bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bifurcation and Chaos Analysis of a Supersonic Slipper–Track System
Authors: Dang Tianjiao , Liu Zhen , Morandini Marco , Ma Linjie , Masarati Pierangelo 
Published: May 2024

Abstract
The slipper is the critical component of a supersonic rocket sled that is in contact with the track. Due to clearance and contact effects, the supersonic slipper–track system displays pronounced nonlinearities. A comprehensive analysis, including bifurcation and chaos detection, is conducted on this system to predict the nonlinear behavior of the slipper. Kinematic and dynamic models of the system are established using the generalized coordinate and Lagrange multiplier methods. This model accounts for slipper–track clearances, track irregularities, and normal contact forces. The dynamic response of the slipper is examined both in time and frequency domain. The bifurcation analysis encompasses various parameters such as slipper velocity and length, and slipper–track clearance. Chaos identification is employed for both qualitative and quantitative assessments, utilizing phase diagrams, Poincaré sections, the trajectory of the slipper's center, and the largest Lyapunov exponent (LLE). The findings revealed significant nonlinear phenomena, including self-excited vibrations, superharmonic responses, jumping phenomena, strange attractors, and combined frequencies. Notably, this study demonstrated the potential for leveraging chaotic response to mitigate the contact forces on the slipper. These insights contribute to the rationalization of control parameters and the optimization of slipper and track design.
The interplay of suppressive soil bacteria and plant root exudates determines germination of microsclerotia of
Verticillium longisporum
Authors: Sarenqimuge Sarenqimuge , Wang Yao , Alhussein Mohammad , Koopmann Birger , von Tiedemann Andreas 
Published: May 2024

ABSTRACT

Dormant microsclerotia play a vital role in the survival and spread of
Verticillium longisporum
, as they can stay viable in the soil and maintain their infectivity for many years. In our previous work, we revealed that soil bacterial volatiles are a key inhibitory factor causing microsclerotia dormancy in the soil. In this study, we further demonstrate that root exudates collected from both host and non-host plants can effectively rescue microsclerotia from bacterial suppression and initiate germination. To identify the specific compounds in root exudates responsible for microsclerotia germination, we fractionated the collected root exudates into polar and non-polar compounds. Subsequently, we conducted comprehensive bioassays with each fraction on germination-suppressed microsclerotia. The result revealed a pivotal role of primary metabolites in root exudates, particularly glutamic acid, in triggering microsclerotia germination and overcoming bacterial inhibition. Moreover, our studies revealed a decrease in inhibitory bacterial volatile fatty acids when bacteria were cultured in the presence of root exudates or glutamic acid. This suggests a potential mechanism, by which root exudates set-off bacterial suppression on microsclerotia. Here, we reveal for the first time that plant root exudates, instead of directly inducing the germination of microsclerotia, enact a set-off effect by counteracting the suppressive impact of soil bacteria on the microsclerotia germination process. This nuanced interaction advances our understanding of the multifaceted dynamics governing microsclerotia dormancy and germination in the soil environment.

IMPORTANCE

Our research provides first-time insights into the crucial interaction between plant root exudates and soil bacteria in regulating the germination of
Verticillium longisporum
microsclerotia, a significant structure in the survival and proliferation of this soil-borne pathogen. We describe so far unknown mechanisms, which are key to understand how root infections on oilseed rape can occur. By pinpointing primary metabolites in root exudates as key factors in overcoming bacteria-induced dormancy and promote microsclerotia germination, our study highlights the potential for exploiting plant - as well as soil microbe-derived - compounds to control
V. longisporum
. This work underscores the importance of elucidating the nuanced interactions within the soil ecosystem to devise innovative strategies for managing root infective plant diseases, thereby contributing to the resilience and health of cropping systems.
Unveiling the immune dynamics of
Neisseria
persistent oral colonization
Authors: Alles Mario , Gunasena Manuja , Zia Tauqir , D'Mello Adonis , Bhattarai Saroj , Mulhern Will , Terry Luke , Scherger Trenton , Wijeratne Saranga , Singh Sachleen , Wijeratne Asela J. , Kasturiratna Dhanuja , Tettelin Hervé , Weyand Nathan J. , Liyanage Namal P. M. 
Published: May 2024

ABSTRACT

Commensal bacteria are crucial in maintaining host physiological homeostasis, immune system development, and protection against pathogens. Despite their significance, the factors influencing persistent bacterial colonization and their impact on the host still need to be fully understood. Animal models have served as valuable tools to investigate these interactions, but most have limitations. The bacterial genus
Neisseria
, which includes both commensal and pathogenic species, has been studied from a pathogenicity to humans perspective but lacks models that study immune responses in the context of long-term persistence.
Neisseria musculi
, a recently described natural commensal of mice, offers a unique opportunity to study long-term host-commensal interactions. In this study, for the first time, we have used this model to study the transcriptional, phenotypic, and functional dynamics of immune cell signatures in the mucosal and systemic tissue of mice in response to
N. musculi
colonization. We found key genes and pathways vital for immune homeostasis in palate tissue, validated by flow cytometry of immune cells from the lung, blood, and spleen. This study offers a novel avenue for advancing our understanding of host-bacteria dynamics and may provide a platform for developing efficacious interventions against mucosal persistence by pathogenic
Neisseria
.
Isolation and identification of uric acid-dependent
Aciduricibacillus chroicocephali
gen. nov., sp. nov. from seagull feces and implications for hyperuricemia treatment
Authors: Liu Wenxuan , Nan Fulong , Liu Fengjun , Yang Xiaoli , Li Zonghui , Jiang Shasha , Zhang Xianjuan , Li Jun , Yu Meng , Wang Yunyang , Wang Bin 
Published: May 2024

ABSTRACT

Hyperuricemia has become the second most prevalent metabolic disease after diabetes, but the limitations of urate-lowering treatment (ULT) drugs and patient nonadherence make ULT far less successful. Thus, more ULT approaches urgently need to be explored. Uric acid-degrading bacteria have potential application value in ULT. In this study, we isolated 44XB
T
, a uric acid-degrading bacterium, from black-headed gull (
Chroicocephalus ridibundus
) feces. Using a polyphasic taxonomic approach, strain 44XB
T
was identified as a novel genus within the family
Bacillaceae
; subsequently, the name
Aciduricibacillus chroicocephali
was proposed. Strain 44XB
T
had a unique uric acid-dependent phenotype and utilized uric acid and allantoin as the sole carbon and nitrogen sources, but not common carbon sources or complex media. In the genome, multiple copies of genes involved in uric acid metabolic pathway (
pucL
,
pucM
,
uraD
, and
allB
) were found. Six copies of
pucL
(encoding urate oxidase) were detected. Of these, five
pucL
copies were in a tandem arrangement and shared 70.42%–99.70% amino acid identity.
In vivo
experiments revealed that 44XB
T
reduced serum uric acid levels and attenuated kidney damage in hyperuricemic mice through uric acid catalysis in the gut and gut microbiota remodeling. In conclusion, our findings discover a strain for studying bacterial uric acid metabolism and may provide valuable insights into ULT.

IMPORTANCE

The increasing disease burden of hyperuricemia highlights the need for new therapeutic drugs and treatment strategies. Our study describes the developmental and application values of natural uric acid-degrading bacteria found in the gut of birds and broadened the source of bacteria with potential therapeutic value. Furthermore, the special physiology characteristics and genomic features of strain 44XB
T
are valuable for further study.
Stratigraphy, eruption, and evolution of the Columbia River Basalt Group
Authors: Soderberg Evan R. , Hart Rachelle , Camp Victor E. , Wolff John A. , Steiner Arron 
Published: May 2024

ABSTRACTThe Miocene Columbia River Basalt Group (CRBG) is world famous and the best studied continental flood basalt province on Earth. Decades of field and laboratory study have resulted in a detailed stratigraphy, consisting of seven formations containing more than 350 flows, a well-constrained chronology, and a large geochemical database. Petrogenesis of the flood basalts is constrained by many thousands of major element, trace element, and isotopic analyses of whole rocks and their constituent minerals. There is broad consensus that the province is the product of a deep mantle plume, although the details of plume interaction with North American lithosphere, and the generation, storage, transport, and eruption of flood basalt magma, are the subjects of continuing research. This field trip focuses on basalt flow sequences, dikes, vents, evolution of basaltic magmas through the lifetime of flood lava activity, and their relation to the larger Yellowstone Hotspot Province. The formations to be examined include the Imnaha, Grande Ronde, Wanapum, and Saddle Mountain Basalts. Trip stops are primarily along the Snake and Grande Ronde Rivers located in and adjacent to the canyon country of southeast Washington, western Idaho, and northeast Oregon.
Evidence of cardiomyopathy associated with Marfan syndrome in children
Authors: Weigand Justin , Stephens-Novy Sara , Sachdeva Shagun , Doan Tam T , Yasso Abigail , Morris Shaine A 
Published: May 2024

ObjectiveMarfan syndrome (MFS)-associated cardiomyopathy, defined as ventricular dilation and dysfunction unexplained by volume loading, is not well defined in children. This study evaluated ventricular size and function in paediatric MFS using cardiac MRI (cMRI).MethodsThis retrospective cohort study examined patients with MFS <19 years old at first cMRI. Left ventricular (LV) ejection fraction (EF) <55% was considered abnormal, as were z-scores >2. Combined mitral and aortic regurgitation indexed to LV stroke volume <20% defined absent/mild volume load. Biventricular volumes and EF on serial cMRI studies were compared with normative paediatric cMRI values, with measures converted to z-scores as appropriate. Longitudinal changes in volumes and EF were evaluated by mixed linear regression. Associations between ventricular, aortic and mitral characteristics were evaluated.Results58 patients (60% male) were evaluated. Median age at initial cMRI was 13.6 years (IQR 10.0–15.8 years). Among patients with absent/mild LV volume load at initial cMRI (n=44, 76%), indexed LV end-diastolic volume (EDV) was significantly increased above normative values (median z-score 1.8, IQR 0.6–3.5, p<0.0001) and LVEF was abnormal in 48% (21/44). In the absence of volume loading, mitral valve prolapse (MVP) was associated with larger ventricular volumes and lower LVEF. Among those with serial cMRIs, LVEF and EDV z-scores did not significantly change over a mean follow-up time between cMRI studies of 1.5 years.ConclusionVentricular dilation and reduced EF are common in children with MFS and occur with no/mild LV volume load, suggesting intrinsic cardiomyopathy. MVP may be associated with cardiomyopathy.
Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes
Authors: Levin Noam , Kim Sanghyun P , Marquardt Charles A , Vale Nolan R , Yu Zhiya , Sindiri Sivasish , Gartner Jared J , Parkhurst Maria , Krishna Sri , Lowery Frank J , Zacharakis Nikolaos , Levy Lior , Prickett Todd D , Benzine Tiffany , Ray Satyajit , Masi Robert V , Gasmi Billel , Li Yong , Islam Rafiqul , Bera Alakesh , Goff Stephanie L , Robbins Paul F , Rosenberg Steven A 
Published: May 2024

BackgroundTumor-infiltrating lymphocytes (TILs) targeting neoantigens can effectively treat a selected set of metastatic solid cancers. However, harnessing TILs for cancer treatments remains challenging because neoantigen-reactive T cells are often rare and exhausted, and ex vivo expansion can further reduce their frequencies. This complicates the identification of neoantigen-reactive T-cell receptors (TCRs) and the development of TIL products with high reactivity for patient treatment.MethodsWe tested whether TILs could be in vitro stimulated against neoantigens to achieve selective expansion of neoantigen-reactive TILs. Given their prevalence, mutant p53 or RAS were studied as models of human neoantigens. An in vitro stimulation method, termed “NeoExpand”, was developed to provide neoantigen-specific stimulation to TILs. 25 consecutive patient TILs from tumors harboring p53 or RAS mutations were subjected to NeoExpand.ResultsWe show that neoantigenic stimulation achieved selective expansion of neoantigen-reactive TILs and broadened the neoantigen-reactive CD4+and CD8+TIL clonal repertoire. This allowed the effective isolation of novel neoantigen-reactive TCRs. Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. Furthermore, neoantigenic stimulation improved the in vivo antitumor efficacy of TILs relative to the conventional OKT3-induced rapid TIL expansion in p53-mutated or KRAS-mutated xenograft mouse models.ConclusionsTaken together, neoantigenic stimulation of TILs selectively expands neoantigen-reactive TILs by frequencies and by their clonal repertoire. NeoExpand led to improved phenotypes and functions of neoantigen-reactive TILs. Our data warrant its clinical evaluation.Trial registration numberNCT00068003,NCT01174121, andNCT03412877.
A cross-diffusion system modeling rivaling gangs: Global existence of bounded solutions and FCT stabilization for numerical simulation
Authors: Fuest Mario , Heydari Shahin 
Published: May 2024

In this paper, we study a gang territorial model consisting of two parabolic and two ordinary differential equations, where a taxis-type mechanism models that the two rivaling gangs are repelled by each other’s graffiti. Our main analytical finding shows the existence of global, bounded classical solutions. By making use of quantitative global estimates, we prove that these solutions converge to homogeneous steady states if the initial data are sufficiently small.Moreover, we perform numerical experiments which show that for different choices of parameters, the system may become diffusion- or convection-dominated, where in the former case the solutions converge toward constant steady states while in the latter case nontrivial asymptotic behavior such as segregation is observed. In order to perform these experiments, we apply a nonlinear finite element flux-corrected transport method (FEM-FCT) which is positivity-preserving. Then we treat the nonlinearities in both the system and the proposed nonlinear scheme simultaneously using fixed-point iteration.
A 5-Hydroxymethylcytosine-Based Noninvasive Model for Early Detection of Colorectal Carcinomas and Advanced Adenomas: The METHOD-2 Study
Authors: Chang Wenju , Zhang Zhou , Jia Baoqing , Ding Kefeng , Pan Zhizhong , Su Guoqiang , Zhang Wei , Liu Tianyu , Zhong Yunshi , He Guodong , Ren Li , Wei Ye , Li Dongdong , Cui Xiaolong , Yang Jun , Shi Yixiang , Bissonnette Marc , He Chuan , Zhang Wei , Fan Jia , Xu Jianmin 
Published: May 2024

Abstract

Purpose:
Detection of colorectal carcinomas at a time when there are more treatment options is associated with better outcomes. This prospective case–control study assessed the 5-hydroxymethylcytosine (5hmC) biomarkers in circulating cell-free DNA (cfDNA) for early detection of colorectal carcinoma and advanced adenomas (AA).

Experimental Design:
Plasma cfDNA samples from 2,576 study participants from the multicenter METHOD-2 study (NCT03676075) were collected, comprising patients with newly diagnosed colorectal carcinoma (n = 1,074), AA (n = 356), other solid tumors (n = 80), and non–colorectal carcinoma/AA controls (n = 1,066), followed by genome-wide 5hmC profiling using the 5hmC-Seal technique and the next-generation sequencing. A weighted diagnostic model for colorectal carcinoma (stage I–III) and AA was developed using the elastic net regularization in a discovery set and validated in independent samples.

Results:
Distribution of 5hmC in cfDNA reflected gene regulatory relevance and tissue of origin. Besides being confirmed in internal validation, a 96-gene model achieved an area under the curve (AUC) of 90.7% for distinguishing stage I–III colorectal carcinoma from controls in 321 samples from multiple centers for external validation, regardless of primary location or mutation status. This model also showed cancer-type specificity as well as high capacity for distinguishing AA from controls with an AUC of 78.6%. Functionally, differential 5hmC features associated with colorectal carcinoma and AA demonstrated relevance to colorectal carcinoma biology, including pathways such as calcium and MAPK signaling.

Conclusions:
Genome-wide mapping of 5hmC in cfDNA shows promise as a highly sensitive and specific noninvasive blood test to be integrated into screening programs for improving early detection of colorectal carcinoma and high-risk AA.
Medication-overuse headache: a narrative review
Authors: Gosalia Helin , Moreno-Ajona David , Goadsby Peter J. 
Published: May 2024

AbstractMedication-overuse headache (MOH), which potentially involves 1–2% of the population, is defined as a headache, on ≥ 15 days a month affected, along with overuse of one or other acute attack medications. MOH presents with significant challenges in the headache community, particularly in clinical settings raising various questions about its pathophysiology. Through a review of the current literature and our clinical experience, we have explored the mechanisms through which MOH may occur, provide an understanding of the current state of treatment and detail some possible views on the understanding and treatment of this condition. We evaluate the variations in treatment methods offered globally and understanding of the disorder. Above all interventions, patient education is crucial, which is underscored by an analysis of the academic publications. Given the condition is preventable, early intervention is imperative and patient awareness is highlighted as key. Globally, there is no uniform treatment methodology, which may be advantageous as approaches need to take local circumstances into account.
MFPINC: prediction of plant ncRNAs based on multi-source feature fusion
Authors: Nie Zhenjun , Gao Mengqing , Jin Xiu , Rao Yuan , Zhang Xiaodan 
Published: May 2024

AbstractNon-coding RNAs (ncRNAs) are recognized as pivotal players in the regulation of essential physiological processes such as nutrient homeostasis, development, and stress responses in plants. Common methods for predicting ncRNAs are susceptible to significant effects of experimental conditions and computational methods, resulting in the need for significant investment of time and resources. Therefore, we constructed an ncRNA predictor(MFPINC), to predict potential ncRNA in plants which is based on the PINC tool proposed by our previous studies. Specifically, sequence features were carefully refined using variance thresholding and F-test methods, while deep features were extracted and feature fusion were performed by applying the GRU model. The comprehensive evaluation of multiple standard datasets shows that MFPINC not only achieves more comprehensive and accurate identification of gene sequences, but also significantly improves the expressive and generalization performance of the model, and MFPINC significantly outperforms the existing competing methods in ncRNA identification. In addition, it is worth mentioning that our tool can also be found on Github (https://github.com/Zhenj-Nie/MFPINC) the data and source code can also be downloaded for free.
Enhancing salt stress tolerance in wheat (Triticum aestivum) seedlings: insights from trehalose and mannitol
Authors: Alhudhaibi Abdulrahman M. , Ibrahim Mervat A. R. , Abd-Elaziz Seham M. S. , Farag Hanaa R. M. , Elsayed Salwa M. , Ibrahim Hemmat A. , Hossain ABM Sharif , Alharbi Basmah M. , Haouala Faouzi , Elkelish Amr , Srour Hany A. M. 
Published: May 2024

AbstractSalinity stress, an ever-present challenge in agriculture and environmental sciences, poses a formidable hurdle for plant growth and productivity in saline-prone regions worldwide. Therefore, this study aimed to explore the effectiveness of trehalose and mannitol induce salt resistance in wheat seedlings. Wheat grains of the commercial variety Sakha 94 were divided into three groups : a group that was pre-soaked in 10 mM trehalose, another group was soaked in 10 mM mannitol, and the last was soaked in distilled water for 1 hour, then the pre soaked grains cultivated in sandy soil, each treatment was divided into two groups, one of which was irrigated with 150 mM NaCl and the other was irrigated with tap water. The results showed that phenols content in wheat seedlings increased and flavonoids reduced due to salt stress. Trehalose and mannitol cause slight increase in total phenols content while total flavonoids were elevated highy in salt-stressed seedlings. Furthermore, Trehalose or mannitol reduced salt-induced lipid peroxidation. Salt stress increases antioxidant enzyme activities of guaiacol peroxidase (G-POX), ascorbate peroxidase (APX), and catalase (CAT) in wheat seedlings, while polyphenol oxidase (PPO) unchanged. Trehalose and mannitol treatments caused an increase in APX, and CAT activities, whereas G-POX not altered but PPO activity were decreased under salt stress conditions. Molecular docking confirmed the interaction of Trehalose or mannitol with peroxidase and ascorbic peroxidase enzymes. Phenyl alanine ammonia layase (PAL) activity was increased in salt-stressed seedlings. We can conclude that pre-soaking of wheat grains in 10 mM trehalose or mannitol improves salinity stress tolerance by enhancing antioxidant defense enzyme and/or phenol biosynthesis, with docking identifying interactions with G-POX, CAT, APX, and PPO.