bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reductive acetogenesis is a dominant process in the ruminant hindgut
Authors: Li Qiushuang , Huo Jiabin , Ni Gaofeng , Zhang Fan , Zhang Shizhe , Zhang Xiumin , Wang Rong , Yu Zhongtang , Pu Xuanxuan , Yue Yipeng , Ungerfeld Emilio M. , Zhang Xiaoli , Wu Jian , Tan Zhiliang , Greening Chris , Wang Min 
Published: June 2024

Abstract

Background
The microbes residing in ruminant gastrointestinal tracts convert plant biomass to nutritious volatile fatty acids, the primary energy source for ruminants. Ruminants´ gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), each with contrasting structures and functions in anaerobic digestion. With most previous studies focusing on the rumen microbiome, the cecal microbiome is much less investigated and understood, including the assembling microbial communities and overriding pathways of hydrogen metabolism.
Results
Here we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as experimental ruminant model. In situ measurements showed that acetate and hydrogen levels were both higher in the cecum than in the rumen. Concurrently, microbes capable of host mucin degradation and fermentative hydrogen production were more abundant in the cecum, whereas fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea were less abundant. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum, and genome-resolved analysis unveiled that cecum acetogens are both phylogenetically and functionally novel. Two in vitro experiments further supported that the pathways of hydrogen metabolism differ between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, a comparative analysis showed a strong enrichment of reductive acetogens in the hindguts of other ruminants.
Conclusions
These findings, by revealing an enrichment of acetogenesis in an important part of the gastrointestinal tract, reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts.
Fecal Microbiota Transplantation Alters the Proteomic Landscape of Inflammation in HIV: Identifying Bacterial Drivers
Authors: Díaz-García Claudio , Moreno Elena , Talavera Alba , Martín-Fernández Lucía , Martín-Pedraza Laura , Pérez-Molina José A. , González-Bodí Sara , Huerta-Cepas Jaime , Dronda Fernando , Gosalbes María José , Luna Laura , Vivancos María Jesús , Moreno Santiago , Serrano-Villar Sergio 
Published: June 2024

Abstract

Background
Despite effective antiretroviral therapy, people with HIV (PWH) experience persistent systemic inflammation, increasing morbidity and mortality. Modulating the gut microbiome through fecal microbiota transplant (FMT) represents a novel therapeutic strategy. We aimed to evaluate proteomic changes in inflammatory pathways following repeated, low-dose FMT versus placebo.
Methods
This double-masked, placebo-controlled pilot study assessed the proteomic impacts of weekly FMT versus placebo over eight weeks on systemic inflammation in 29 PWH on stable antiretroviral therapy (ART). Three stool donors with high Faecalibacterium and butyrate profiles were selected. Proteomic changes in 344 inflammatory proteins in plasma were quantified using the Proximity Extension Assay, with samples collected at baseline and weeks 1, 8, and 24. Concurrently, we characterized shifts in gut microbiota composition and annotated functions through shotgun metagenomics. We fitted generalized additive models to evaluate the dynamics of protein expression. We selected the most relevant proteins to explore their correlations with the microbiome composition and functionality over time using linear mixed models.
Results
FMT significantly reduced plasma levels of 45 inflammatory proteins, including established mortality predictors like IL-6 and TNF. We found notable reductions persisting up to 16 weeks after the final FMT procedure, including proteins like CCL20 and CD22. We identified changes in FT3LG, IL17A, IL6, IL10RB, and others, which correlated with multiple bacterial species. We found specific bacterial species within the Ruminococcaceae, Succinivibrionaceae, Prevotellaceae, and the Clostridium genus, along with their associated genes and functions, to be significantly correlated with changes in inflammatory markers.
Conclusions
Targeted modulation of the gut microbiome through FMT effectively modulated systemic inflammation in PWH, with sustained effects. These findings suggest the potential of the microbiome as a therapeutic target to mitigate inflammation-related complications in this population, encouraging further research and development of microbiome-based interventions.
Feasibility and safety of a non-indwelling urinary catheter after flexible ureteroscopy with intelligent control of renal pelvis pressure: A retrospective study
Authors: mei Huang , Baihua Yang , Xiaohua Luo , Leming Song , Xiaolin Deng 
Published: June 2024

Abstract

Background
To explore the feasibility and safety of a non-indwelling urinary catheter after flexible ureteroscopy with intelligent control of renal pelvic pressure (FUS-ICP).
Methods
In this retrospective study, we assessed patients with upper urinary tract stones who were treated with FUS-ICP at the Ganzhou People's Hospital from February 2022 to December 2023. Patients were divided into the non-urinary catheter (non-UC) and urinary catheter (UC) groups according to whether an indwelling catheter was used after surgery.
Results
In total, 142 patients were included in the study. There was no significant difference in the preoperative general data between the two groups. Patients in the non-UC group performed better than those in the UC group in terms of catheter-related bladder irritation (P = 0.001), the Sedation-Agitation Scale score (P = 0.012), and the numerical rating scale (P = 0.003). The incidences of urinary retention (P = 0.620), urinary tract infection (P = 0.529), and re-indwelling urinary catheters (P = 0.438) in the UC group were inferior to those in the non-UC group, but there was no statistical significance.
Conclusions
Non-indwelling urinary catheters are safe and feasible for patients undergoing FUS-ICP.
Effects of fish protein fertilizer on soil properties, bamboo growth and bamboo shoot yield of Lei bamboo (Phyllostachys violascensʻPrevernalisʼ) forest
Authors: Zhao Jiancheng , Ni Huijing , Wang Bo , Yang Zhenya 
Published: June 2024

Abstract

Lei bamboo (Phyllostachys violascensʻPrevernalisʼ) is a high economic value species with high yield and good quality of bamboo shoots. However, heavy chemical fertilizer and covering cultivation are used to produce off-season bamboo shoots, resulting in soil degradation and a decline in soil productivity. This study introduced an amino acid fertilizer called fish protein fertilizer to replace part of chemical fertilizer, and investigated the effect of different fertilizer combinations on bamboo growth, shoot yield and soil properties to clarify the growth-promoting mechanism of amino acid fertilizer. Results showed that after replacing 45 kg of compound fertilizer with 10 kg or 20 kg of fish protein fertilizer (1) bamboo shoot yield increased by 23.24% or 26.19%, respectively; (2) growth of leaves and roots were enhanced, thick root proportion increased, and proportion of root in the topsoil layer decreased; (3) soil pH, contents of AP (available phosphate), SOC (soil organic carbon), MBC (microbial biomass carbon) and MBN (microbial biomass nitrogen), soil enzyme activity increased; (4) contents of N and P in leaf increased, while the N/P and K/P decreased. Overall, amino acid fertilizer can promote microbial growth and improve soil enzyme activity through supplying carbon sources and nitrogen sources, thus promoting phosphorus activation and increasing soil phosphorus effectiveness, and then improving the foraging scale of root systems, and ultimately enhancing nutrients absorption and increasing bamboo shoot yield.
Differences in the DNA Methylome of T cells in Adults With Asthma of Varying Severity
Authors: Liao Yixuan , Cavalcante Raymond , Waller Jonathan , Deng Furong , Scruggs Anne , Huang Yvonne , Atasoy Ulus , Chen Yahong , Huang Steven 
Published: June 2024

Abstract

Background
DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity or asthma endotypes are less well-defined.
Objective
To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation.
Methods
Peripheral blood T cells from 35 adults with asthma in Beijing, China were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores.
Results
Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway.
Conclusion
These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to the phenotype and severity of their overall disease.
Modeling Two-Phase Gas-Solid Flow in Axisymmetric Diffusers using Cut Cell Technique: An Eulerian-Eulerian Approach
Authors: Salem Khaled M. , Elreafay Adel M. , Abumandour Ramzy M. , Dawood A. S. 
Published: June 2024

Abstract

Axisymmetric diffusers find wide applications in various industrial processes, including combustion systems, pneumatic conveying, and fluidized bed reactors. Understanding and accurately modeling the behavior of two-phase flows in these devices are critical for optimizing their performance and efficiency. The cut cell technique is employed, providing a flexible and efficient means of representing intricate geometries within axisymmetric domains. The paper discusses the governing equations, numerical discretization schemes, and boundary conditions used in the Eulerian-Eulerian approach with the cut cell technique for axisymmetric diffusers. Various aspects of the two-phase gas-solid flow, including particle-particle and particle-wall interactions, interphase momentum transfer, and phase segregation, are investigated. The governing equations are solved using house developed code called FORTRAN, a widely used programming language in scientific and engineering simulations. The results of this study will provide valuable insights into the behavior of gas-solid two-phase flows in axisymmetric diffuser. A parametric study of the impact of particles diameters (100, 200,300\(\mu m\)), the solid volume loading ratios \((0.005, 0.008, 0.01)\) and cant angle (4.5°, 7°, 9.5°) effect of axisymmetric diffuser on the local skin friction, pressure, velocity, turbulent kinetic energy, and separation zone.
A Prediction Method for the Initiation Pressure of Pre-CO 2 Fracturing Considering the Modification of Rock Mechanical Parameters after CO 2 Treatment
Authors: Kong Cuilong , Sun Yuxue , Wei Jianguang , Li Guo , Yang Ying , Tang Chao , Wei Xu , Jiang Xingwen , Cong Ziyuan 
Published: June 2024

Abstract

The utilization of CO2 fracturing fluid presents a notable reduction in the challenges associated with reservoir opening, particularly in dense and unconventional reservoirs. The widespread adoption of this technique underscores its efficacy. The establishment of a more realistic CO2 fracturing model serves to elucidate the intricate mechanisms underlying CO2 fracturing transformation. Additionally, it furnishes a foundational framework for devising comprehensive fracturing construction plans. However, current research has neglected to consider the influence of CO2 on rock properties during CO2 fracturing, resulting in an inability to precisely replicate the alterations in the reservoir post-CO2 injection into the formation. This disparity from the actual conditions poses a substantial limitation to the application and advancement of CO2 fracturing technology. This work integrates the variations in physical parameters of rocks after complete contact and reaction with CO2 into the numerical model of crack propagation. This comprehensive approach fully acknowledges the impact of pre-CO2 exposure on the mechanical parameters of reservoir rocks. Consequently, it authentically restores the reservoir state following CO2 injection, ensuring a more accurate representation of the post-fracturing conditions. The research findings reveal that post-CO2 treatment, the elastic modulus of reservoir shale experiences a reduction of 12.5%, Poisson's ratio decreases by 11.8%, tensile strength decreases by 7.9%, permeability increased by 180%. Additionally, the pre-injection of CO2 into the reservoir induces a notable increase in pore pressure in the near wellbore zone. In comparison with conventional numerical simulation methods, the approach outlined in this paper yields a reduction in the error associated with predicting fracturing pressure by 9.8%. The model and methodology presented herein serve as a practical tool for accurately forecasting the initiation pressure of CO2 fracturing.
Propagation of periodic director and flow patterns in a cholesteric liquid crystal under electroconvection
Authors: Yoshioka Jun , Nobori Hiroki , Fukao Koji , Araoka Fumito 
Published: June 2024

Abstract

The electroconvection of liquid crystals is a typical example of a dissipative structure generated by complicated interactions between three factors: convective flow, structural deformation, and the migration of charge carriers. In this study, we found that the periodic structural deformation of a cholesteric liquid crystal propagates in space, like a wave, under an alternating-current electric field. The existence of convection and charge carriers was confirmed by flow-field measurements and dielectric relaxation spectroscopy. Given that the wave phenomenon results from electroconvection, we suggest a possible model for describing the mechanism of wave generation. The validity of the model was examined using the Onsager variational principle. Consequently, it was suggested that wave generation can be described by four effects: the electrostatic potential, mixing entropy, anisotropic friction due to charge migration, and viscous dissipation of the liquid crystal.
Research on photovoltaic MPPT Control strategy Based on Improved Manta Ray Foraging Optimization Algorithm
Authors: Zhou ZiJian , Fang YanHong 
Published: June 2024

Abstract

In order to solve the problem that the multi-peak power voltage (P-U) characteristic curve generated by a photovoltaic power generation system under unbalanced illumination and the traditional maximum power point tracking (MPPT) algorithm easily falls into the local optimal solution, a photovoltaic multi-peak MPPT method based on an improved manta ray foraging algorithm is proposed.The algorithm combines several mathematical optimization strategies with the original manta ray foraging optimization algorithm. Firstly, chaos mapping is used to initialize the search population, increasing population diversity. At the same time, reverse learning is integrated after summarizing the characteristics of photovoltaic P-V characteristic curves to improve the distribution efficiency of the population; Secondly, a nonlinear change function is introduced to provide a better balance between the development and exploration of the algorithm; Then the linear change curve is introduced to improve the ability of the algorithm to jump out of the local extreme value; Finally, levy flight strategy is introduced to improve the search ability of the algorithm. It is proved by the simulation results of MATLAB/Simulink, In the process of tracking, the algorithm has a small oscillation amplitude, good tracking accuracy, and good convergence time.
Modular Simulation Framework for the Design of Air-Spring-Dampers
Authors: Schnieders Marco , Rexer Manuel , Jericho Christian , Dietrich Ingo , Pelz Peter F. 
Published: June 2024

Abstract

Air-spring-dampers offer a novel alternative to traditional hydraulic damping within suspension systems. However, due to the intricate damping behavior and a multitude of configuration possibilities, the design process of air-spring-dampers proves to be challenging. This paper proposes a solution to address these challenges by introducing a simulation framework integrated with parameter optimization, enabling the simulation and design of any air-spring-damper. The simulation framework incorporates three fundamental modules: volume, mass exchange, and heat exchange. By abstracting the air-spring-damper as a graph and representing it via adjacency matrices, these modules will automatically be connected to construct a simulation model for any air-spring-damper configuration. Furthermore, leveraging the framework simplifies the design process through a parameter optimization. This method allows for a target damping curve to be set. The optimization algorithm then adjusts the air-spring-damper's design parameters until the target curve is achieved. A comparison of algorithms is conducted to determine the most suitable for this optimization problem. The pattern search and surrogate algorithms emerge as strong performers, effectively producing the target damping curve. To simplify the design process further, the common objective of enhancing driving safety and comfort is transformed into an optimization problem within the framework. This leads to the generation of a pareto front, which presents design recommendations that balance safety and comfort optimally.
Genotyping-by-sequencing reveals the genetic diversity and population structure of Peruvian highland maize races
Authors: Arbizu Carlos I. , Soto Isamar Bazo , Flores Joel , Ortiz Rodomiro , Blas Raul , García-Mendoza Pedro J. , Sevilla Ricardo , Crossa José , Grobman Alexander 
Published: June 2024

Abstract

Peruvian maize exhibits abundant morphological diversity, with landraces cultivated from sea level (sl) up to 3,500 m above sl. Previous research based on morphological descriptors, defined at least 52 Peruvian maize races, but its genetic diversity and population structure remains largely unknown. Here we used genotyping-by-sequencing (GBS) to obtain single nucleotide polymorphisms (SNPs) that allow inferring the genetic structure and diversity of 423 maize accessions from the genebank of Universidad Nacional Agraria la Molina (UNALM) and Universidad Nacional Autónoma de Tayacaja (UNAT). These accessions represent nine races and one sub-race, along with 15 open-pollinated lines (purple corn) and two yellow maize hybrids. It was possible to obtain 14,235 high-quality SNPs distributed along the 10 maize chromosomes of maize. Gene diversity ranged from 0.33 (sub-race Pachia) to 0.362 (race Ancashino), with race Cusco showing the lowest inbreeding coefficient (0.205) and Ancashino the highest (0.274) for the landraces. Population divergence (FST) was very low (mean = 0.017), thus depicting extensive interbreeding among Peruvian maize. Population structure analysis indicated that these 423 distinct genotypes can be included in 10 groups, with some maize races clustering together. Peruvian maize races failed to be recovered as monophyletic; instead, our phylogenetic tree identified two clades corresponding to the groups of the classification of the races of Peruvian maize based on their chronological origin, i.e., anciently derived or primary races and lately derived or secondary races. Additionally, these two clades are also congruent with the geographic origin of these maize races, reflecting their mixed evolutionary backgrounds and constant evolution. Peruvian maize germplasm needs further investigation with modern technologies to better use them massively in breeding programs that favor agriculture mainly in the South American highlands. We also expect this work will pave a path for establishing more accurate conservation strategies for this precious crop genetic resource.
Disrupting Notch signaling related HES1 in myeloid cells reinvigorates antitumor T cell responses
Authors: Kim Myung Sup , Kang Hyeokgu , Baek Jung-Hwan , Cho Moon-Gyu , Chung EunJoo , Kim Seok-Jun , Chung Joon-Yong , Chun Kyung-Hee 
Published: June 2024

Abstract

Background: Tumor-associated macrophages (TAMs) are immunosuppressive cells within the tumor microenvironment (TME) that hinder anti-tumor immunity. Notch signaling is a pathway crucial for TAM differentiation and function. Here, we investigate the role of HES1, a downstream target of Notch signaling, in TAM-mediated immunosuppression and explore its potential as a target for cancer immunotherapy.
Methods: In this work, we constructed conditional Hes1 knockout mice to selectively delete Hes1 in TAMs. We further analyzed the TME composition, T cell infiltration and activation, and anti-tumor effects in these mice, both alone and in combination with PD-1 checkpoint blockade.
Results: Our study showed that expression levels of Notch target Hes1 were increase in TAMs and mice with conditional knockout of Hes1 gene in TAMs exhibited decreased tumor growth, with increased infiltration and activation of cytotoxic T cells in tumors. Expression of tumor promoting factors was critically altered in Hes1-conditional KO TAMs, leading to the improved tumor microenvironment. Notably, arginase-1 expression was decreased in Hes1-conditional KO mice. Arg1 is known to deplete arginine and deactivate T cells in the TME. Administration of anti-PD-1 monoclonal antibody inhibited tumor growth to a greater extent in Hes1-conditional KO mice than in WT mice.
Conclusions: We identified a pivotal role for the Notch signaling pathway in shaping TAM function, suggesting that T-cell dysfunction in the TME is caused when the Notch target, HES1, in TAMs is upregulated by tumor-associated factors (TAFs), which, in turn, increases the expression of arginase-1. Targeting HES1 in TAMs appears to be a promising strategy for cancer immunotherapy.