bluuebunny/crossref_metadata_2025_split huggingface dataset:
New MiniPromoter Ple389 (ADORA2A) Drives Selective Expression in Medium Spiny Neurons in Mice and Non-human Primates
Authors: Gomes Alissandra de Moura , Petkau Terri L. , Korecki Andrea J. , Fornes Oriol , Galvan Adriana , Lu Ge , Hill Austin M. , Lam Siu Ling , Yao Anqi , Farkas Rachelle A. , Wasserman Wyeth , Smith Yoland , Simpson Elizabeth , Leavitt Blair 
Published: November 2024

Abstract

Compact cell type-specific promoters are important tools for basic and preclinical research and clinical delivery of gene therapy. In this work, we designed novel MiniPromoters to target D1 and D2 type dopaminoceptive medium spiny neurons in the striatum by manually identifying candidate regulatory regions or employing the OnTarget webserver. We then empirically tested the designs in rAAV-PHP.B for specificity and robustness in three systems: intravenous injection in mice, intracerebroventricular injection in mice, and intracerebroventricular injection in non-human primates. Twelve MiniPromoters were designed from eight genes: seven manually and five using OnTarget. When delivered intravenously in mice, three MiniPromoters demonstrated highly selective expression in the striatum, with Ple389 (ADORA2A) showing high levels of dopamine D2-receptor cell co-localization. The same three MiniPromoters also displayed enriched expression in the striatum when delivered intracerebroventricularly in mice with high levels of DARPP32 co-localization. Finally, Ple389 (ADORA2A) was intracerebroventricularly injected in non-human primates and showed enriched expression in the striatum as in the mouse. Ple389 (ADORA2A) demonstrated expression in the medium spiny neurons in all three systems tested and exhibited the highest level of D2-MSNs and DARPP32 co-labeling in mice, demonstrating its potential as a tool for gene therapy approaches for Parkinson and Huntington disease treatment.
Biofabricated SnO2 Nanoparticles derived from Leaves Extract of Morinda citrifolia and Pandanus amaryllifolius for Photocatalytic Degradation
Authors: Buniyamin Irmaizatussyehdany , Asli Noor Asnida , Ak Rabiatuladawiyah Md , Jafar Salifairus Mohammad , Eswar Kevin Alvin , Mahmood Mohd Khairil Adzhar , Idorus Mohd Yusri , Shamsudin Muhammad Salleh , Rahman Motiur , Mahmood Mohamad Rusop , Khusaimi Zuraida 
Published: November 2024

Abstract

This study investigates the biofabrication of SnO₂ nanoparticles (NPs) utilizing leaf extracts from Morinda citrifolia and Pandanus amaryllifolius for photocatalytic degradation of methylene blue (MB). The synthesis method integrates tin chloride pentahydrate with the leaf extracts, followed by calcination. Comprehensive characterization via FTIR, XRD, FESEM, EDX, HRTEM, and UV-Vis spectroscopy confirmed the successful formation of SnO₂ NPs, revealing distinct morphological and crystalline properties. Photocatalytic tests demonstrated that SnO₂ NPs derived from M. citrifolia achieved a superior degradation rate of 97%, compared to 80% from P. amaryllifolius, with optimal activity under neutral pH. Radical scavenger experiments identified electrons as the primary active species. Reusability tests indicated a gradual decline in efficiency over five cycles, demonstrating its stability. These findings underscore the potential of biofabricated SnO₂ NPs as sustainable and efficient solutions for dye-polluted water remediation, offering a promising avenue for environmental conservation and resource management.
Halogen bond-modulated solid-state reordering and symmetry breaking of azahelicenes
Authors: Qiu Huibin , Liang Juncong , Gan Fuwei , Zhang Guoli , Shen Chengshuo 
Published: November 2024

Abstract

Spontaneous symmetry breaking plays an essential role in revealing the origin of homochirality in nature. However, previous studies have prevalently focused on the emergence of symmetry breaking upon the aggregation of discrete molecules in solution. Herein, we report a unique solid-state symmetry breaking process of dynamically chiral azahelicenes that emerged in vacuum-driven transformation of halogen bond-woven crystals. Aza[6]helicene with fixed chirality is first employed to co-crystallized with various halides to explore the strength of intermolecular halogen bonds. Due to the weak feature of the halogen bonding, the halides in the cocrystals can be completely removed under vacuum at an elevated temperature, allowing the residual aza[6]helicene molecules to reorder into single crystals. Particularly, the micron sheet of the cocrystal formed with 1,3,5-trifluoro-2,4,6-triiodobenzene directly transforms into tightly packed slim blocks. Further, aza[4]helicene which possesses chiral conformations but rapidly enantiomerizes in solution is adopted to prepare halogen bond-woven cocrystals. While all the cocrystals are comprised by equal amount of P and M isomers, the solid formed after the removal of pentafluoroiodobenzene is found to be chiroptically active. The aza[4]helicene molecules released from the halogen bond network solely adopt one chiral conformation upon reordering and symmetry breaking instantly occurs in a solid state. The Cotton effects gradually increase with the extension of vacuum–heating treatment, indicating a unidirectional transformation of the chiral conformations and an amplification of symmetry breaking during the solid-state reorganization. Precise manipulation for the absolute configuration of the solid-state symmetry breaking is further accomplished by using aza[6]helicene as a chiral inducer. This work provides new insights into the origin of homochiral solid biostructures and expands the pathway to versatile chiral organic materials from achiral/racemic precursors.
Temperature-sensitive shape memory polyamide elastomers with tunable segments: achieving excellent performances and application prospects
Authors: Yuan Chengke , Li Yingchun , Xue Jianyu , Mi Jia , Wang Yu , Toktarbay Zhexenbek 
Published: November 2024

Abstract

Thermoplastic polyamide elastomers (TPAEs) possess remarkable characteristics such as high-temperature tolerance, superior mechanical properties, and the shape memory effect (SME). In the current study, a type of TPAEs with SME is developed by fabricating the long carbon chain polyamide (PA512) and polyethylene glycol (PEG) through a two-step melt polycondensation process. The properties of TPAEs were investigated by varying the PA512 prepolymer's molecular weight and the amount of PEG. During synthesizing TPAEs with SME, the crucial balance of COOH and OH groups was skillfully achieved by introducing biobased butanediol (BDO). The chemical structure of TPAEs is confirmed by FTIR and 1H NMR tests. By meticulously engineering the PA512 molecular weight and refining the PEG domain content, TPAEs are fabricated to elongate at a break of 592.4% at room temperature while maintaining a tensile strength of 23.1 MPa. TPAEs, which have two distinct melting temperatures, exhibit microphase separation between the PEG and PA512 domains. This phenomenon is further corroborated by the scanning electron microscope (SEM) test. Additionally, TPAEs exhibit the SME, which can fix a temporary shape when heated, twisted, and cooled, then recover to its original shape upon reheating, with TPAE230 demonstrating the most outstanding shape memory effect, achieving an average shape fixity ratio of 91.2% and a shape recovery ratio of 94.4%. This behavior is attributed to the fixing force provided by the PEG domains and the entropy elasticity of the physically cross-linked PA512 domains. The findings indicate that TPAEs exhibit enhanced SME in response to temperature changes. Leveraging this property, the development of a temperature-sensitive device holds promise for achieving breakthroughs in the realm of elastic temperature sensing applications.
Origin of the depth-dependent anisotropy in the Earth’s inner core
Authors: Kolesnikov Efim , Li Xiang , Müller Susanne , Rohrbach Arno , Klemme Stephan , Berndt Jasper , Liermann Hanns-Peter , Sanchez-Valle Carmen , Kupenko Ilya 
Published: November 2024

Abstract

The understanding of the origin of seismic anisotropy in the Earth’s inner core (IC) remains a subject of debate and requires examining the deformation behavior of potential core materials. In this research, we investigated the effect of silicon and carbon on the deformation of the hexagonal close-packed iron alloy employing radial X-ray diffraction at high-pressure, high-temperature conditions. We revealed the low anisotropy of the sound velocity (~2 %) of the Fe-Si-C alloy that is compatible with the anisotropy observed in the IC’s outer shells. This finding provides an explanation for the heterogeneous depth-dependent elastic anisotropy in the IC originating from the stratification of silicon and carbon within the inner core upon its crystallization.
Decision Support System Using the Expert-Fuzzy Method in Validating Real-Time Acid Rain Measurements
Authors: Ramadhan Ardiansyah , Chandra Indra , Indrawati Asri , Tanti Dyah Aries , Mendonça Israel , Aritsugi Masayoshi 
Published: November 2024

Abstract

The measurement of acid rain is a very important instrument for evaluating the environmental effects of air pollution on ecosystems. However, the existing manual methods use few parameters, leading to inefficacy and incomplete data for suitable decision-making. A new system for real-time information is proposed in this study, which employs the Expert-Fuzzy method within a Decision Support System (DSS) that enhances the precision and consistency of acid rain measurements. Such improvements include individual sensor range detection, outlier identification, dynamic windowing, and averaging from their integration into Raspberry Pi, an advanced statistical technique. These enhancements improve confidence intervals and precision in the real-time validation of data. From May 7 until June 7 2023, field testing was taking place at two locations (-6.9729594 107.6274528; − 6.969282, 107.6255821) where key parameters like pH, temperature, and conductivity, among others, were being monitored to ensure a confidence level of approximately 95%. The little discrepancies between raw data and validated allude to this system’s precision since after validation, pH readings were 5.99, conductivity measured 14.47 ms/cm, and temperatures showed 25.01℃. The more support for the stability of these measurements from the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model, which traces back the sources of possible neutralization pollutants. This research shows that acid rain classification and decision-making can be enhanced by combining expert knowledge with fuzzy logic. Using the Expert-Fuzzy method, environmental monitoring measurements can be made more precise.
YTHDF2 promotes anaplastic thyroid cancer progression via activating the DDIT4/AKT/mTOR signaling
Authors: Dai Bao , Xu Lei , Rong Shikuo , Song Muye , Lan Ziteng , Chen Weijian , Liu Yongchen , Wang Linhe , Li Jinghua , Chen Jian , Wu Zeyu 
Published: November 2024

Abstract

Background RNA methylation, an important reversible post-transcriptional modification in eukaryotes, has emerged as a prevalent epigenetic alteration. However, the role of the m6A reader YTH domain family 2 (YTHDF2) has not been reported in anaplastic thyroid cancer (ATC) and its biological mechanism is unclear.Methods The relationship between YTHDF2 expression and ATC was determined through the utilization of data sets and tissue samples. A range of analytical techniques were employed to investigate the regulatory mechanism of YTHDF2 in ATC, including bioinformatics analysis, M6A dot-blot analysis, methylated RNA immunoprecipitation sequencing (MeRIP-seq), RNA immunoprecipitation (RIP) assays, RNA sequencing, RNA stability assays and dual luciferase reporter gene assays. In vitro and in vivo assays were also conducted to determine the contribution of YTHDF2 to ATC development.Results In this study, we found that YTHDF2 expression was significantly increased in ATC. Our comprehensive in vitro and in vivo experiments demonstrated that YTHDF2 knockdown significantly attenuated ATC proliferation, invasion, migration, and promotion of apoptosis, whereas the opposite trend was obtained with YTHDF2 overexpression. Mechanically, RNA-seq, MeRIP-seq and RIP-seq analysis, and molecular biology experiments demonstrated that YTHDF2 accelerated the degradation of DNA damage and Development 1 (DDIT4, or REDD1) mRNA in an m6A-dependent manner, which in turn activated the AKT/mTOR signaling pathway and induced activation of epithelial-mesenchymal transition (EMT), thereby promoting ATC tumor progression.Conclusions This study is the first to demonstrate that elevated YTHDF2 expression levels suppress DDIT4 expression in an m6A-dependent manner and activate the AKT/mTOR signaling pathway, thereby promoting ATC progression. YTHDF2 plays a pivotal role in ATC progression, and it may serve as a promising therapeutic target in the future.
Python-Driven Mapping of Artificial Groundwater Recharge Zones: Application in Dhar District, Madhya Pradesh, India
Authors: Rathore Ankit Kailashi , Khan Shafia , Verma Pramod K , Chaure Shailesh K 
Published: November 2024

Abstract

In regions with limited rainfall and ephemeral drainage patterns, groundwater is an invaluable resource for sustaining life and supporting agriculture. This study focuses on identifying groundwater potential recharge zones in Madhya Pradesh's tribal-dominated Dhar district, which was declared a 'water scarce' area in 2022 and restricted for groundwater use, even for irrigation. Dhar's geological setting suggests over 95% of impervious rocks (Basalt, Gneiss, and Granite), while aquifer rocks (sandstone and limestone) are less than 4%, poses significant challenges for groundwater recharge. This study leverages Python and open-source tools instead of proprietary software for identifying groundwater recharge zones. The Python integrates various factors influencing the groundwater availability into a composite map and categorizes the Dhar district into six distinct groundwater recharge classes: excellent (about 4.5% area), good (41% area), fine (34%), moderate (10% area), bad (6% area), and unaccepted (about 2.7% area). The Python-generated integrated map has been validated by groundwater level monitoring station data of IWRIS (India Water Resources Information System), confirming the model accuracy. This study substantiate the effectiveness of Python and open-source tools for groundwater management, can provide a scalable solution for water-scarce regions.
Identification and functional analysis of NPR2 truncating mutations in two Chinese families with Short Stature
Authors: Wei Shuoshuo , Li Rong , He Dongye , Zhang Chuanpeng , Zhang Mei , Li Yanying , Chen Shuxiong , Liu Fupeng , Ban Bo , Zhao Qianqian 
Published: November 2024

Abstract

Background: The signaling pathway of C-type natriuretic peptide (CNP) and its receptor (natriuretic peptide receptor 2, NPR2) is implicated in the process of endochondral ossification, which is crucial for the linear growth of long bones. Loss-of-function mutations in the NPR2 gene cause short stature. This study aimed to identify and characterize truncating mutations in NPR2 among Chinese families with short stature.
Methods: Whole-exome sequencing and Sanger sequencing were conducted to identify potential mutations. Bioinformatic analysis was utilized to assess the pathogenicity of two mutations. The effects of candidate mutation on gene expression, subcellular localization, protein stability, and protein function were further assessed through in vitro assays.
Results: In this study, A novel mutation, c.2629_2630delAG, p.S877Hfs*10 and a previously reported mutation, c.1162C>T, p.R388* (ClinVar database) in NPR2, were identified in the individuals, and these variants were inherited from the mother and father, respectively. Both mutations were predicted to be deleterious and have a significant impact on protein structure based on bioinformatics analysis. In vitro experiments demonstrated that mutant mRNAs evaded nonsense-mediated mRNA decay (NMD) to produce truncated NPR2 proteins with reduced stability and increased degradation. Furthermore, two truncated NPR2 proteins exhibited impaired localization at the cell membrane and almost completely lost their ability to stimulate cyclic guanosine monophosphate (cGMP) production in HEK293T cells compared to wild-type (WT) NPR2 (p <0.05).
Conclusion: Our study identified two loss-of-function mutations of the NPR2 gene in two Chinese families and offered new insights on the pathogenesis of short stature caused by NPR2 truncating mutations.
Detection of small-magnitude events using unsupervised machine learning for waveform-based source imaging through grouped time reversals
Authors: Dalai Bijayananda , Kumar Prakash 
Published: November 2024

Abstract

Efficient arrival picking is one of the crucial steps for seismic data processing both in active and passive seismology. We employ the unsupervised Fuzzy C-means clustering to improve the picking of the arrivals of small magnitude earthquake events, and then source location is computed by grouped time-reversal imaging approach by first splitting the receivers into groups and then backward propagating the wavefield. Once the arrivals are auto picked, P-wave signals are identified and extracted from the entire waveforms. Finally, a high-resolution source location image is obtained by multidimensional cross-correlation of the wavefields. The performance of the approach has been tested on a suite of synthetic data and field data sets obtained from the North-West Himalayan region of Jammu and Kashmir. The estimated uncertainties reveal the improvement of the locations over the conventional travel time inversion method. We demonstrate that these two independent approaches can effectively be used to analyze seismological data sets in a complex medium, and even works with sparse seismic networks for locating the small-magnitude earthquakes. The present approach can be used to locate the seismic sources utilizing the single-component waveform data.
A nature-is-enhancing mindset improves depressive emotions through a chain mediation model
Authors: Chen Yue , Zhang Xiaoqi , Chen Yidi 
Published: November 2024

Abstract

It is widely acknowledged that nature benefits human well-being, both physically and psychologically. However, the role of mindsets in this relationship between humans and nature has not received sufficient attention. This study conducted two investigations to explore the role of mindsets in the context of nature and to reveal the underlying mediating mechanism between nature-is-enhancing mindsets and depression. Study 1 introduced a reliable and valid four-item tool to measure the nature-is-enhancing mindset, which evaluates individuals' beliefs about nature as beneficial. Study 2 illustrated that a nature-is-enhancing mindset could significantly decrease depression. Furthermore, nature contact and perceived stress were identified as mediators in the association between nature-is-enhancing mindsets and depression. Perceived stress had a significant mediating effect. This study proposes a strong antecedent variable that explains the beneficial effects of natural contact, providing new perspectives and directions for cognitive interventions aimed at promoting engagement with nature.
O-GlcNAcylation of irf3 by a novel Zebrafish O-GlcNAc transferase isoform Ogtb_tv3 facilitates its sufficient activation and innate antiviral response
Authors: LU CAO , Aoling Xu , Jie Zhang , Hai Huang , Dandan Xu , Songlin Liu , yan Zhao , Jing Zhou , Liu Hongtao 
Published: November 2024

Abstract

Metabolic pathways are crucial for regulating immune responses, yet the specific mechanisms influencing innate immunity in fish during viral infections remain poorly understood. This study aims to bridge this gap by elucidating the role of the hexosamine biosynthesis pathway (HBP)–associated O-linked β-N-acetylglucosamine (O-GlcNAc) signaling in enhancing antiviral innate immunity in zebrafish. We discovered that infection with spring viremia of carp virus (SVCV) significantly activates the HBP, leading to enhanced protein O-GlcNAcylation in zebrafish. We identified a novel O-GlcNAc transferase isoform, Ogtb_tv3, essential for the O-GlcNAcylation of the transcription factor IRF3. This modification is crucial for the full activation of IRF3 and the subsequent initiation of antiviral gene expression. Pharmacological enhancement of the HBP - O-GlcNAc pathway further potentiated these antiviral responses, directly linking metabolic activity to immune efficacy. Our findings demonstrate that O-GlcNAcylation mediated by Ogtb_tv3 within the HBP is critical for activating IRF3 during SVCV infection, thus enhancing the immune response in zebrafish. This study highlights the significant role of glucose metabolism in antiviral innate immunity and suggests targeting metabolic pathways as a novel therapeutic strategy against viral infections.
Dietary Influences on Osteoporosis: Insights from a Natural Population Cohort in Sichuan, China
Authors: Yang Rong , Zhao Qian , Yao Yi , Li Jieling , Fu Wenjun , Wu Miaomiao , Xiong Jing 
Published: November 2024

Abstract

Purpose:This study aims to assess the impact of dietary factors on osteoporosis prevalence within a natural population in Sichuan, China, to establish a foundation for future dietary intervention strategies.
Methods: Participants were drawn from a prospective natural population cohort study centered in Sichuan, selecting representative sites and employing cluster random sampling to execute cohort projects across various locations in Southwestern China. This approach enabled the collection of data from populations with diverse geographical, economic and cultural characteristics, and ethnicities. Based on baseline data, univariate and multivariate ordinal logistic regression analyses were performed to evaluate the impact of diet on the prevalence of osteoporosis.
Results: The study included 1,099 participants, with an average age of 63.1 years, comprising 345 men (31.39%) and 754 women (68.61%), Of these, 277 individuals (25.20%) were diagnosed with osteoporosis. After adjusting for age and gender, preliminary analysis revealed that consuming tea once to twice a week was associated with a reduced risk of osteoporosis (RR=0.645, 95% CI 0.418-0.997), while no other dietary factors demonstrated a significant effect. Further analysis indicated that among women, consuming tea once to twice a week was associated with a reduced risk of osteoporosis (RR=0.576, 95% CI 0.353-0.940). Among men, a preference for spicy foods was linked to a lower risk of osteoporosis (RR=0.110, 95% CI 0.014-0.885), and the use of olive oil as a dietary oil was identified as a potential risk factor for osteoporosis (RR=36.120, 95% CI 2.231-584.820).
Conclusion: This study, leveraging a natural population cohort in the Sichuan area, explores the influence of diet on osteoporosis. The findings suggest that in women, drinking tea once to twice a week may serve as a preventative measure against osteoporosis, whereas in men, a preference for spicy flavors can provide similar protection and using olive oil as a dietary oil was identified as a risk factor for osteoporosis.
Trial registration number: ChiCTR1900024623
Date of registration: 2019-07-19