calibration of field sensors, examination of relationship to nutrients and other drivers, evaluation of temporal trends, and other applications addressing local to national scale concerns.
Comprehensive Dataset on Electrical Load Profiles for Energy Community in Ireland
Authors: Trivedi Rohit , Bahloul Mohamed , Saif Aziz , Patra Sandipan , Khadem Shafi 
Published: June 2024

AbstractThis paper describes a comprehensive energy-related dataset, collected from residential electricity households within an energy community in Ireland, as part of StoreNet project. The data includes local weather parameters and per household power (W) and energy (Wh) components for various aspects such as active power consumption, PV generation, grid import and export, charging and discharging, and the state of charge of energy storage. Additionally, it provides weather data for the location at a 1-minute temporal resolution for the year 2020. The dataset has been validated by comparing measurements that should yield identical results to standard load profiles, with no significant inconsistencies discovered. Validation examples have also been given through the published articles where this dataset has been used to analyse peer-to-peer energy trading benefits for the energy community and decision-making support for aggregators. The dataset aids in understanding patterns in electrical load curves and the duty cycle of energy storage within an energy community. Furthermore, it can assist in comprehending the impact on distribution networks caused by distributed energy storage.
MEDUSA: Marine benthic Ecological Data from Underwater imagery Surveys of sub-Antarctic Crozet environments
Authors: Lelièvre Yann , Motreuil Sébastien , Specq Léa , Marschal Christian , Dubois Philippe , Wauters Lisa , Guéné Mathilde , Saucède Thomas 
Published: June 2024

AbstractInscribed on the UNESCO World Heritage list, the sub-Antarctic Crozet archipelago is located in a region facing significant environmental changes impacting a poorly known marine biodiversity. Underwater imagery constitutes a valuable non-invasive approach for gathering ecological data and improving our knowledge of ecosystems’ vulnerability. We here compiled two datasets, encompassing 17 video-imagery surveys of Crozet nearshore environments conducted in 2021 and 2022 at two sites of Ile de la Possession: Baie du Marin and Crique du Sphinx. Faunal abundance and algal cover data related to each survey are also provided. A total of 755 images were analysed, comprising 52 faunal and 14 algal taxa identified in 2021, as well as 45 faunal and 14 algal taxa identified in 2022. Video-transects were performed in shallow waters by scuba divers using a GoPro®HERO7 multiple camera set-up, and in deeper waters using a remotely operated vehicle. These data provide a first baseline for biodiversity and ecosystem studies, and for monitoring the long-term dynamics of Crozet benthic habitats facing natural and anthropogenic disturbances.
Targeting the ZMIZ1-Notch1 signaling axis for the treatment of tongue squamous cell carcinoma
Authors: Pang Yunqing , Sun Yunjie , Wu Yuyan , Li Jiamin , Qin Pingchuan , Guo Shanchuan , Zhou Wenlian , Chen Jian , Wang Jing 
Published: June 2024

AbstractZinc finger MIZ-type containing 1 (ZMIZ1) is a transcriptional coactivator related to the protein inhibitors of activated STATs (PIAS) family. Mounting evidence suggests that ZMIZ1 plays a crucial role in the occurrence and development of cancers. The function of ZMIZ1 in tongue squamous cell carcinoma (TSCC) and the mechanisms underpinning its role in this disease have not been fully clarified. We performed qualitative ZMIZ1 protein expression analyses using immunohistochemistry in 20 patient-derived, paraffin-embedded TSCC tissue sections. We used RNAi to knock down ZMIZ1 expression in the CAL-27 TSCC cell line and quantified the impact of ZMIZ1 knock down on proliferation, migration and apoptosis via CCK-8, scratch assay and flow cytometry, respectively. We used qRT-PCR and western blotting to investigate the role of ZMIZ1 in this cell line. Finally, we established a model of lung metastasis in nude mice to replicate the in vitro results. ZMIZ1 protein was significantly more abundant in TSCC case tissue samples. ZMIZ1 knockdown reduced the invasion and metastases of TSCC tumor cells and promoted apoptosis. ZMIZ1 knockdown was associated with the down-regulation of Notch signaling pathway related factors Jagged1 and Notch1, and invasion and metastasis related factors MKP-1, SSBP2 and MMP7 in vitro and in vivo, at the mRNA level. In vitro and in vivo data suggest that knock down of ZMIZ1 may inhibit TSCC invasion and metastasis by modulating Notch signaling. ZMIZ1 inhibition may therefore represent a new therapeutic target for TSCC.
Effect of salt-alkali stress on seed germination of the halophyte Halostachys caspica
Authors: Zhang Rui , Zhang Huizhen , Wang Lai , Zeng Youling 
Published: June 2024

AbstractThe increasing global phenomenon of soil salinization has prompted heightened interest in the physiological ecology of plant salt and alkali tolerance. Halostachys caspica belonging to Amaranthaceae, an exceptionally salt-tolerant halophyte, is widely distributed in the arid and saline-alkali regions of Xinjiang, in Northwest China. Soil salinization and alkalinization frequently co-occur in nature, but very few studies focus on the interactive effects of various salt and alkali stress on plants. In this study, the impacts on the H. caspica seed germination, germination recovery and seedling growth were investigated under the salt and alkali stress. The results showed that the seed germination percentage was not significantly reduced at low salinity at pH 5.30–9.60, but decreased with elevated salt concentration and pH. Immediately after, salt was removed, ungerminated seeds under high salt concentration treatment exhibited a higher recovery germination percentage, indicating seed germination of H. caspica was inhibited under the condition of high salt-alkali stress. Stepwise regression analysis indicated that, at the same salt concentrations, alkaline salts exerted a more severe inhibition on seed germination, compared to neutral salts. The detrimental effects of salinity or high pH alone were less serious than their combination. Salt concentration, pH value, and their interactions had inhibitory effects on seed germination, with salinity being the decisive factor, while pH played a secondary role in salt-alkali mixed stress.
Biomechanical analysis of adjacent segments after correction surgery for adult idiopathic scoliosis: a finite element analysis
Authors: Wang Dong-hai , Wu Dan-ni , Xin Da-qi , Shi Qin , Wang Wen-xuan , Xing Wen-hua , Yang Hui-lin 
Published: June 2024

AbstractThe biomechanical aspects of adjacent segment degeneration after Adult Idiopathic Scoliosis (AdIS) corrective surgery involving postoperative changes in motion and stress of adjacent segments have yet to be investigated. The objective of this study was to evaluate the biomechanical effects of corrective surgery on adjacent segments in adult idiopathic scoliosis by finite element analysis. Based on computed tomography data of the consecutive spine from T1–S1 of a 28-year-old male patient with adult idiopathic scoliosis, a three-dimensional finite element model was established to simulate the biomechanics. Two posterior long-segment fixation and fusion operations were designed: Strategy A, pedicle screws implanted in all segments of both sides, and Strategy B, alternate screws instrumentation on both sides. The range of motion (ROM), Maximum von Mises stress value of intervertebral disc (IVD), and Maximum von Mises stress of the facet joint (FJ) at the fixation adjacent segment were calculated and compared with data of the preoperative AdIS model. Corrective surgery decreased the IVD on the adjacent segments, increased the FJ on the adjacent segments, and decreased the ROM of the adjacent segments. A greater decrease of Maximum von Mises stress was observed on the distal adjacent segment compared with the proximal adjacent segment. The decrease of Maximum von Mises stress and increment of Maximum von Mises stress on adjacent FJ in strategy B was greater than that in strategy A. Under the six operation modes, the change of the Maximum von Mises stress on the adjacent IVD and FJ was significant. The decrease in ROM in the proximal adjacent segment was greater than that of the distal adjacent segment, and the decrease of ROM in strategy A was greater than that in strategy B. This study clarified the biomechanical characteristics of adjacent segments after AdIS corrective surgery, and further biomechanical analysis of two different posterior pedicle screw placement schemes by finite element method. Our study provides a theoretical basis for the pathogenesis, prevention, and treatment of adjacent segment degeneration after corrective surgery for AdIS.
Effects of weight loss intervention on anxiety, depression and quality of life in women with severe obesity and polycystic ovary syndrome
Authors: Kataoka Josefin , Olsson Marie , Lindgren Eva , Larsson Ingrid , Schmidt Johanna , Benrick Anna , Stener-Victorin Elisabet 
Published: June 2024

AbstractPolycystic ovary syndrome (PCOS) is a common endocrine disorder in women that is associated with an increased risk of anxiety and depression and with a lower health-related quality of life (HRQoL). PCOS is closely associated with obesity, which per se can lead to symptoms of anxiety and depression and lower HRQoL. The first-line treatment for PCOS is weight loss through lifestyle intervention, which has been shown to improve all symptoms of the syndrome. The aim of this study was to investigate symptoms of anxiety and depression and HRQoL in women with severe obesity (BMI ≥ 35) with and without PCOS, and to evaluate the effect of a one-year structured weight loss intervention. A total of 246 women with severe obesity (PCOS n = 63, non-PCOS n = 183) were included. The comprehensive psychopathological rating scale self-rating scale for affective symptoms (CPRS-S-A) and the short form-36 (SF-36) were used to assess symptoms of anxiety and depression and HRQoL. In total 72 women of the 246 women with severe obesity completed a one-year weight loss programme and were followed up and compared with baseline data. In women with severe obesity, there were no differences in symptoms of anxiety and depression and HRQoL between women with and without PCOS at baseline. Clinically relevant anxiety symptoms were present in 71.3% (PCOS) and 65.6% (non-PCOS), and depression symptoms were present in 56.4% (PCOS) and 52.2% (non-PCOS). Significant weight loss improved physical HRQoL in all women, but reduced symptoms of anxiety and depression only in women without PCOS. There were no differences when comparing the changes between the groups. Women with severe obesity are severely affected by symptoms of anxiety and depression, independent of PCOS. Weight loss improved symptoms of anxiety and depression in women without PCOS, but there were no differences between groups in change from baseline to follow-up.Trial registration number: Clinical trial.gov: NCT01319162, March 18, 2011. Date of registration and enrolment of the first subject September 2011.
Induction and antiviral activity of ferret myxovirus resistance (Mx) protein 1 against influenza A viruses
Authors: Farrukee Rubaiyea , Schwab Lara S. U. , Barnes James B. , Brooks Andrew G. , Londrigan Sarah L. , Hartmann Gunther , Zillinger Thomas , Reading Patrick C. 
Published: June 2024

AbstractMyxovirus resistance (Mx) proteins are products of interferon stimulated genes (ISGs) and Mx proteins of different species have been reported to mediate antiviral activity against a number of viruses, including influenza A viruses (IAV). Ferrets are widely considered to represent the ‘gold standard’ small animal model for studying pathogenesis and immunity to human IAV infections, however little is known regarding the antiviral activity of ferret Mx proteins. Herein, we report induction of ferret (f)Mx1/2 in a ferret lung cell line and in airway tissues from IAV-infected ferrets, noting that fMx1 was induced to higher levels that fMx2 both in vitro and in vivo. Overexpression confirmed cytoplasmic expression of fMx1 as well as its ability to inhibit infection and replication of IAV, noting that this antiviral effect of fMx1was modest when compared to cells overexpressing either human MxA or mouse Mx1. Together, these studies provide the first insights regarding the role of fMx1 in cell innate antiviral immunity to influenza viruses. Understanding similarities and differences in the antiviral activities of human and ferret ISGs provides critical context for evaluating results when studying human IAV infections in the ferret model.