bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stoichiometry validation of supramolecular complexes with a hydrocarbon cage host by van ’t Hoff analyses
Authors: Fukunaga Toshiya M. , Onaka Yuzuka , Kato Takahide , Ikemoto Koki , Isobe Hiroyuki 
Published: December 2023

AbstractDefining chemical processes with equations is the first important step in characterizing equilibria for the assembly of supramolecular complexes, and the stoichiometry of the assembled components must be defined to generate the equation. Recently, this subject has attracted renewed interest, and statistical and/or information-theoretic measures were introduced to examine the validities of the equilibrium models used during curve fitting analyses of titration. The present study shows that these measures may not always be appropriate for credibility examinations and that further reformation of the protocols used to determine the overall stoichiometry is necessary. Hydrocarbon cage hosts and their chloroform complexes formed via weak CH-π hydrogen bonds were studied, which allowed us to introduce van ’t Hoff analyses for effective validation of the stoichiometries of supramolecular complexes. This study shows that the stoichiometries of supramolecular complexes should be carefully examined by adopting multiple measures with different origins.
Theta mediated dynamics of human hippocampal-neocortical learning systems in memory formation and retrieval
Authors: Gattas Sandra , Larson Myra Sarai , Mnatsakanyan Lilit , Sen-Gupta Indranil , Vadera Sumeet , Swindlehurst A. Lee , Rapp Paul E. , Lin Jack J. , Yassa Michael A. 
Published: December 2023

AbstractEpisodic memory arises as a function of dynamic interactions between the hippocampus and the neocortex, yet the mechanisms have remained elusive. Here, using human intracranial recordings during a mnemonic discrimination task, we report that 4-5 Hz (theta) power is differentially recruited during discrimination vs. overgeneralization, and its phase supports hippocampal-neocortical when memories are being formed and correctly retrieved. Interactions were largely bidirectional, with small but significant net directional biases; a hippocampus-to-neocortex bias during acquisition of new information that was subsequently correctly discriminated, and a neocortex-to-hippocampus bias during accurate discrimination of new stimuli from similar previously learned stimuli. The 4-5 Hz rhythm may facilitate the initial stages of information acquisition by neocortex during learning and the recall of stored information from cortex during retrieval. Future work should further probe these dynamics across different types of tasks and stimuli and computational models may need to be expanded accordingly to accommodate these findings.
BACH1 controls hepatic insulin signaling and glucose homeostasis in mice
Authors: Jin Jiayu , He Yunquan , Guo Jieyu , Pan Qi , Wei Xiangxiang , Xu Chen , Qi Zhiyuan , Li Qinhan , Ma Siyu , Lin Jiayi , Jiang Nan , Ma Jinghua , Wang Xinhong , Jiang Lindi , Ding Qiurong , Osto Elena , Zhi Xiuling , Meng Dan 
Published: December 2023

AbstractHepatic insulin resistance is central to the metabolic syndrome. Here we investigate the role of BTB and CNC homology 1 (BACH1) in hepatic insulin signaling. BACH1 is elevated in the hepatocytes of individuals with obesity and patients with non-alcoholic fatty liver disease (NAFLD). Hepatocyte-specific Bach1 deletion in male mice on a high-fat diet (HFD) ameliorates hyperglycemia and insulin resistance, improves glucose homeostasis, and protects against steatosis, whereas hepatic overexpression of Bach1 in male mice leads to the opposite phenotype. BACH1 directly interacts with the protein-tyrosine phosphatase 1B (PTP1B) and the insulin receptor β (IR-β), and loss of BACH1 reduces the interaction between PTP1B and IR-β upon insulin stimulation and enhances insulin signaling in hepatocytes. Inhibition of PTP1B significantly attenuates BACH1-mediated suppression of insulin signaling in HFD-fed male mice. Hepatic BACH1 knockdown ameliorates hyperglycemia and improves insulin sensitivity in diabetic male mice. These results demonstrate a critical function for hepatic BACH1 in the regulation of insulin signaling and glucose homeostasis.
Hypothalamic CRH neurons represent physiological memory of positive and negative experience
Authors: Füzesi Tamás , Rasiah Neilen P. , Rosenegger David G. , Rojas-Carvajal Mijail , Chomiak Taylor , Daviu Núria , Molina Leonardo A. , Simone Kathryn , Sterley Toni-Lee , Nicola Wilten , Bains Jaideep S. 
Published: December 2023

AbstractRecalling a salient experience provokes specific behaviors and changes in the physiology or internal state. Relatively little is known about how physiological memories are encoded. We examined the neural substrates of physiological memory by probing CRHPVN neurons of mice, which control the endocrine response to stress. Here we show these cells exhibit contextual memory following exposure to a stimulus with negative or positive valence. Specifically, a negative stimulus invokes a two-factor learning rule that favors an increase in the activity of weak cells during recall. In contrast, the contextual memory of positive valence relies on a one-factor rule to decrease activity of CRHPVN neurons. Finally, the aversive memory in CRHPVN neurons outlasts the behavioral response. These observations provide information about how specific physiological memories of aversive and appetitive experience are represented and demonstrate that behavioral readouts may not accurately reflect physiological changes invoked by the memory of salient experiences.
Unique adipose tissue invariant natural killer T cell subpopulations control adipocyte turnover in mice
Authors: Han Sang Mun , Park Eun Seo , Park Jeu , Nahmgoong Hahn , Choi Yoon Ha , Oh Jiyoung , Yim Kyung Min , Lee Won Taek , Lee Yun Kyung , Jeon Yong Geun , Shin Kyung Cheul , Huh Jin Young , Choi Sung Hee , Park Jiyoung , Kim Jong Kyoung , Kim Jae Bum 
Published: December 2023

AbstractAdipose tissue invariant natural killer T (iNKT) cells are a crucial cell type for adipose tissue homeostasis in obese animals. However, heterogeneity of adipose iNKT cells and their function in adipocyte turnover are not thoroughly understood. Here, we investigate transcriptional heterogeneity in adipose iNKT cells and their hierarchy using single-cell RNA sequencing in lean and obese mice. We report that distinct subpopulations of adipose iNKT cells modulate adipose tissue homeostasis through adipocyte death and birth. We identify KLRG1+ iNKT cells as a unique iNKT cell subpopulation in adipose tissue. Adoptive transfer experiments showed that KLRG1+ iNKT cells are selectively generated within adipose tissue microenvironment and differentiate into a CX3CR1+ cytotoxic subpopulation in obese mice. In addition, CX3CR1+ iNKT cells specifically kill enlarged and inflamed adipocytes and recruit macrophages through CCL5. Furthermore, adipose iNKT17 cells have the potential to secrete AREG, and AREG is involved in stimulating adipose stem cell proliferation. Collectively, our data suggest that each adipose iNKT cell subpopulation plays key roles in the control of adipocyte turnover via interaction with adipocytes, adipose stem cells, and macrophages in adipose tissue.
Solvent-pair surfactants enabled assembly of clusters and copolymers towards programmed mesoporous metal oxides
Authors: Xie Wenhe , Ren Yuan , Jiang Fengluan , Huang Xin-Yu , Yu Bingjie , Liu Jianhong , Li Jichun , Chen Keyu , Zou Yidong , Hu Bingwen , Deng Yonghui 
Published: December 2023

AbstractOrganic-inorganic molecular assembly has led to numerous nano/mesostructured materials with fantastic properties, but it is dependent on and limited to the direct interaction between host organic structure-directing molecules and guest inorganic species. Here, we report a “solvent-pair surfactants” enabled assembly (SPEA) method to achieve a general synthesis of mesostructured materials requiring no direct host-guest interaction. Taking the synthesis of mesoporous metal oxides as an example, the dimethylformamide/water solvent pairs behave as surfactants and induce the formation of mesostructured polyoxometalates/copolymers nanocomposites, which can be converted into metal oxides. This SPEA method enables the synthesis of functional ordered mesoporous metal oxides with different pore sizes, structures, compositions and tailored pore-wall microenvironments that are difficult to access via conventional direct organic-inorganic assembly. Typically, nitrogen-doped mesoporous ε-WO3 with high specific surface area, uniform mesopores and stable framework is obtained and exhibits great application potentials such as gas sensing.
Atroposelective hydroarylation of biaryl phosphines directed by phosphorus centres
Authors: Li Zexian , Wang Minyan , Yang Youqing , Liang Yong , Chen Xiangyang , Zhao Yue , Houk K. N. , Shi Zhuangzhi 
Published: December 2023

AbstractPrized for their ability to generate chemical complexity rapidly, catalytic carbon–hydrogen (C–H) activation and functionalization reactions have enabled a paradigm shift in the standard logic of synthetic chemistry. Directing group strategies have been used extensively in C–H activation reactions to control regio- and enantioselectivity with transition metal catalysts. However, current methods rely heavily on coordination with nitrogen and/or oxygen atoms in molecules and have therefore been found to exhibit limited generality in asymmetric syntheses. Here, we report enantioselective C–H activation with unsaturated hydrocarbons directed by phosphorus centres to rapidly construct libraries of axially chiral phosphines through dynamic kinetic resolution. High reactivity and enantioselectivity are derived from modular assembly of an iridium catalyst with an endogenous phosphorus atom and an exogenous chiral phosphorus ligand, as confirmed by detailed experimental and computational studies. This reaction mode significantly expands the pool of enantiomerically enriched functional phosphines, some of which have shown excellent efficiency for asymmetric catalysis.
Redox-enabled electronic interrogation and feedback control of hierarchical and networked biological systems
Authors: Wang Sally , Chen Chen-Yu , Rzasa John R. , Tsao Chen-Yu , Li Jinyang , VanArsdale Eric , Kim Eunkyoung , Zakaria Fauziah Rahma , Payne Gregory F. , Bentley William E. 
Published: December 2023

AbstractMicroelectronic devices can directly communicate with biology, as electronic information can be transmitted via redox reactions within biological systems. By engineering biology’s native redox networks, we enable electronic interrogation and control of biological systems at several hierarchical levels: proteins, cells, and cell consortia. First, electro-biofabrication facilitates on-device biological component assembly. Then, electrode-actuated redox data transmission and redox-linked synthetic biology allows programming of enzyme activity and closed-loop electrogenetic control of cellular function. Specifically, horseradish peroxidase is assembled onto interdigitated electrodes where electrode-generated hydrogen peroxide controls its activity. E. coli’s stress response regulon, oxyRS, is rewired to enable algorithm-based feedback control of gene expression, including an eCRISPR module that switches cell-cell quorum sensing communication from one autoinducer to another—creating an electronically controlled ‘bilingual’ cell. Then, these disparate redox-guided devices are wirelessly connected, enabling real-time communication and user-based control. We suggest these methodologies will help us to better understand and develop sophisticated control for biology.
Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction
Authors: Tung Lin Wei , Groppa Elena , Soliman Hesham , Lin Bruce , Chang Chihkai , Cheung Chun Wai , Ritso Morten , Guo David , Rempel Lucas , Sinha Sarthak , Eisner Christine , Brassard Julyanne , McNagny Kelly , Biernaskie Jeff , Rossi Fabio 
Published: December 2023

AbstractTherapeutic angiogenesis represents a promising avenue to revascularize the ischemic heart. Its limited success is partly due to our poor understanding of the cardiac stroma, specifically mural cells, and their response to ischemic injury. Here, we combine single-cell and positional transcriptomics to assess the behavior of mural cells within the healing heart. In response to myocardial infarction, mural cells adopt an altered state closely associated with the infarct and retain a distinct lineage from fibroblasts. This response is concurrent with vascular rarefaction and reduced vascular coverage by mural cells. Positional transcriptomics reveals that the infarcted heart is governed by regional-dependent and temporally regulated programs. While the remote zone acts as an important source of pro-angiogenic signals, the infarct zone is accentuated by chronic activation of anti-angiogenic, pro-fibrotic, and inflammatory cues. Together, our work unveils the spatiotemporal programs underlying cardiac repair and establishes an association between vascular deterioration and mural cell dysfunction.
Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
Authors: Aguilar-Bultet Lisandra , García-Martín Ana B. , Vock Isabelle , Maurer Pekerman Laura , Stadler Rahel , Schindler Ruth , Battegay Manuel , Stadler Tanja , Gómez-Sanz Elena , Tschudin-Sutter Sarah 
Published: December 2023

AbstractDespite recognition of the immediate impact of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-Klebsiella pneumoniae species complex and ESBL-Escherichia coli in individual patients over time, we performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-K. pneumoniae species complex and 284 ESBL-E. coli isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-K. pneumoniae species complex, and 83.6% of patients colonized with ESBL-E. coli. We frequently observed isolates of the same strain recovered from different body sites associated with either colonization or infection. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at prolonged risk of recurrent infection with colonizing strains.
Physics-aware differentiable design of magnetically actuated kirigami for shape morphing
Authors: Wang Liwei , Chang Yilong , Wu Shuai , Zhao Ruike Renee , Chen Wei 
Published: December 2023

AbstractShape morphing that transforms morphologies in response to stimuli is crucial for future multifunctional systems. While kirigami holds great promise in enhancing shape-morphing, existing designs primarily focus on kinematics and overlook the underlying physics. This study introduces a differentiable inverse design framework that considers the physical interplay between geometry, materials, and stimuli of active kirigami, made by soft material embedded with magnetic particles, to realize target shape-morphing upon magnetic excitation. We achieve this by combining differentiable kinematics and energy models into a constrained optimization, simultaneously designing the cuts and magnetization orientations to ensure kinematic and physical feasibility. Complex kirigami designs are obtained automatically with unparalleled efficiency, which can be remotely controlled to morph into intricate target shapes and even multiple states. The proposed framework can be extended to accommodate various active systems, bridging geometry and physics to push the frontiers in shape-morphing applications, like flexible electronics and minimally invasive surgery.
A broad-spectrum gas sensor based on correlated two-dimensional electron gas
Authors: Hong Yuhao , Wei Long , Zhang Qinghua , Deng Zhixiong , Liao Xiaxia , Zhou Yangbo , Wang Lei , Li Tongrui , Liu Junhua , Xiao Wen , Hu Shilin , Wang Lingfei , Li Lin , Huijben Mark , Gan Yulin , Chen Kai , Koster Gertjan , Rijnders Guus , Liao Zhaoliang 
Published: December 2023

AbstractDesigning a broad-spectrum gas sensor capable of identifying gas components in complex environments, such as mixed atmospheres or extreme temperatures, is a significant concern for various technologies, including energy, geological science, and planetary exploration. The main challenge lies in finding materials that exhibit high chemical stability and wide working temperature range. Materials that amplify signals through non-chemical methods could open up new sensing avenues. Here, we present the discovery of a broad-spectrum gas sensor utilizing correlated two-dimensional electron gas at a delta-doped LaAlO3/SrTiO3 interface with LaFeO3. Our study reveals that a back-gating on this two-dimensional electron gas can induce a non-volatile metal to insulator transition, which consequently can activate the two-dimensional electron gas to sensitively and quantitatively probe very broad gas species, no matter whether they are polar, non-polar, or inert gases. Different gas species cause resistance change at their sublimation or boiling temperature and a well-defined phase transition angle can quantitatively determine their partial pressures. Such unique correlated two-dimensional electron gas sensor is not affected by gas mixtures and maintains a wide operating temperature range. Furthermore, its readout is a simple measurement of electric resistance change, thus providing a very low-cost and high-efficient broad-spectrum sensing technique.
Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution
Authors: Buda Karol , Miton Charlotte M. , Tokuriki Nobuhiko 
Published: December 2023

AbstractEnzyme evolution is characterized by constant alterations of the intramolecular residue networks supporting their functions. The rewiring of these network interactions can give rise to epistasis. As mutations accumulate, the epistasis observed across diverse genotypes may appear idiosyncratic, that is, exhibit unique effects in different genetic backgrounds. Here, we unveil a quantitative picture of the prevalence and patterns of epistasis in enzyme evolution by analyzing 41 fitness landscapes generated from seven enzymes. We show that >94% of all mutational and epistatic effects appear highly idiosyncratic, which greatly distorted the functional prediction of the evolved enzymes. By examining seemingly idiosyncratic changes in epistasis along adaptive trajectories, we expose several instances of higher-order, intramolecular rewiring. Using complementary structural data, we outline putative molecular mechanisms explaining higher-order epistasis along two enzyme trajectories. Our work emphasizes the prevalence of epistasis and provides an approach to exploring this phenomenon through a molecular lens.
A human lower-limb biomechanics and wearable sensors dataset during cyclic and non-cyclic activities
Authors: Scherpereel Keaton , Molinaro Dean , Inan Omer , Shepherd Max , Young Aaron 
Published: December 2023

AbstractTasks of daily living are often sporadic, highly variable, and asymmetric. Analyzing these real-world non-cyclic activities is integral for expanding the applicability of exoskeletons, protheses, wearable sensing, and activity classification to real life, and could provide new insights into human biomechanics. Yet, currently available biomechanics datasets focus on either highly consistent, continuous, and symmetric activities, such as walking and running, or only a single specific non-cyclic task. To capture a more holistic picture of lower limb movements in everyday life, we collected data from 12 participants performing 20 non-cyclic activities (e.g. sit-to-stand, jumping, squatting, lunging, cutting) as well as 11 cyclic activities (e.g. walking, running) while kinematics (motion capture and IMUs), kinetics (force plates), and electromyography (EMG) were collected. This dataset provides normative biomechanics for a highly diverse range of activities and common tasks from a consistent set of participants and sensors.
Improved chromosome-level genome assembly of Indian sandalwood (Santalum album)
Authors: Zhang Xinhua , Li MingZhi , Bian Zhan , Chen Xiaohong , Li Yuan , Xiong Yuping , Fang Lin , Wu Kunlin , Zeng Songjun , Jian Shuguang , Wang Rujiang , Ren Hai , Teixeira da Silva Jaime A. , Ma Guohua 
Published: December 2023

AbstractSantalum album is a well-known aromatic and medicinal plant that is highly valued for the essential oil (EO) extracted from its heartwood. In this study, we present a high-quality chromosome-level genome assembly of S. album after integrating PacBio Sequel, Illumina HiSeq paired-end and high-throughput chromosome conformation capture sequencing technologies. The assembled genome size is 207.39 M with a contig N50 of 7.33 M and scaffold N50 size of 18.31 M. Compared with three previously published sandalwood genomes, the N50 length of the genome assembly was longer. In total, 94.26% of the assembly was assigned to 10 pseudo-chromosomes, and the anchor rate far exceeded that of a recently released value. BUSCO analysis yielded a completeness score of 94.91%. In addition, we predicted 23,283 protein-coding genes, 89.68% of which were functionally annotated. This high-quality genome will provide a foundation for sandalwood functional genomics studies, and also for elucidating the genetic basis of EO biosynthesis in S. album.