bluuebunny/crossref_metadata_2025_split huggingface dataset:
TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
Authors: Wang Feng , Xu Yang , Wang Robert , Zhang Beatrice , Smith Noah , Notaro Amber , Gaerlan Samantha , Kutschera Eric , Kadash-Edmondson Kathryn E. , Xing Yi , Lin Lan 
Published: August 2023

AbstractLong-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism
Authors: Nakashima Yu , Kawakami Atsushi , Ogasawara Yasushi , Maeki Masatoshi , Tokeshi Manabu , Dairi Tohru , Morita Hiroyuki 
Published: August 2023

AbstractThe lasso peptide MS-271 is a ribosomally synthesized and post-translationally modified peptide (RiPP) consisting of 21 amino acids with D-tryptophan at the C-terminus, and is derived from the precursor peptide MslA. MslH, encoded in the MS-271 biosynthetic gene cluster (msl), catalyzes the epimerization at the Cα center of the MslA C-terminal Trp21, leading to epi-MslA. The detailed catalytic process, including the catalytic site and cofactors, has remained enigmatic. Herein, based on X-ray crystallographic studies in association with MslA core peptide analogues, we show that MslH is a metallo-dependent peptide epimerase with a calcineurin-like fold. The crystal structure analysis, followed by site-directed mutagenesis, docking simulation, and ICP-MS studies demonstrate that MslH employs acid/base chemistry to facilitate the reversible epimerization of the C-terminal Trp21 of MslA, by utilizing two pairs of His/Asp catalytic residues that are electrostatically tethered to a six-coordination motif with a Ca(II) ion via water molecules.
Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community
Authors: Weiss Anna S. , Niedermeier Lisa S. , von Strempel Alexandra , Burrichter Anna G. , Ring Diana , Meng Chen , Kleigrewe Karin , Lincetto Chiara , Hübner Johannes , Stecher Bärbel 
Published: August 2023

AbstractA challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further,Bacteroides caecimurisandBlautia coccoidesare found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
Development of high-voltage and high-energy membrane-free nonaqueous lithium-based organic redox flow batteries
Authors: Gautam Rajeev K. , Wang Xiao , Lashgari Amir , Sinha Soumalya , McGrath Jack , Siwakoti Rabin , Jiang Jianbing “Jimmy” 
Published: August 2023

AbstractLithium-based nonaqueous redox flow batteries (LRFBs) are alternative systems to conventional aqueous redox flow batteries because of their higher operating voltage and theoretical energy density. However, the use of ion-selective membranes limits the large-scale applicability of LRFBs. Here, we report high-voltage membrane-free LRFBs based on an all-organic biphasic system that uses Li metal anode and 2,4,6-tri-(1-cyclohexyloxy-4-imino-2,2,6,6-tetramethylpiperidine)-1,3,5-triazine (Tri-TEMPO), N-propyl phenothiazine (C3-PTZ), and tris(dialkylamino)cyclopropenium (CP) cathodes. Under static conditions, the Li||Tri-TEMPO, Li||C3-PTZ, and Li||CP batteries with 0.5 M redox-active material deliver capacity retentions of 98%, 98%, and 92%, respectively, for 100 cycles over ~55 days at the current density of 1 mA/cm2 and a temperature of 27 °C. Moreover, the Li||Tri-TEMPO (0.5 M) flow battery delivers an initial average cell discharge voltage of 3.45 V and an energy density of ~33 Wh/L. This flow battery also demonstrates 81% of capacity for 100 cycles over ~45 days with average Coulombic efficiency of 96% and energy efficiency of 82% at the current density of 1.5 mA/cm2 and at a temperature of 27 °C.
A BLADE-ON-PETIOLE orthologue regulates corolla differentiation in the proximal region in Torenia fournieri
Authors: Su Shihao , Lei Yawen , Zhou Xuan , Suzuki Takamasa , Xiao Wei , Higashiyama Tetsuya 
Published: August 2023

AbstractThe three-dimensional shape of a flower is integrated by morphogenesis along different axes. Differentiation along the petal proximodistal axis is tightly linked to the specification of pollinators; however, it is still unclear how a petal patterns this axis. The corolla of Torenia fournieri exhibits strong differentiation along the proximodistal axis, and we previously found a proximal regulator, TfALOG3, controlling corolla neck differentiation. Here, we report another gene, TfBOP2, which is predominantly expressed in the proximal region of the corolla. TfBOP2 mutants have shorter proximal corolla tubes and longer distal lobe, demonstrating its function as a proximal regulator. Arabidopsis BOPs mutant shows similar defects, favouring a shared role of BOPs homologues. Genetic analysis demonstrates the interaction between TfBOP2 and TfALOG3, and we further found that TfALOG3 physically interacts with TfBOP2 and can recruit TfBOP2 to the nuclear region. Our study favours a hypothetical shared BOP-ALOG complex that is recruited to regulate corolla differentiation in the proximal region axis of T. fournieri.
Selective CO2 reduction to CH3OH over atomic dual-metal sites embedded in a metal-organic framework with high-energy radiation
Authors: Hu Changjiang , Jiang Zhiwen , Wu Qunyan , Cao Shuiyan , Li Qiuhao , Chen Chong , Yuan Liyong , Wang Yunlong , Yang Wenyun , Yang Jinbo , Peng Jing , Shi Weiqun , Zhai Maolin , Mostafavi Mehran , Ma Jun 
Published: August 2023

AbstractThe efficient use of renewable X/γ-rays or accelerated electrons for chemical transformation of CO2 and water to fuels holds promise for a carbon-neutral economy; however, such processes are challenging to implement and require the assistance of catalysts capable of sensitizing secondary electron scattering and providing active metal sites to bind intermediates. Here we show atomic Cu-Ni dual-metal sites embedded in a metal-organic framework enable efficient and selective CH3OH production (~98%) over multiple irradiated cycles. The usage of practical electron-beam irradiation (200 keV; 40 kGy min−1) with a cost-effective hydroxyl radical scavenger promotes CH3OH production rate to 0.27 mmol g−1 min−1. Moreover, time-resolved experiments with calculations reveal the direct generation of CO2•‒ radical anions via aqueous electrons attachment occurred on nanosecond timescale, and cascade hydrogenation steps. Our study highlights a radiolytic route to produce CH3OH with CO2 feedstock and introduces a desirable atomic structure to improve performance.
A mosaic adeno-associated virus vector as a versatile tool that exhibits high levels of transgene expression and neuron specificity in primate brain
Authors: Kimura Kei , Nagai Yuji , Hatanaka Gaku , Fang Yang , Tanabe Soshi , Zheng Andi , Fujiwara Maki , Nakano Mayuko , Hori Yukiko , Takeuchi Ryosuke F. , Inagaki Mikio , Minamimoto Takafumi , Fujita Ichiro , Inoue Ken-ichi , Takada Masahiko 
Published: August 2023

AbstractRecent emphasis has been placed on gene transduction mediated through recombinant adeno-associated virus (AAV) vector to manipulate activity of neurons and their circuitry in the primate brain. In the present study, we created a novel vector of which capsid was composed of capsid proteins derived from both of the AAV serotypes 1 and 2 (AAV1 and AAV2). Following the injection into the frontal cortex of macaque monkeys, this mosaic vector, termed AAV2.1 vector, was found to exhibit the excellence in transgene expression (for AAV1 vector) and neuron specificity (for AAV2 vector) simultaneously. To explore its applicability to chemogenetic manipulation and in vivo calcium imaging, the AAV2.1 vector expressing excitatory DREADDs or GCaMP was injected into the striatum or the visual cortex of macaque monkeys, respectively. Our results have defined that such vectors secure intense and stable expression of the target proteins and yield conspicuous modulation and imaging of neuronal activity.
A synthetic metastatic niche reveals antitumor neutrophils drive breast cancer metastatic dormancy in the lungs
Authors: Wang Jing , Ocadiz-Ruiz Ramon , Hall Matthew S. , Bushnell Grace G. , Orbach Sophia M. , Decker Joseph T. , Raghani Ravi M. , Zhang Yining , Morris Aaron H. , Jeruss Jacqueline S. , Shea Lonnie D. 
Published: August 2023

AbstractBiomaterial scaffolds mimicking the environment in metastatic organs can deconstruct complex signals and facilitate the study of cancer progression and metastasis. Here we report that a subcutaneous scaffold implant in mouse models of metastatic breast cancer in female mice recruits lung-tropic circulating tumor cells yet suppresses their growth through potent in situ antitumor immunity. In contrast, the lung, the endogenous metastatic organ for these models, develops lethal metastases in aggressive breast cancer, with less aggressive tumor models developing dormant lungs suppressing tumor growth. Our study reveals multifaceted roles of neutrophils in regulating metastasis. Breast cancer-educated neutrophils infiltrate the scaffold implants and lungs, secreting the same signal to attract lung-tropic circulating tumor cells. Second, antitumor and pro-tumor neutrophils are selectively recruited to the dormant scaffolds and lungs, respectively, responding to distinct groups of chemoattractants to establish activated or suppressive immune environments that direct different fates of cancer cells.
SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development
Authors: Matsui Yurika , Djekidel Mohamed Nadhir , Lindsay Katherine , Samir Parimal , Connolly Nina , Wu Gang , Yang Xiaoyang , Fan Yiping , Xu Beisi , Peng Jamy C. 
Published: August 2023

AbstractStem cell survival versus death is a developmentally programmed process essential for morphogenesis, sizing, and quality control of genome integrity and cell fates. Cell death is pervasive during development, but its programming is little known. Here, we report that Smad nuclear interacting protein 1 (SNIP1) promotes neural progenitor cell survival and neurogenesis and is, therefore, integral to brain development. The SNIP1-depleted brain exhibits dysplasia with robust induction of caspase 9-dependent apoptosis. Mechanistically, SNIP1 regulates target genes that promote cell survival and neurogenesis, and its activities are influenced by TGFβ and NFκB signaling pathways. Further, SNIP1 facilitates the genomic occupancy of Polycomb complex PRC2 and instructs H3K27me3 turnover at target genes. Depletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and to partially restore genetic programs in the SNIP1-depleted brain in vivo. These findings suggest a loci-specific regulation of PRC2 and H3K27 marks to toggle cell survival and death in the developing brain.
Intermittent dietary methionine deprivation facilitates tumoral ferroptosis and synergizes with checkpoint blockade
Authors: Xue Ying , Lu Fujia , Chang Zhenzhen , Li Jing , Gao Yuan , Zhou Jie , Luo Ying , Lai Yongfeng , Cao Siyuan , Li Xiaoxiao , Zhou Yuhan , Li Yan , Tan Zheng , Cheng Xiang , Li Xiong , Chen Jing , Wang Weimin 
Published: August 2023

AbstractDietary methionine interventions are beneficial to apoptosis-inducing chemotherapy and radiotherapy for cancer, while their effects on ferroptosis-targeting therapy and immunotherapy are unknown. Here we show the length of time methionine deprivation affects tumoral ferroptosis differently. Prolonged methionine deprivation prevents glutathione (GSH) depletion from exceeding the death threshold by blocking cation transport regulator homolog 1 (CHAC1) protein synthesis. Whereas, short-term methionine starvation accelerates ferroptosis by stimulating CHAC1 transcription. In vivo, dietary methionine with intermittent but not sustained deprivation augments tumoral ferroptosis. Intermittent methionine deprivation also sensitizes tumor cells against CD8+ T cell-mediated cytotoxicity and synergize checkpoint blockade therapy by CHAC1 upregulation. Clinically, tumor CHAC1 correlates with clinical benefits and improved survival in cancer patients treated with checkpoint blockades. Lastly, the triple combination of methionine intermittent deprivation, system xc- inhibitor and PD-1 blockade shows superior antitumor efficacy. Thus, intermittent methionine deprivation is a promising regimen to target ferroptosis and augment cancer immunotherapy.
Bonding wood with uncondensed lignins as adhesives
Authors: Yang Guangxu , Gong Zhenggang , Luo Xiaolin , Chen Lihui , Shuai Li 
Published: August 2023

AbstractPlywood is widely used in construction, such as for flooring and interior walls, as well as in the manufacture of household items such as furniture and cabinets. Such items are made of wood veneers that are bonded together with adhesives such as urea–formaldehyde and phenol–formaldehyde resins1,2. Researchers in academia and industry have long aimed to synthesize lignin–phenol–formaldehyde resin adhesives using biomass-derived lignin, a phenolic polymer that can be used to substitute the petroleum-derived phenol3–6. However, lignin–phenol–formaldehyde resin adhesives are less attractive to plywood manufacturers than urea–formaldehyde and phenol–formaldehyde resins owing to their appearance and cost. Here we report a simple and practical strategy for preparing lignin-based wood adhesives from lignocellulosic biomass. Our strategy involves separation of uncondensed or slightly condensed lignins from biomass followed by direct application of a suspension of the lignin and water as an adhesive on wood veneers. Plywood products with superior performances could be prepared with such lignin adhesives at a wide range of hot-pressing temperatures, enabling the use of these adhesives as promising alternatives to traditional wood adhesives in different market segments. Mechanistic studies indicate that the adhesion mechanism of such lignin adhesives may involve softening of lignin by water, filling of vessels with softened lignin and crosslinking of lignins in adhesives with those in the cell wall.
MedalCare-XL: 16,900 healthy and pathological synthetic 12 lead ECGs from electrophysiological simulations
Authors: Gillette Karli , Gsell Matthias A. F. , Nagel Claudia , Bender Jule , Winkler Benjamin , Williams Steven E. , Bär Markus , Schäffter Tobias , Dössel Olaf , Plank Gernot , Loewe Axel 
Published: August 2023

AbstractMechanistic cardiac electrophysiology models allow for personalized simulations of the electrical activity in the heart and the ensuing electrocardiogram (ECG) on the body surface. As such, synthetic signals possess known ground truth labels of the underlying disease and can be employed for validation of machine learning ECG analysis tools in addition to clinical signals. Recently, synthetic ECGs were used to enrich sparse clinical data or even replace them completely during training leading to improved performance on real-world clinical test data. We thus generated a novel synthetic database comprising a total of 16,900 12 lead ECGs based on electrophysiological simulations equally distributed into healthy control and 7 pathology classes. The pathological case of myocardial infraction had 6 sub-classes. A comparison of extracted features between the virtual cohort and a publicly available clinical ECG database demonstrated that the synthetic signals represent clinical ECGs for healthy and pathological subpopulations with high fidelity. The ECG database is split into training, validation, and test folds for development and objective assessment of novel machine learning algorithms.
ThoughtSource: A central hub for large language model reasoning data
Authors: Ott Simon , Hebenstreit Konstantin , Liévin Valentin , Hother Christoffer Egeberg , Moradi Milad , Mayrhauser Maximilian , Praas Robert , Winther Ole , Samwald Matthias 
Published: August 2023

AbstractLarge language models (LLMs) such as GPT-4 have recently demonstrated impressive results across a wide range of tasks. LLMs are still limited, however, in that they frequently fail at complex reasoning, their reasoning processes are opaque, they are prone to ‘hallucinate’ facts, and there are concerns about their underlying biases. Letting models verbalize reasoning steps as natural language, a technique known as chain-of-thought prompting, has recently been proposed as a way to address some of these issues. Here we present ThoughtSource, a meta-dataset and software library for chain-of-thought (CoT) reasoning. The goal of ThoughtSource is to improve future artificial intelligence systems by facilitating qualitative understanding of CoTs, enabling empirical evaluations, and providing training data. This first release of ThoughtSource integrates seven scientific/medical, three general-domain and five math word question answering datasets.
Regulation of brain cognitive states through auditory, gustatory, and olfactory stimulation with wearable monitoring
Authors: Fekri Azgomi Hamid , F. Branco Luciano R. , Amin Md. Rafiul , Khazaei Saman , Faghih Rose T. 
Published: August 2023

AbstractInspired by advances in wearable technologies, we design and perform human-subject experiments. We aim to investigate the effects of applying safe actuation (i.e., auditory, gustatory, and olfactory) for the purpose of regulating cognitive arousal and enhancing the performance states. In two proposed experiments, subjects are asked to perform a working memory experiment calledn-back tasks. Next, we incorporate listening to different types of music, drinking coffee, and smelling perfume as safe actuators. We employ signal processing methods to seamlessly infer participants’ brain cognitive states. The results demonstrate the effectiveness of the proposed safe actuation in regulating the arousal state and enhancing performance levels. Employing only wearable devices for human monitoring and using safe actuation intervention are the key components of the proposed experiments. Our dataset fills the existing gap of the lack of publicly available datasets for the self-management of internal brain states using wearable devices and safe everyday actuators. This dataset enables further machine learning and system identification investigations to facilitate future smart work environments. This would lead us to the ultimate idea of developing practical automated personalized closed-loop architectures for managing internal brain states and enhancing the quality of life.
Dependence of the acoustic propulsion of nano- and microcones on their orientation and aspect ratio
Authors: Voß Johannes , Wittkowski Raphael 
Published: August 2023

AbstractRecent research revealed the orientation-dependent propulsion of a cone-shaped colloidal particle that is exposed to a planar traveling ultrasound wave. Here, we extend the previous research by considering nano- and microcones with different aspect ratios and studying how the propulsion of a particle depends on its orientation and aspect ratio. We also study how the orientation-averaged propulsion of a cone-shaped particle, which corresponds to an isotropic ultrasound field, depends on its aspect ratio and identify an aspect ratio of 1/2 where the orientation-averaged propulsion is particularly strong. To make our simulation results easier reusable for follow-up research, we provide a corresponding simple analytic representation.
Pure and doped carbon quantum dots as fluorescent probes for the detection of phenol compounds and antibiotics in aquariums
Authors: Mousa Mahmoud A. , Abdelrahman Hanaa H. , Fahmy Mamdouh A. , Ebrahim Dina G. , Moustafa Amira H. E. 
Published: August 2023

AbstractThe resulting antibiotic residue and organic chemicals from continuous climatic change, urbanization and increasing food demand have a detrimental impact on environmental and human health protection. So, we created a unique B, N-CQDs (Boron, Nitrogen doping carbon quantum dots) based fluorescent nanosensor to investigate novel sensing methodologies for the precise and concentrated identification of antibiotics and phenol derivatives substances to ensure that they are included in the permitted percentages. The as-prepared highly fluorescent B, N-CQDs had a limited range of sizes between 1 and 6 nm and average sizes of 2.5 nm in our study. The novel B, N-CQDs showed high sensitivity and selectivity for phenolic derivatives such as hydroquinone, resorcinol, and para aminophenol, as well as organic solvents such as hexane, with low detection limits of 0.05, 0.024, 0.032 and 0.013 µM respectively in an aqueous medium. The high fluorescence B, N-CQDs probes were examined using transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and UV/VIS spectroscopy. The outcomes were compared to carbon quantum dots (CQDs) previously generated from Urea.