bluuebunny/crossref_metadata_2025_split huggingface dataset:
How molecular architecture defines quantum yields
Authors: Pashley-Johnson Fred , Munaweera Rangika , Hossain Sheikh I. , Gauci Steven C. , Delafresnaye Laura , Frisch Hendrik , O’Mara Megan L. , Du Prez Filip E. , Barner-Kowollik Christopher 
Published: July 2024

AbstractUnderstanding the intricate relationship between molecular architecture and function underpins most challenges at the forefront of chemical innovation. Bond-forming reactions are particularly influenced by the topology of a chemical structure, both on small molecule scale and in larger macromolecular frameworks. Herein, we elucidate the impact that molecular architecture has on the photo-induced cyclisations of a series of monodisperse macromolecules with defined spacers between photodimerisable moieties, and examine the relationship between propensity for intramolecular cyclisation and intermolecular network formation. We demonstrate a goldilocks zone of maximum reactivity between the sterically hindered and entropically limited regimes with a quantum yield of intramolecular cyclisation that is nearly an order of magnitude higher than the lowest value. As a result of the molecular design of trifunctional macromolecules, their quantum yields can be deconvoluted into the formation of two different cyclic isomers, as rationalised with molecular dynamics simulations. Critically, we visualise our solution-based studies with light-based additive manufacturing. We formulate four photoresists for microprinting, revealing that the precise positioning of functional groups is critical for resist performance, with lower intramolecular quantum yields leading to higher-quality printing in most cases.
Learning interpretable dynamics of stochastic complex systems from experimental data
Authors: Gao Ting-Ting , Barzel Baruch , Yan Gang 
Published: July 2024

AbstractComplex systems with many interacting nodes are inherently stochastic and best described by stochastic differential equations. Despite increasing observation data, inferring these equations from empirical data remains challenging. Here, we propose the Langevin graph network approach to learn the hidden stochastic differential equations of complex networked systems, outperforming five state-of-the-art methods. We apply our approach to two real systems: bird flock movement and tau pathology diffusion in brains. The inferred equation for bird flocks closely resembles the second-order Vicsek model, providing unprecedented evidence that the Vicsek model captures genuine flocking dynamics. Moreover, our approach uncovers the governing equation for the spread of abnormal tau proteins in mouse brains, enabling early prediction of tau occupation in each brain region and revealing distinct pathology dynamics in mutant mice. By learning interpretable stochastic dynamics of complex systems, our findings open new avenues for downstream applications such as control.
Turning copper into an efficient and stable CO evolution catalyst beyond noble metals
Authors: Xue Jing , Dong Xue , Liu Chunxiao , Li Jiawei , Dai Yizhou , Xue Weiqing , Luo Laihao , Ji Yuan , Zhang Xiao , Li Xu , Jiang Qiu , Zheng Tingting , Xiao Jianping , Xia Chuan 
Published: July 2024

AbstractUsing renewable electricity to convert CO2 into CO offers a sustainable route to produce a versatile intermediate to synthesize various chemicals and fuels. For economic CO2-to-CO conversion at scale, however, there exists a trade-off between selectivity and activity, necessitating the delicate design of efficient catalysts to hit the sweet spot. We demonstrate here that copper co-alloyed with isolated antimony and palladium atoms can efficiently activate and convert CO2 molecules into CO. This trimetallic single-atom alloy catalyst (Cu92Sb5Pd3) achieves an outstanding CO selectivity of 100% (±1.5%) at −402 mA cm−2 and a high activity up to −1 A cm−2 in a neutral electrolyte, surpassing numerous state-of-the-art noble metal catalysts. Moreover, it exhibits long-term stability over 528 h at −100 mA cm−2 with an FECO above 95%. Operando spectroscopy and theoretical simulation provide explicit evidence for the charge redistribution between Sb/Pd additions and Cu base, demonstrating that Sb and Pd single atoms synergistically shift the electronic structure of Cu for CO production and suppress hydrogen evolution. Additionally, the collaborative interactions enhance the overall stability of the catalyst. These results showcase that Sb/Pd-doped Cu can steadily carry out efficient CO2 electrolysis under mild conditions, challenging the monopoly of noble metals in large-scale CO2-to-CO conversion.
Reversible modulation of superconductivity in thin-film NbSe2 via plasmon coupling
Authors: Cheng Guanghui , Lin Meng-Hsien , Chen Hung-Ying , Wang Dongli , Wang Zheyan , Qin Wei , Zhang Zhenyu , Zeng Changgan 
Published: July 2024

AbstractIn recent years, lightwave has stood out as an ultrafast, non-contact control knob for developing compact superconducting circuitry. However, the modulation efficiency is limited by the low photoresponse of superconductors. Plasmons, with the advantages of strong light-matter interaction, present a promising route to overcome the limitations. Here we achieve effective modulation of superconductivity in thin-film NbSe2 via near-field coupling to plasmons in gold nanoparticles. Upon resonant plasmon excitation, the superconductivity of NbSe2 is substantially suppressed. The modulation factor exceeds 40% at a photon flux of 9.36 × 1013 s−1mm−2, and the effect is significantly diminished for thicker NbSe2 samples. Our observations can be theoretically interpreted by invoking the non-equilibrium electron distribution in NbSe2 driven by the plasmon-associated evanescent field. Finally, a reversible plasmon-driven superconducting switch is realized in this system. These findings highlight plasmonic tailoring of quantum states as an innovative strategy for superconducting electronics.
Maternal preconceptional and prenatal exposure to El Niño Southern Oscillation levels and child mortality: a multi-country study
Authors: Xu Hongbing , Zhuang Castiel Chen , Oddo Vanessa M. , Malembaka Espoir Bwenge , He Xinghou , Zhang Qinghong , Huang Wei 
Published: July 2024

AbstractEl Niño Southern Oscillation (ENSO) has been shown to relate to the epidemiology of childhood infectious diseases, but evidence for whether they increase child deaths is limited. Here, we investigate the impact of mothers’ ENSO exposure during and prior to delivery on child mortality by constructing a retrospective cohort study in 38 low- and middle-income countries. We find that high levels of ENSO indices cumulated over 0–12 lagged months before delivery are associated with significant increases in risks of under-five mortality; with the hazard ratio ranging from 1.33 (95% confidence interval [CI], 1.26, 1.40) to 1.89 (95% CI, 1.78, 2.00). Child mortality risks are particularly related to maternal exposure to El Niño-like conditions in the 0th–1st and 6th–12th lagged months. The El Niño effects are larger in rural populations and those with unsafe sources of drinking water and less education. Thus, preventive interventions are particularly warranted for the socio-economically disadvantaged.
Exploration on the potential efficacy and mechanism of methyl salicylate glycosides in the treatment of schizophrenia based on bioinformatics, molecular docking and dynamics simulation
Authors: Wang Xiuhuan , Ma Jiamu , Dong Ying , Ren Xueyang , Li Ruoming , Yang Guigang , She Gaimei , Tan Yunlong , Chen Song 
Published: July 2024

AbstractThe etiological and therapeutic complexities of schizophrenia (SCZ) persist, prompting exploration of anti-inflammatory therapy as a potential treatment approach. Methyl salicylate glycosides (MSGs), possessing a structural parent nucleus akin to aspirin, are being investigated for their therapeutic potential in schizophrenia. Utilizing bioinformation mining, network pharmacology, molecular docking and dynamics simulation, the potential value and mechanism of MSGs (including MSTG-A, MSTG-B, and Gaultherin) in the treatment of SCZ, as well as the underlying pathogenesis of the disorder, were examined. 581 differentially expressed genes related to SCZ were identified in patients and healthy individuals, with 349 up-regulated genes and 232 down-regulated genes. 29 core targets were characterized by protein-protein interaction (PPI) network, with the top 10 core targets being BDNF, VEGFA, PVALB, KCNA1, GRIN2A, ATP2B2, KCNA2, APOE, PPARGC1A and SCN1A. The pathogenesis of SCZ primarily involves cAMP signaling, neurodegenerative diseases and other pathways, as well as regulation of ion transmembrane transport. Molecular docking analysis revealed that the three candidates exhibited binding activity with certain targets with binding affinities ranging from −4.7 to −109.2 kcal/mol. MSTG-A, MSTG-B and Gaultherin show promise for use in the treatment of SCZ, potentially through their ability to modulate the expression of multiple genes involved in synaptic structure and function, ion transport, energy metabolism. Molecular dynamics simulation revealed good binding abilities between MSTG-A, MSTG-B, Gaultherin and ATP2B2. It suggests new avenues for further investigation in this area.
Mechanical release of homogenous proteins from supramolecular gels
Authors: Bianco Simona , Hasan Muhammad , Ahmad Ashfaq , Richards Sarah-Jane , Dietrich Bart , Wallace Matthew , Tang Qiao , Smith Andrew J. , Gibson Matthew I. , Adams Dave J. 
Published: July 2024

AbstractA long-standing challenge is how to formulate proteins and vaccines to retain function during storage and transport and to remove the burdens of cold-chain management. Any solution must be practical to use, with the protein being released or applied using clinically relevant triggers. Advanced biologic therapies are distributed cold, using substantial energy, limiting equitable distribution in low-resource countries and placing responsibility on the user for correct storage and handling. Cold-chain management is the best solution at present for protein transport but requires substantial infrastructure and energy. For example, in research laboratories, a single freezer at −80 °C consumes as much energy per day as a small household1. Of biological (protein or cell) therapies and all vaccines, 75% require cold-chain management; the cost of cold-chain management in clinical trials has increased by about 20% since 2015, reflecting this complexity. Bespoke formulations and excipients are now required, with trehalose2, sucrose or polymers3 widely used, which stabilize proteins by replacing surface water molecules and thereby make denaturation thermodynamically less likely; this has enabled both freeze-dried proteins and frozen proteins. For example, the human papilloma virus vaccine requires aluminium salt adjuvants to function, but these render it unstable against freeze–thaw4, leading to a very complex and expensive supply chain. Other ideas involve ensilication5 and chemical modification of proteins6. In short, protein stabilization is a challenge with no universal solution7,8. Here we designed a stiff hydrogel that stabilizes proteins against thermal denaturation even at 50 °C, and that can, unlike present technologies, deliver pure, excipient-free protein by mechanically releasing it from a syringe. Macromolecules can be loaded at up to 10 wt% without affecting the mechanism of release. This unique stabilization and excipient-free release synergy offers a practical, scalable and versatile solution to enable the low-cost, cold-chain-free and equitable delivery of therapies worldwide.
Psilocybin desynchronizes the human brain
Authors: Siegel Joshua S. , Subramanian Subha , Perry Demetrius , Kay Benjamin P. , Gordon Evan M. , Laumann Timothy O. , Reneau T. Rick , Metcalf Nicholas V. , Chacko Ravi V. , Gratton Caterina , Horan Christine , Krimmel Samuel R. , Shimony Joshua S. , Schweiger Julie A. , Wong Dean F. , Bender David A. , Scheidter Kristen M. , Whiting Forrest I. , Padawer-Curry Jonah A. , Shinohara Russell T. , Chen Yong , Moser Julia , Yacoub Essa , Nelson Steven M. , Vizioli Luca , Fair Damien A. , Lenze Eric J. , Carhart-Harris Robin , Raison Charles L. , Raichle Marcus E. , Snyder Abraham Z. , Nicol Ginger E. , Dosenbach Nico U. F. 
Published: July 2024

AbstractA single dose of psilocybin, a psychedelic that acutely causes distortions of space–time perception and ego dissolution, produces rapid and persistent therapeutic effects in human clinical trials1–4. In animal models, psilocybin induces neuroplasticity in cortex and hippocampus5–8. It remains unclear how human brain network changes relate to subjective and lasting effects of psychedelics. Here we tracked individual-specific brain changes with longitudinal precision functional mapping (roughly 18 magnetic resonance imaging visits per participant). Healthy adults were tracked before, during and for 3 weeks after high-dose psilocybin (25 mg) and methylphenidate (40 mg), and brought back for an additional psilocybin dose 6–12 months later. Psilocybin massively disrupted functional connectivity (FC) in cortex and subcortex, acutely causing more than threefold greater change than methylphenidate. These FC changes were driven by brain desynchronization across spatial scales (areal, global), which dissolved network distinctions by reducing correlations within and anticorrelations between networks. Psilocybin-driven FC changes were strongest in the default mode network, which is connected to the anterior hippocampus and is thought to create our sense of space, time and self. Individual differences in FC changes were strongly linked to the subjective psychedelic experience. Performing a perceptual task reduced psilocybin-driven FC changes. Psilocybin caused persistent decrease in FC between the anterior hippocampus and default mode network, lasting for weeks. Persistent reduction of hippocampal-default mode network connectivity may represent a neuroanatomical and mechanistic correlate of the proplasticity and therapeutic effects of psychedelics.
Normative longitudinal EEG recordings during sleep stage II in the first year of age
Authors: Harmony Thalía , Otero-Ojeda Gloria , Aubert-Vázquez Eduardo , Fernández Thalía , Cubero-Rego Lourdes 
Published: July 2024

AbstractThe electroencephalogram (EEG) is a fundamental diagnostic procedure that explores brain function. This manuscript describes the characteristics of a sample of healthy at-term infants. One hundred and three (103) infants from Mexico between 15 days and 12.5 months of age were recorded during physiological sleep. Referential EEG recordings were obtained using linked ear lobes as reference. The amplifier gain was 10,000, the bandwidth was set between 0.3 and 30 Hz, and the sample rate was 200 Hz. Sample windows of 2.56 s were marked for later quantitative analysis. To our knowledge, this is the first dataset of normal infants during the first year of age.
A diffusion MRI tractography atlas for concurrent white matter mapping across Eastern and Western populations
Authors: Li Yijie , Zhang Wei , Wu Ye , Yin Li , Zhu Ce , Chen Yuqian , Cetin-Karayumak Suheyla , Cho Kang Ik K. , Zekelman Leo R. , Rushmore Jarrett , Rathi Yogesh , Makris Nikos , O’Donnell Lauren J. , Zhang Fan 
Published: July 2024

AbstractThe study of brain differences across Eastern and Western populations provides vital insights for understanding potential cultural and genetic influences on cognition and mental health. Diffusion MRI (dMRI) tractography is an important tool in assessing white matter (WM) connectivity and brain tissue microstructure across different populations. However, a comprehensive investigation into WM fiber tracts between Eastern and Western populations is challenged due to the lack of a cross-population WM atlas and the large site-specific variability of dMRI data. This study presents a dMRI tractography atlas, namely theEast-West WM Atlas, for concurrent WM mapping between Eastern and Western populations and creates a large, harmonized dMRI dataset (n=306) based on the Human Connectome Project and the Chinese Human Connectome Project. The curated WM atlas, as well as subject-specific data including the harmonized dMRI data, the whole brain tractography data, and parcellated WM fiber tracts and their diffusion measures, are publicly released. This resource is a valuable addition to facilitating the exploration of brain commonalities and differences across diverse cultural backgrounds.
A Multi-Center, Multi-Parametric MRI Dataset of Primary and Secondary Brain Tumors
Authors: Gong Zhenyu , Xu Tao , Peng Nan , Cheng Xing , Niu Chen , Wiestler Benedikt , Hong Fan , Li Hongwei Bran 
Published: July 2024

AbstractBrain metastases (BMs) and high-grade gliomas (HGGs) are the most common and aggressive types of malignant brain tumors in adults, with often poor prognosis and short survival. As their clinical symptoms and image appearances on conventional magnetic resonance imaging (MRI) can be astonishingly similar, their accurate differentiation based solely on clinical and radiological information can be very challenging, particularly for “cancer of unknown primary”, where no systemic malignancy is known or found. Non-invasive multiparametric MRI and radiomics offer the potential to identify these distinct biological properties, aiding in the characterization and differentiation of HGGs and BMs. However, there is a scarcity of publicly available multi-origin brain tumor imaging data for tumor characterization. In this paper, we introduce a multi-center, multi-origin brain tumor MRI (MOTUM) imaging dataset obtained from 67 patients: 29 with high-grade gliomas, 20 with lung metastases, 10 with breast metastases, 2 with gastric metastasis, 4 with ovarian metastasis, and 2 with melanoma metastasis. This dataset includes anonymized DICOM files alongside processed FLAIR, T1-weighted, contrast-enhanced T1-weighted, T2-weighted sequences images, segmentation masks of two tumor regions, and clinical data. Our data-sharing initiative is to support the benchmarking of automated tumor segmentation, multi-modal machine learning, and disease differentiation of multi-origin brain tumors in a multi-center setting.
Chromosome-level genome assembly of Aquilaria yunnanensis
Authors: Li Meifei , Zhang Yingmin , Wang Yi , Yin Yue , Zhou Meijun , Zhang Yonghong 
Published: July 2024

AbstractAquilaria yunnanensis is an endangered agarwood-producing tree currently listed on the IUCN Red List of Threatened Species. The agarwood it produces has important medicinal and economic value, but its population has sharply declined due to human destruction and habitat reduction. Therefore, obtaining genomic information on A. yunnanensis is beneficial for its protection work. We assembled a chromosome-level reference genome of A. yunnanensis by using BGI short reads, PacBio HiFi long reads, coupled with Hi-C technology. The final genome assembly of A. yunnanensis is 847.04 Mb, with N50 size of 99.68 Mb, in which 805.49 Mb of the bases were anchored on eight pseudo-chromosomes. Two gapless pseudo-chromosomes were detected in the assembly. A total of 27,955 protein-coding genes as well as 74.65% repetitive elements were annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of A. yunnanensis, as well as the molecular phylogenetics and evolutionary patterns in Aquilaria.
Trends in hepatitis C virus seroprevalence and associated risk factors among msm in Pakistan: insights from a community-based study
Authors: Tirmizi Raza , Munir Rimsha , Zaidi Nousheen 
Published: July 2024

AbstractPakistan bears a substantial burden of hepatitis C virus (HCV) infection, with the second-highest prevalence globally. This community-based cross-sectional study, conducted from January to December 2022 in Punjab, Pakistan, investigates the seroprevalence of HCV among the men who have sex with men (MSM) population. The study identifies demographic and behavioral risk factors associated with HCV infection within this population group. Among the 501 participants, the study found an HCV seroprevalence of 14.86%. The association between demographic characteristics and seroprevalence is assessed by calculating the percentage of positive cases, revealing notable associations with age, education level, and self-identified sexual orientation. Furthermore, the study identified several behavioral risk factors positively associated with HCV seroprevalence, including sharing personal items such as razors and toothbrushes, histories of surgery, blood transfusion, dental procedures, intravenous drug use, and therapeutic injection histories. These risk factors were identified through structured interviews, and the prevalence of HCV seropositivity among the exposed groups was calculated accordingly. Interestingly, a lower HCV positivity rate was observed among self-reported HIV-positive individuals, contradicting previous research. The findings underscore the need for comprehensive, targeted prevention strategies such as risk factor awareness campaigns and educational programs tailored for the MSM population in Pakistan. Further research is warranted to validate these findings and better understand the complex interplay of factors contributing to HCV seroprevalence in this high-risk population.
Thymoquinone’ potent impairment of multidrug-resistant Staphylococcus aureus NorA efflux pump activity
Authors: Ahmad Adel Attia M. , Abdelgalil Sara Y. , Khamis Tarek , Abdelwahab Ashraf M. O. , Atwa Dina Nader , Elmowalid Gamal A. 
Published: July 2024

AbstractThe drug efflux pump is a crucial mechanism implicated in resistance to multiple antimicrobials. Thymoquinone (TQ) has evidently demonstrated multiple activities, antibacterial being the most effective. Knowledge about TQ activity against multidrug-resistant Staphylococcus aureus is very scarce. Therefore, the present study was conducted to investigate TQ resistance modulation in ciprofloxacin (CIP) and doxycycline (DO) multidrug-resistant S. aureus. Forty-seven samples were collected from different sources, and S. aureus was isolated and identified. Then, S. aureus resistance profiles to antimicrobials, N. sativa essential oil, and TQ; the correlation between TQ-MIC readings and disc diffusion; cartwheel and ethidium bromide (EtBr) accumulation assays; and norA gene expression were all described within silico molecular docking for TQ interactions with norA efflux pump protein. TQ-MICs ranged from 5–320 µg/ml. TQ down-regulated norA gene expression, resulting in a drop in efflux pump activity of 77.5–90.6% in the examined strains, comparable to that observed with verapamil. Exposure of S. aureus strains to CIP and DO raises the initial basal efflux pumping expression to 34.2 and 22.9 times, respectively. This induced efflux pumping overexpression was substantially reduced by 97.7% when TQ was combined with CIP or DO. There was a significant reduction of MICs of CIP and DO MICs by 2–15 and 2–4 folds, respectively, after treatment with 0.5XMIC-TQ in resistance modulation assays. These results refer to TQ ligand inhibitory interactions with NorA protein in molecular docking. Interpretations of inhibition zone diameters (IZDs) of disc diffusion and TQ-MICs exhibit independence of MICs from IZDs, as indicated by invalid linear regression analysis. TQ significantly reduced efflux pumping S. aureus induced by CIP and DO, but further investigations are needed to improve TQ-pharmacokinetics to restore CIP and DO activity and suppress fluoroquinolone and doxycycline-resistant S. aureus selection in clinical and animal settings.