bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phononic bath engineering of a superconducting qubit
Authors: Kitzman J. M. , Lane J. R. , Undershute C. , Harrington P. M. , Beysengulov N. R. , Mikolas C. A. , Murch K. W. , Pollanen J. 
Published: July 2023

AbstractPhonons, the ubiquitous quanta of vibrational energy, play a vital role in the performance of quantum technologies. Conversely, unintended coupling to phonons degrades qubit performance and can lead to correlated errors in superconducting qubit systems. Regardless of whether phonons play an enabling or deleterious role, they do not typically admit control over their spectral properties, nor the possibility of engineering their dissipation to be used as a resource. Here we show that coupling a superconducting qubit to a bath of piezoelectric surface acoustic wave phonons enables a novel platform for investigating open quantum systems. By shaping the loss spectrum of the qubit via the bath of lossy surface phonons, we demonstrate preparation and dynamical stabilization of superposition states through the combined effects of drive and dissipation. These experiments highlight the versatility of engineered phononic dissipation and advance the understanding of mechanical losses in superconducting qubit systems.
Longevity gene responsible for robust blue organic materials employing thermally activated delayed fluorescence
Authors: Meng Qing-Yu , Wang Rui , Wang Yi-Lei , Guo Xing-Wei , Liu Yu-Qi , Wen Xue-Liang , Yao Cheng-Yu , Qiao Juan 
Published: July 2023

AbstractThe 3rd-Gen OLED materials employing thermally-activated delayed fluorescence (TADF) combine advantages of first two for high-efficiency and low-cost devices. Though urgently needed, blue TADF emitters have not met stability requirement for applications. It is essential to elucidate the degradation mechanism and identify the tailored descriptor for material stability and device lifetime. Here, via in-material chemistry, we demonstrate chemical degradation of TADF materials involves critical role of bond cleavage at triplet state rather than singlet, and disclose the difference between bond dissociation energy of fragile bonds and first triplet state energy (BDE-ET1) is linearly correlated with logarithm of reported device lifetime for various blue TADF emitters. This significant quantitative correlation strongly reveals the degradation mechanism of TADF materials have general characteristic in essence and BDE-ET1 could be the shared “longevity gene”. Our findings provide a critical molecular descriptor for high-throughput-virtual-screening and rational design to unlock the full potential of TADF materials and devices.
Site-specific bioorthogonal protein labelling by tetrazine ligation using endogenous β-amino acid dienophiles
Authors: Richter Daniel , Lakis Edgars , Piel Jörn 
Published: July 2023

AbstractThe tetrazine ligation is an inverse electron-demand Diels–Alder reaction widely used for bioorthogonal modifications due to its versatility, site specificity and fast reaction kinetics. A major limitation has been the incorporation of dienophiles in biomolecules and organisms, which relies on externally added reagents. Available methods require the incorporation of tetrazine-reactive groups by enzyme-mediated ligations or unnatural amino acid incorporation. Here we report a tetrazine ligation strategy, termed TyrEx (tyramine excision) cycloaddition, permitting autonomous dienophile generation in bacteria. It utilizes a unique aminopyruvate unit introduced by post-translational protein splicing at a short tag. Tetrazine conjugation occurs rapidly with a rate constant of 0.625 (15) M−1 s−1 and was applied to produce a radiolabel chelator-modified Her2-binding Affibody and intracellular, fluorescently labelled cell division protein FtsZ. We anticipate the labelling strategy to be useful for intracellular studies of proteins, as a stable conjugation method for protein therapeutics, as well as other applications.
Demonstration of momentum cooling to enhance the potential of cancer treatment with proton therapy
Authors: Maradia Vivek , Meer David , Dölling Rudolf , Weber Damien C. , Lomax Antony J. , Psoroulas Serena 
Published: July 2023

AbstractIn recent years, there has been a considerable push towards ultrahigh dose rates in proton therapy to effectively utilize motion mitigation strategies and potentially increase the sparing of healthy tissue through the so-called FLASH effect. However, in cyclotron-based proton therapy facilities, it is difficult to reach ultrahigh dose rates for low-energy beams. The main reason for this lies in the large momentum spread that such beams have after reducing their energy to levels required for proton therapy, incurring large losses in conventionally used momentum or energy selection slits. Here we propose momentum cooling by using a wedge in the energy selection system (instead of a slit) to reduce the momentum spread of the beam without introducing substantial beam losses. We demonstrate this concept in our eye treatment beamline and obtain a factor of two higher transmission, which could eventually halve the treatment delivery time. Furthermore, we show that with a gantry design incorporating this feature, we can achieve almost a factor of 100 higher transmission for a 70 MeV beam compared with conventional cyclotron-based facilities. This concept could enhance the potential of proton therapy by opening up possibilities of treating new indications and reducing the cost.
Physics-informed reinforcement learning for motion control of a fish-like swimming robot
Authors: Rodwell Colin , Tallapragada Phanindra 
Published: July 2023

AbstractMotion control of fish-like swimming robots presents many challenges due to the unstructured environment and unmodelled governing physics of the fluid–robot interaction. Commonly used low-fidelity control models using simplified formulas for drag and lift forces do not capture key physics that can play an important role in the dynamics of small-sized robots with limited actuation. Deep Reinforcement Learning (DRL) holds considerable promise for motion control of robots with complex dynamics. Reinforcement learning methods require large amounts of training data exploring a large subset of the relevant state space, which can be expensive, time consuming, or unsafe to obtain. Data from simulations can be used in the initial stages of DRL, but in the case of swimming robots, the complexity of fluid–body interactions makes large numbers of simulations infeasible from the perspective of time and computational resources. Surrogate models that capture the primary physics of the system can be a useful starting point for training a DRL agent which is subsequently transferred to train with a higher fidelity simulation. We demonstrate the utility of such physics-informed reinforcement learning to train a policy that can enable velocity and path tracking for a planar swimming (fish-like) rigid Joukowski hydrofoil. This is done through a curriculum where the DRL agent is first trained to track limit cycles in a velocity space for a representative nonholonomic system, and then transferred to train on a small simulation data set of the swimmer. The results show the utility of physics-informed reinforcement learning for the control of fish-like swimming robots.
Impact of corn processing and weaning age on calf performance, blood metabolites, rumen fermentation, and behavior
Authors: Rahimi A. , Ghorbani G. R. , Hashemzadeh F. , Mirzaei M. , Saberipour H. R. , Ahmadi F. , Ghaffari M. H. 
Published: July 2023

AbstractThis study examined the impact of two corn processing methods (steam-flaked (SFC) vs. ground) combined with two weaning ages (50 or 75 days) on calf performance, blood metabolites, rumen fermentation, nutrient digestion, and behavior. The study involved 48 three-day-old Holstein calves, with an average body weight of 41.4 ± 2.2 kg. The experimental design was a 2 × 2 factorial arrangement, resulting in four treatment groups: SFC50 (SFC and weaning at 50 days), SFC75 (SFC and weaning at 75 days), GC50 (ground corn and weaning at 50 days), and GC75 (ground corn and weaning at 75 days). Calves were given whole milk at 4 L/ day from day 3–15 and 7 L/ day from day 16 to either 43 or 68, depending on weaning age. Weaning occurred between days 44 and 50 for early-weaned calves and between days 69 and 75 for late-weaned calves. The study lasted until calves were 93 days old. The starter ration consisted of soybean meal, corn grain, 5% chopped wheat straw and premix. Results indicated that the SFC-based starter feed improved calf performance and nutrient digestion, as evidenced by increased weight gain, dry matter, crude protein, and neutral detergent fiber digestibility. Calves fed the SFC-based starter diet had lower blood albumin and urea N concentrations, while blood total protein and globulin concentrations were higher, especially in early-weaned calves. No significant changes in rumen pH and ammonia-N concentration were observed. In addition, the SFC starter feed resulted in higher volatile fatty acids concentration and longer feeding time in weaned calves compared to ground corn. Overall, these results suggest that an SFC-based starter feed may be beneficial for both early and late weaned calves.
The genomic and transcriptomic landscape of advanced renal cell cancer for individualized treatment strategies
Authors: de Joode K. , van de Geer W. S. , van Leenders G. J. L. H. , Hamberg P. , Westgeest H. M. , Beeker A. , Oosting S. F. , van Rooijen J. M. , Beerepoot L. V. , Labots M. , Mathijssen R. H. J. , Lolkema M. P. , Cuppen E. , Sleijfer S. , van de Werken H. J. G. , van der Veldt A. A. M. 
Published: July 2023

AbstractDifferences in the clinical course and treatment responses in individual patients with advanced renal cell carcinoma (RCC) can largely be explained by the different genomics of this disease. To improve the personalized treatment strategy and survival outcomes for patients with advanced RCC, the genomic make-up in patients with advanced RCC was investigated to identify putative actionable variants and signatures. In this prospective multicenter study (NCT01855477), whole-genome sequencing (WGS) data of locally advanced and metastatic tissue biopsies and matched whole-blood samples were collected from 91 patients with histopathologically confirmed RCC. WGS data were analyzed for small somatic variants, copy-number alterations and structural variants. For a subgroup of patients, RNA sequencing (RNA-Seq) data could be analyzed. RNA-Seq data were clustered on immunogenic and angiogenic gene expression patterns according to a previously developed angio-immunogenic gene signature. In all patients with papillary and clear cell RCC, putative actionable drug targets were detected by WGS, of which 94% were on-label available. RNA-Seq data of clear cell and papillary RCC were clustered using a previously developed angio-immunogenic gene signature. Analyses of driver mutations and RNA-Seq data revealed clear differences among different RCC subtypes, showing the added value of WGS and RNA-Seq over clinicopathological data. By improving both histological subtyping and the selection of treatment according to actionable targets and immune signatures, WGS and RNA-Seq may improve therapeutic decision making for most patients with advanced RCC, including patients with non-clear cell RCC for whom no standard treatment is available to data. Prospective clinical trials are needed to evaluate the impact of genomic and transcriptomic diagnostics on survival outcome for advanced RCC patients.
Survival analysis of a stochastic impulsive single-species population model with migration driven by environmental toxicant
Authors: Dai Xiangjun , Jiao Jianjun , Quan Qi 
Published: July 2023

AbstractConsidering the influence of environmental toxicant on population migration between patches, we propose and study a stochastic impulsive single-species population model with migration driven by environmental toxicant in this paper. We first discuss the existence and uniqueness of global positive solutions of the model by constructing the Lyapunov function. Then, we obtain sufficient conditions for extinction, stochastic persistence and persistence in the mean of the single-species population. Finally, we present some numerical simulations to illustrate our results. These results provide insights for the conservation and management of species in polluted environments.
Bacterial community structure in the rumen and hindgut is associated with nitrogen efficiency in Holstein cows
Authors: De La Guardia-Hidrogo V. M. , Paz H. A. 
Published: July 2023

AbstractNitrogen efficiency (Neff; milk N/N intake) in dairy cows is limited and most of the consumed N is excreted in manure. Despite the crucial role of the gastrointestinal microbiome on N metabolism, associations between bacterial communities at different sections and Neff are not fully elucidated. Enhanced understanding of host-microbiome interactions can provide insights to improve Neff in dairy cows. Twenty-three Holstein cows were selected, and their Neff were determined using a N balance approach. From the cohort of cows, six cows were classified as low Neff and five cows as high Neff and their rumen and fecal bacterial communities were profiled using amplicon sequence variants (ASV) based on 16S rRNA gene sequencing. Then, relationships between differentially abundant bacterial features and Neff were evaluated. Neff in low and high cows averaged 22.8 and 30.3%, respectively. With similar N intake, high Neff cows wasted less N in manure compared to low Neff cows (P < 0.01, 11.0 ± 0.59 vs 14.3 ± 0.54 g of N/kg of milk). Rumen fermentation and plasma profiles were similar between Neff groups, but for plasma Gln which was greater (P = 0.02) in high compared to low Neff cows. In both rumen and feces, the phylogenetic composition of the bacterial communities was similar (P ≥ 0.65) between Neff groups, but differences were observed at the species -level (amplicon sequence variants). In the rumen, differentially abundant species from the genus Prevotella showed strong positive correlations with Neff, whereas in feces, differentially abundant species from the class Clostridia showed strong negative correlations with Neff. Our results revealed that Holstein cows with divergent Neff display distinctive bacterial community structure at the species-level in both the rumen and feces. Strong correlations between differentially abundant species and Neff in both sample sites, support the importance of the rumen bacterial composition on productive responses and suggest a more relevant role of the hindgut microbiome. Targeting both pre- and post-gastric bacterial communities may provide novel opportunities to enhance Neff in dairy cows.
Heat transfer analysis of buoyancy opposing radiated flow of alumina nanoparticles scattered in water-based fluid past a vertical cylinder
Authors: Alharbi Sayer Obaid , Khan Umair , Zaib Aurang , Ishak Anuar , Raizah Zehba , Eldin Sayed M. , Pop Ioan 
Published: July 2023

AbstractCooling and heating are two critical processes in the transportation and manufacturing industries. Fluid solutions containing metal nanoparticles have higher thermal conductivity than conventional fluids, allowing for more effective cooling. Thus, the current paper is a comparative exploration of the time-independent buoyancy opposing and heat transfer flow of alumina nanoparticles scattered in water as a regular fluid induced via a vertical cylinder with mutual effect of stagnation-point and radiation. Based on some reasonable assumptions, the model of nonlinear equations is developed and then tackled numerically employing the built-in bvp4c MATLAB solver. The impacts of assorted control parameters on gradients are investigated. The outcomes divulge that the aspect of friction factor and heat transport upsurge by incorporating alumina nanoparticles. The involvement of the radiation parameter shows an increasing tendency in the heat transfer rate, resulting in an enhancement in thermal flow efficacy. In addition, the temperature distribution uplifts due to radiation and curvature parameters. It is discerned that the branch of dual outcomes exists in the opposing flow case. Moreover, for higher values of the nanoparticle volume fraction, the reduced shear stress and the reduced heat transfer rate increased respectively by almost 1.30% and 0.0031% for the solution of the first branch, while nearly 1.24%, and 3.13% for the lower branch solution.
Identification of novel biomarkers and immune infiltration features of recurrent pregnancy loss by machine learning
Authors: Luo Yujia , Zhou Yuanyuan 
Published: July 2023

AbstractRecurrent pregnancy loss (RPL) is a complex reproductive disorder. The incompletely understood pathophysiology of RPL makes early detection and exact treatment difficult. The purpose of this work was to discover optimally characterized genes (OFGs) of RPL and to investigate immune cell infiltration in RPL. It will aid in better understanding the etiology of RPL and in the early detection of RPL. The RPL-related datasets were obtained from the Gene Expression Omnibus (GEO), namely GSE165004 and GSE26787. We performed functional enrichment analysis on the screened differentially expressed genes (DEGs). Three machine learning techniques are used to generate the OFGs. A CIBERSORT analysis was conducted to examine the immune infiltration in RPL patients compared with normal controls and to investigate the correlation between OFGs and immune cells. Between the RPL and control groups, 42 DEGs were discovered. These DEGs were found to be involved in cell signal transduction, cytokine receptor interactions, and immunological response, according to the functional enrichment analysis. By integrating OFGs from the LASSO, SVM-REF, and RF algorithms (AUC > 0.880), we screened for three down-regulated genes: ZNF90, TPT1P8, FGF2, and an up-regulated FAM166B. Immune infiltration study revealed that RPL samples had more monocytes (P < 0.001) and fewer T cells (P = 0.005) than controls, which may contribute to RPL pathogenesis. Additionally, all OFGs linked with various invading immune cells to varying degrees. In conclusion, ZNF90, TPT1P8, FGF2, and FAM166B are potential RPL biomarkers, offering new avenues for research into the molecular mechanisms of RPL immune modulation and early detection.
The Elk-3 target Abhd10 ameliorates hepatotoxic injury and fibrosis in alcoholic liver disease
Authors: Li Tian-Zhu , Bai Chun-Ying , Wu Bao , Zhang Cong-Ying ,   SIRIGULENG, Wang Wen-Tao , Shi Tie-Wei , Zhou Jing 
Published: July 2023

AbstractAlcoholic liver disease (ALD) and other forms of chronic hepatotoxic injury can lead to transforming growth factor β1 (TGFβ1)-induced hepatic fibrosis and compromised liver function, underscoring the need to develop novel treatments for these conditions. Herein, our analyses of liver tissue samples from severe alcoholic hepatitis (SAH) patients and two murine models of ALD reveals that the ALD phenotype was associated with upregulation of the transcription factor ETS domain-containing protein (ELK-3) and ELK-3 signaling activity coupled with downregulation of α/β hydrolase domain containing 10 (ABHD10) and upregulation of deactivating S-palmitoylation of the antioxidant protein Peroxiredoxin 5 (PRDX5). In vitro, we further demonstrate that ELK-3 can directly bind to the ABHD10 promoter to inhibit its transactivation. TGFβ1 and epidermal growth factor (EGF) signaling induce ABHD10 downregulation and PRDX5 S-palmitoylation via ELK-3. This ELK-3-mediated ABHD10 downregulation drives oxidative stress and disrupts mature hepatocyte function via enhancing S-palmitoylation of PRDX5’s Cys100 residue. In vivo, ectopic Abhd10 overexpression ameliorates liver damage in ALD model mice. Overall, these data suggest that the therapeutic targeting of the ABHD10-PRDX5 axis may represent a viable approach to treating ALD and other forms of hepatotoxicity.
Thermodynamics, statistical mechanics and the vanishing pore width limit of confined fluids
Authors: Dong W. , Franosch T. , Schilling R. 
Published: July 2023

AbstractTemperature, particle number and volume are the independent variables of the Helmholtz free energy for a bulk fluid. For a fluid confined in a slit pore between two walls, they are usually complemented by the surface area. However, an alternative choice is possible with the volume replaced by the pore width. Although the formulations with such two sets of independent variables are different, we show they are equivalent and present their relations. Corresponding general statistical-mechanics results are also presented. When the pore width becomes very small, the system behaves rather like a two-dimensional (2D) fluid and one can wonder if thermodynamics still holds. We find it remains valid even in the limit of vanishing pore width and show how to treat the divergences in the normal pressure and the chemical potential so that the corresponding 2D results can be obtained. Thus, we show that the Gibbs surface thermodynamics is perfectly capable of describing small systems.
Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress
Authors: Osburn Ernest D , Yang Gaowen , Rillig Matthias C , Strickland Michael S 
Published: July 2023

Abstract
Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.
Unveiling a remarkable enhancement role by designing a confined structure Ho-TNTs@Mn catalyst for low-temperature NH3-SCR reaction
Authors: Zhao Tian , Huang Xiaosheng , Cui Rongji , Zhang Guodong , Tang Zhicheng 
Published: July 2023

This work clarifies how the pore confinement effect of TNTs and modification of Ho affects the NH3-SCR activity, sulfur resistance and N2 selectivity, allowing us to design an effective catalyst with the desired SO2 resistance and N2 selectivity.