bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaccination with Mincle agonist UM-1098 and mycobacterial antigens induces protective Th1 and Th17 responses
Authors: Rungelrath Viktoria , Ahmed Mushtaq , Hicks Linda , Miller Shannon M. , Ryter Kendal T. , Montgomery Kyle , Ettenger George , Riffey Alexander , Abdelwahab Walid M. , Khader Shabaana Abdul , Evans Jay T. 
Published: June 2024

AbstractTuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of the top infectious killers in the world. The only licensed vaccine against TB, Bacille Calmette-Guérin (BCG), provides variable protection against pulmonary TB, especially in adults. Hence, novel TB vaccine approaches are urgently needed. Both Th1 and Th17 responses are necessary for protection against TB, yet effective adjuvants and vaccine delivery systems for inducing robust Th1 and Th17 immunity are lacking. Herein we describe a synthetic Mincle agonist, UM-1098, and a silica nanoparticle delivery system that drives Th1/Th17 responses to Mtb antigens. Stimulation of human peripheral blood mononuclear cells (hPBMCs) with UM-1098 induced high levels of Th17 polarizing cytokines IL-6, IL-1β, IL-23 as well as IL-12p70, IL-4 and TNF-α in vitro. PBMCs from both C57BL/6 and BALB/c mice responded with a similar cytokine pattern in vitro and in vivo. Importantly, intramuscular (I.M.) vaccination with UM-1098-adjuvanted TB antigen M72 resulted in significantly higher antigen-specific IFN-γ and IL-17A levels in C57BL/6 wt mice than Mincle KO mice. Vaccination of C57BL/6 wt mice with immunodominant Mtb antigens ESAT6/Ag85B or M72 resulted in predominantly Th1 and Th17 responses and induced antigen-specific serum antibodies. Notably, in a virulent Mtb challenge model, vaccination with UM-1098 adjuvanted ESAT6/Ag85B or M72 significantly reduced lung bacterial burden when compared with unvaccinated mice and protection occurred in the absence of pulmonary inflammation. These data demonstrate that the synthetic Mincle agonist UM-1098 induces strong Th1 and Th17 immunity after vaccination with Mtb antigens and provides protection against Mtb infection in mice.
Sustainability of global small-scale constructed wetlands for multiple pollutant control
Authors: Chen Guogui , Mo Yuanyuan , Gu Xuan , Jeppesen Erik , Xie Tian , Ning Zhonghua , Li Yina , Li Dongxue , Chen Cong , Cui Baoshan , Wu Haiming 
Published: June 2024

AbstractThe global wastewater surge demands constructed wetlands (CWs) to achieve the UN’s Sustainable Development Goals (SDG); yet the pollutant removal interactions and global sustainability of small CWs are unclear. This study synthesizes small CW data from 364 sites worldwide. The removal efficiency of organic matter and nutrient pollutants of small CWs had a 75th percentile of 68.8–84.0%. Bivariate analysis found consistent synergies between pollutant removals, lasting 3–12 years. The optimal thresholds for maintaining the synergistic effects were as follows: area size—17587 m2, hydraulic loading rate—0.45 m/d, hydraulic retention time—8.2 days, and temperature—20.2 °C. When considering the co-benefits and sustainability of small CWs for multi-pollutants control, promoting small-scale CWs could be an effective and sustainable solution for managing diverse wastewater pollutants while simultaneously minimizing land requirements. This solution holds the potential to address the challenges posed by global water scarcity resulting from wastewater discharge and water pollution.
Harmonized Database of Western U.S. Water Rights (HarDWR) v.1
Authors: Lisk Matthew D. , Grogan Danielle S. , Zuidema Shan , Zheng Jiameng , Caccese Robert , Peklak Darrah , Fisher-Vanden Karen , Lammers Richard B. , Olmstead Sheila M. , Fowler Lara 
Published: June 2024

AbstractIn the arid and semi-arid Western U.S., access to water is regulated through a legal system of water rights. Individuals, companies, organizations, municipalities, and tribal entities have documents that declare their water rights. State water regulatory agencies collate and maintain these records, which can be used in legal disputes over access to water. While these records are publicly available data in all Western U.S. states, the data have not yet been readily available in digital form from all states. Furthermore, there are many differences in data format, terminology, and definitions between state water regulatory agencies. Here, we have collected water rights data from 11 Western U.S. state agencies, harmonized terminology and use definitions, formatted them for consistency, and tied them to a Western U.S.-wide shapefile of water administrative boundaries.
Exercise may delay cognitive decline in Chinese older adults: a causal inference for ordered multi-categorical exposures with a Mendelian randomization approach
Authors: Han Lizhen , Zeng Yi , Huang Tao , Jia Jinzhu 
Published: June 2024

AbstractThe cognitive problems are prominent in the context of global aging, and the traditional Mendelian randomization method is not applicable to ordered multi-categorical exposures. Therefore, we aimed to address this issue through the development of a method and to investigate the causal inference of cognitive-related lifestyle factors. The study sample was derived from the Chinese Longitudinal Healthy Longevity Survey, which included 897 older adults aged 65 + . This study used genome-wide association analysis to screen genetic loci as instrumental variables and innovatively combined maximum likelihood estimation to infer causal associations between ordered multi-categorical exposures (diet, exercise, etc.) and continuous outcomes (cognitive level). The causal inference method for ordered multi-categorical exposures developed in this study was simple, easy to implement, and able to effectively and reliably discover the potential causal associations between variables. Through this method, we found a potential positive causal association between exercise status and cognitive level in Chinese older adults ($$\widehat{\beta }$$

β
^

= 1.883, 95%CI 0.182–3.512), in which there was no horizontal pleiotropy (p = 0.370). The study provided a causal inference method applicable to ordered multi-categorical exposures, that addressed the limitations of the traditional Mendelian randomization method.
Quality evaluation of chicken soup based on entropy weight method and grey correlation degree method
Authors: Cao Zhongwen , Zhang Tanglei , Tong XiKui 
Published: June 2024

AbstractThis study aimed to develop an assessment framework for evaluating the quality of different chicken soup variants. Three types of chicken soup, traditional chicken soup (TCS), concentrated chicken soup (CCS), and blended chicken soup (BCS), were prepared and analyzed for various physicochemical parameters, including gross protein content, crude fat content, pH level, solid content, viscosity, and chromatic aberration value. Sensory evaluation was also conducted to assess overall quality. Correlation analysis helped identify three key evaluation indicators: gross protein content, L* value (lightness), and b* value (chromatic aberration). The weight assigned to gross protein content was the highest using the entropy weight method (EWM). Moreover, the grey correlation degree method was comprehensively applied to evaluate the chicken soup's quality. This analysis identified TCS and CCS as varieties with superior overall quality, showing a positive correlation with sensory evaluation, consistent with the results of nuclear magnetic resonance (NMR) used in this paper. These results provide theoretical support for assessing comprehensive quality and selecting chicken soup varieties.
Integrated transmission expansion planning incorporating fault current limiting devices and thyristor-controlled series compensation using meta-heuristic optimization techniques
Authors: Almalaq Abdulaziz , Alqunun Khalid , Abbassi Rabeh , Ali Ziad M. , Refaat Mohamed M. , Abdel Aleem Shady H. E. 
Published: June 2024

Abstract
Transmission expansion planning (TEP) is a vital process of ensuring power systems' reliable and efficient operation. The optimization of TEP is a complex challenge, necessitating the application of mathematical programming techniques and meta-heuristics. However, selecting the right optimization algorithm is crucial, as each algorithm has its strengths and limitations. Therefore, testing new optimization algorithms is essential to enhance the toolbox of methods. This paper presents a comprehensive study on the application of ten recent meta-heuristic algorithms for solving the TEP problem across three distinct power networks varying in scale. The ten meta-heuristic algorithms considered in this study include Sinh Cosh Optimizer, Walrus Optimizer, Snow Geese Algorithm, Triangulation Topology Aggregation Optimizer, Electric Eel Foraging Optimization, Kepler Optimization Algorithm (KOA), Dung Beetle Optimizer, Sea-Horse Optimizer, Special Relativity Search, and White Shark Optimizer (WSO). Three TEP models incorporating fault current limiters and thyristor-controlled series compensation devices are utilized to evaluate the performance of the meta-heuristic algorithms, each representing a different scale and complexity level. Factors such as convergence speed, solution quality, and scalability are considered in evaluating the algorithms’ performance. The results demonstrated that KOA achieved the best performance across all tested systems in terms of solution quality. KOA’s average value was 6.8% lower than the second-best algorithm in some case studies. Additionally, the results indicated that WSO required approximately 2–3 times less time than the other algorithms. However, despite WSO’s rapid convergence, its average solution value was comparatively higher than that of some other algorithms. In TEP, prioritizing solution quality is paramount over algorithm speed.
A randomized controlled trial of alpha phase-locked auditory stimulation to treat symptoms of sleep onset insomnia
Authors: Bressler Scott , Neely Ryan , Yost Ryan M , Wang David 
Published: June 2024

AbstractSleep onset insomnia is a pervasive problem that contributes significantly to the poor health outcomes associated with insufficient sleep. Auditory stimuli phase-locked to slow-wave sleep oscillations have been shown to augment deep sleep, but it is unknown whether a similar approach can be used to accelerate sleep onset. The present randomized controlled crossover trial enrolled adults with objectively verified sleep onset latencies (SOLs) greater than 30 min to test the effect of auditory stimuli delivered at specific phases of participants’ alpha oscillations prior to sleep onset. During the intervention week, participants wore an electroencephalogram (EEG)-enabled headband that delivered acoustic pulses timed to arrive anti-phase with alpha for 30 min (Stimulation). During the Sham week, the headband silently recorded EEG. The primary outcome was SOL determined by blinded scoring of EEG records. For the 21 subjects included in the analyses, stimulation had a significant effect on SOL according to a linear mixed effects model (p = 0.0019), and weekly average SOL decreased by 10.5 ± 15.9 min (29.3 ± 44.4%). These data suggest that phase-locked acoustic stimulation can be a viable alternative to pharmaceuticals to accelerate sleep onset in individuals with prolonged sleep onset latencies. Trial Registration: This trial was first registered on clinicaltrials.gov on 24/02/2023 under the name Sounds Locked to ElectroEncephalogram Phase For the Acceleration of Sleep Onset Time (SLEEPFAST), and assigned registry number NCT05743114.
Direct resection is a safe and effective strategy to control seizures in patients with hypothalamic hamartoma
Authors: Ou Yunwei , Yuan Jingzhe , Li Chunde 
Published: June 2024

AbstractAchieving favorable seizure outcomes is challenging in patients with seizures resulting from hypothalamic hamartoma. Although minimally invasive and non-invasive surgical procedures are used to treat this population, these procedures have limitations. Therefore, we analyzed the outcomes of patients with hypothalamic hamartoma following direct resection. We included 159 patients with hypothalamic hamartoma who underwent direct resection using the transcallosal interforniceal approach between 2011 and 2018. The relationships between clinical parameters and seizure outcomes were analyzed. In total, 55.3% achieved gross total resection and 25.2% underwent near-total resection. Of all patients, 79.2% were overall seizure-free at one year, but this number dropped to 77.0% at more than five years. Moreover, 88.4% (129/146) reached gelastic seizure (GS)-free status at one year and this number increased to 89.0% (97/109) at more than five years. Seventy-one patients took antiseizure medication (ASM) long-term, 68 took it for one year, and 11 took it for one-half year. The duration of ASM consumption (p < 0.001) and extent of hypothalamic hamartoma resection (p = 0.016) were significant independent predictors of long-term overall seizure-free survival, while the duration of ASM consumption (p = 0.011) and extent of hypothalamic hamartoma resection (p = 0.026) were significant independent predictors of long-term GS-free survival. Most patients' behavior, school performance, and intelligence were not affected after surgery. Direct resection is effective and safe strategy for patients with hypothalamic hamartomas. Hypothalamic hamartomas should be removed as completely as possible, and patients should take ASM long-term following surgery to reach long-term overall seizure-free or GS-free status.
Modulation of response times in early-stage Parkinson’s disease during emotional processing of embodied and non-embodied stimuli
Authors: Botta Alessandro , Pelosin Elisa , Lagravinese Giovanna , Marchese Roberta , Di Biasio Francesca , Bonassi Gaia , Terranova Sara , Ravizzotti Elisa , Putzolu Martina , Mezzarobba Susanna , Cosentino Carola , Avenanti Alessio , Avanzino Laura 
Published: June 2024

AbstractValence (positive and negative) and content (embodied vs non-embodied) characteristics of visual stimuli have been shown to influence motor readiness, as tested with response time paradigms. Both embodiment and emotional processing are affected in Parkinson’s disease (PD) due to basal ganglia dysfunction. Here we aimed to investigate, using a two-choice response time paradigm, motor readiness when processing embodied (emotional body language [EBL] and emotional facial expressions [FACS]) vs non-embodied (emotional scenes [IAPS]) stimuli with neutral, happy, and fearful content. We enrolled twenty-five patients with early-stage PD and twenty-five age matched healthy participants. Motor response during emotional processing was assessed by measuring response times (RTs) in a home-based, forced two-choice discrimination task where participants were asked to discriminate the emotional stimulus from the neutral one. Rating of valence and arousal was also performed. A clinical and neuropsychological evaluation was performed on PD patients. Results showed that RTs for PD patients were longer for all conditions compared to HC and that RTs were generally longer in both groups for EBL compared to FACS and IAPS, with the sole exception retrieved for PD, where in discriminating fearful stimuli, RTs for EBL were longer compared to FACS but not to IAPS. Furthermore, in PD only, when discriminating fearful respect to neutral stimuli, RTs were shorter when discriminating FACS compared to IAPS. This study shows that PD patients were faster in discriminating fearful embodied stimuli, allowing us to speculate on mechanisms involving an alternative, compensatory, emotional motor pathway for PD patients undergoing fear processing.
Bound states in the continuum in divided triangular hole metasurfaces
Authors: Chern Ruey-Lin , Hsu Ti-Jung 
Published: June 2024

AbstractWe investigate the bound states in the continuum (BICs) in dielectric metasurfaces consisting of a two-part divided triangular hole in the unit cell of a square lattice, with emphasis on the generation, splitting, and merging of BICs. At the smallest height ratio between the upper triangular and the lower trapezoidal holes, the accidental BIC with an extremely large quality factor emerges on an isolated dispersion band at the Brillouin zone center, which is recognized as a polarization singularity (V point) with an integer topological charge. As the height ratio increases, the accidental BIC is split into a pair of circularly polarized states, which are polarization singularities (C points) with half-integer topological charges. The two states depart from each other to a maximum distance, and then approach each other as the height ratio continues to change. They finally merge to another polarization singularity (V point) with an integer topological charge, which is identified as the Friedrich-Wintgen BIC that occurs near the avoided crossing between two interacting dispersion bands.
Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle
Authors: Faleiros Camila A. , Nunes Alanne T. , Gonçalves Osiel S. , Alexandre Pâmela A. , Poleti Mirele D. , Mattos Elisângela C. , Perna-Junior Flavio , Rodrigues Paulo H. Mazza , Fukumasu Heidge 
Published: June 2024

AbstractMetagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.
A remarkable permeability enhancement of Ni1−xZnxFe2O4 (x = 0.65 and 0.70), using a multi-compound calcined additive
Authors: Shatooti S. , Mozaffari M. 
Published: June 2024

Abstract
In this study, entanglement of composition, additive and/or sintering conditions and their effects on magnetic properties of soft ferrites, nickel zinc spinel ferrites (Ni1−xZnxFe2O4, x = 0.65 and 0.70) which were prepared via conventional solid-state reaction method investigated. Also an equiponderant calcined mixture of Bi2O3, CaO, CeO2, SiO2, Al2O3, Y2O3 and nanotitania was mixed thoroughly and used as a multi-compound calcined additive (MCCA). Calcined ferrite powders were crushed, dry and wet milled, dried, mixed with different amounts of MCCA (0.0, 0.5, 1.0, 1.5 and 2.0 wt%), formed in toroidal shapes and finally sintered at different temperatures, from 1150 up to 1360 °C for 3 h. X-ray diffraction assessment confirmed formation of the single phase cubic spinel structures. Initial permeability and Q-factor spectra of the toroids were obtained from 0.1 to 1000 kHz, using an LCR meter. The results show that initial permeability of each sample has a maximum and addition of MCCA to the ferrites leads to a marvelous increase in permeabilities. Additionally, MCCA decreases the optimum sintering temperature too. The optimum amounts of additive were 1.0 and 0.5 wt% for the x = 0.65 (μ′ = 492, Ts = 1280 °C) and x = 0.70 (μ′ = 478, Ts = 1320 °C), respectively. Permeability spectra illustrate that utility zone of the Ni0.35Zn0.65Fe2O4 and Ni0.3Zn0.7Fe2O4 are both less than 100 and 10 kHz, respectively. The results represent that there is a strong entanglement between composition, additive and/or sintering conditions. It can be concluded the MCCA added Ni0.35Zn0.65Fe2O4, is suitable for application in the switching power supplies.
Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding
Authors: Yu Xinghai , Zhou Jinghua , Ye Wenkai , Xu Jingxiu , Li Rui , Huang Li , Chai Yi , Wen Miaomiao , Xu Suhong , Zhou Yu 
Published: June 2024

AbstractWounding initiates intricate responses crucial for tissue repair and regeneration. Yet, the gene regulatory networks governing wound healing remain poorly understood. Here, employing single-worm RNA sequencing (swRNA-seq) across 12 time-points, we delineated a three-stage wound repair process in C. elegans: response, repair, and remodeling. Integrating diverse datasets, we constructed a dynamic regulatory network comprising 241 transcription regulators and their inferred targets. We identified potentially seven autoregulatory TFs and five cross-autoregulatory loops involving pqm-1 and jun-1. We revealed that TFs might interact with chromatin factors and form TF-TF combinatory modules via intrinsically disordered regions to enhance response robustness. We experimentally validated six regulators functioning in transcriptional and translocation-dependent manners. Notably, nhr-76, daf-16, nhr-84, and oef-1 are potentially required for efficient repair, while elt-2 may act as an inhibitor. These findings elucidate transcriptional responses and hierarchical regulatory networks during C. elegans wound repair, shedding light on mechanisms underlying tissue repair and regeneration.
OliTag-seq enhances in cellulo detection of CRISPR-Cas9 off-targets
Authors: Yang Zhi-Xue , Deng Dong-Hao , Gao Zhu-Ying , Zhang Zhi-Kang , Fu Ya-Wen , Wen Wei , Zhang Feng , Li Xiang , Li Hua-Yu , Zhang Jian-Ping , Zhang Xiao-Bing 
Published: June 2024

AbstractThe potential for off-target mutations is a critical concern for the therapeutic application of CRISPR-Cas9 gene editing. Current detection methodologies, such as GUIDE-seq, exhibit limitations in oligonucleotide integration efficiency and sensitivity, which could hinder their utility in clinical settings. To address these issues, we introduce OliTag-seq, an in-cellulo assay specifically engineered to enhance the detection of off-target events. OliTag-seq employs a stable oligonucleotide for precise break tagging and an innovative triple-priming amplification strategy, significantly improving the scope and accuracy of off-target site identification. This method surpasses traditional assays by providing comprehensive coverage across various sgRNAs and genomic targets. Our research particularly highlights the superior sensitivity of induced pluripotent stem cells (iPSCs) in detecting off-target mutations, advocating for using patient-derived iPSCs for refined off-target analysis in therapeutic gene editing. Furthermore, we provide evidence that prolonged Cas9 expression and transient HDAC inhibitor treatments enhance the assay’s ability to uncover off-target events. OliTag-seq merges the high sensitivity typical of in vitro assays with the practical application of cellular contexts. This approach significantly improves the safety and efficacy profiles of CRISPR-Cas9 interventions in research and clinical environments, positioning it as an essential tool for the precise assessment and refinement of genome editing applications.