bluuebunny/crossref_metadata_2025_split huggingface dataset:
Little rip, pseudo rip and bounce cosmology with generalized equation of state in non-standard backgrounds
Authors: Trivedi Oem , Timoshkin Alexander V. 
Published: March 2024

AbstractThe discovery of universe’s late-time acceleration and dark energy has overseen a great deal of research into cosmological singularities and particularly future singularities. Perhaps the most extreme of such singlarities is the big rip, which has propelled a lot of work into ways of moderating it or seeking out alternatives to it and two such alternatives to the big rip are the Little rip and Pseudo rip. Another possibility to consider the far future of the universe is through bounce cosmologies, which presents its own interesting ideas. So in this work we investigate the Little rip, Pseudo rip and Bounce cosmology in non-standard cosmological backgrounds with a generalized equation of state in the presence of a viscous fluid. In particular we discuss about Chern-Simons cosmology and the RS-II Braneworld and discuss how the exotic and non-conventional nature of gravity in such cosmologies affect universal evolution in these scenarios. We find out that there are very significant differences in the behaviour of such cosmic scenarios in these universes in comparison to how they appear in the simple general relativistic universe.
Modeling the spread of rice blast in rice plant group based on cellular automata
Authors: Ding Wei-Long , Zhu Wei , Fan Cheng-Cheng , Xu Li-Feng , Zhang Yu-Ping 
Published: March 2024

Studying and modeling the process of the disease and spread of blast can guide fertilization and reduce the amount of pesticide application. Since most of the existing research focuses on the pathogenesis of the rice blast fungus and the interaction between the plant structure and the fungus, this paper presents a method to simulate the spread of rice blast among rice populations. The method is divided into the following processes. First, based on the cellular automata grid dynamics model, the cell state corresponds to the degree of infection of the rice blast fungus, and its ability to simulate the spatiotemporal evolution of complex systems is used to simulate the spread of disease spots on the surface of rice leaves. Second, according to the biological mechanism of the rice blast fungus and the position of the first infected leaf in a single rice plant, the normal distribution function is used to calculate the infection probability of the remaining leaves, and then the transmission mode of the disease inside a single rice plant is simulated. Then, in view of the natural phenomenon that the blast fungus spores spread with the wind, the wind factor is added to propose a method for the spread of the rice blast fungus among the population of rice plants, and thus a model for the spread of the pathogen among the entire plant population was established. Finally, we set up a simulation system for the spread of rice blasts in rice fields and visualized the spread and spread trend of rice blasts in rice populations. In the simulation experiment, the infection process of rice blast on the surface of the rice leaf was simulated, and the change process of the shape of the diseased spot can be visually seen. This paper not only provides a new idea for the research on pathogen propagation and diffusion between plants in agricultural production but also provides a reference for how to realistically visualize the pathogen propagation model in the virtual agricultural scene.
NAVIDRO, a CARES architectural style for configuring drone co-simulation
Authors: Salmon Loic , Pillain Pierre-Yves , Guillou Goulven , Babau Jean-Philippe 
Published: March 2024

One primary objective of drone simulation is to evaluate diverse drone configurations and contexts aligned with specific user objectives. The initial challenge for simulator designers involves managing the heterogeneity of drone components, encompassing both software and hardware systems, as well as the drone’s behavior. To facilitate the integration of these diverse models, the Functional Mock-Up Interface (FMI) for co-simulation proposes a generic data-oriented interface. However, an additional challenge lies in simplifying the configuration of co-simulation, necessitating an approach to guide the modeling of parametric features and operational conditions such as failures or environment changes.
The article addresses this challenge by introducing CARES, a model-driven engineering and component-based approach for designing drone simulators, integrating the FMI for co-simulation. The proposed models incorporate concepts from component-based software engineering and FMI. The NAVIDRO architectural style is presented for designing and configuring drone co-simulation. CARES utilizes a code generator to produce structural glue code (Java or C++), facilitating the integration of FMI-based domain-specific code. The approach is evaluated through the development of a simulator for navigation functions in an autonomous underwater vehicle, demonstrating its effectiveness in assessing various autonomous underwater vehicle configurations and contexts.
Loss of Dnmt3a increases self-renewal and resistance to pegIFN-α in JAK2-V617F–positive myeloproliferative neoplasms
Authors: Usart Marc , Stetka Jan , Luque Paz Damien , Hansen Nils , Kimmerlin Quentin , Almeida Fonseca Tiago , Lock Melissa , Kubovcakova Lucia , Karjalainen Riikka , Hao-Shen Hui , Börsch Anastasiya , El Taher Athimed , Schulz Jessica , Leroux Jean-Christophe , Dirnhofer Stefan , Skoda Radek C. 
Published: March 2024

Abstract
Pegylated interferon alfa (pegIFN-α) can induce molecular remissions in patients with JAK2-V617F–positive myeloproliferative neoplasms (MPNs) by targeting long-term hematopoietic stem cells (LT-HSCs). Additional somatic mutations in genes regulating LT-HSC self-renewal, such as DNMT3A, have been reported to have poorer responses to pegIFN-α. We investigated whether DNMT3A loss leads to alterations in JAK2-V617F LT-HSC functions conferring resistance to pegIFN-α treatment in a mouse model of MPN and in hematopoietic progenitors from patients with MPN. Long-term treatment with pegIFN-α normalized blood parameters and reduced splenomegaly and JAK2-V617F chimerism in single-mutant JAK2-V617F (VF) mice. However, pegIFN-α in VF;Dnmt3aΔ/Δ (VF;DmΔ/Δ) mice worsened splenomegaly and failed to reduce JAK2-V617F chimerism. Furthermore, LT-HSCs from VF;DmΔ/Δ mice compared with VF were less prone to accumulate DNA damage and exit dormancy upon pegIFN-α treatment. RNA sequencing showed that IFN-α induced stronger upregulation of inflammatory pathways in LT-HSCs from VF;DmΔ/Δ than from VF mice, indicating that the resistance of VF;DmΔ/Δ LT-HSC was not due to failure in IFN-α signaling. Transplantations of bone marrow from pegIFN-α–treated VF;DmΔ/Δ mice gave rise to more aggressive disease in secondary and tertiary recipients. Liquid cultures of hematopoietic progenitors from patients with MPN with JAK2-V617F and DNMT3A mutation showed increased percentages of JAK2-V617F–positive colonies upon IFN-α exposure, whereas in patients with JAK2-V617F alone, the percentages of JAK2-V617F–positive colonies decreased or remained unchanged. PegIFN-α combined with 5-azacytidine only partially overcame resistance in VF;DmΔ/Δ mice. However, this combination strongly decreased the JAK2-mutant allele burden in mice carrying VF mutation only, showing potential to inflict substantial damage preferentially to the JAK2-mutant clone.
Integration of ζ-deficient CARs into the CD3
ζ gene conveys potent cytotoxicity in T and NK cells
Authors: Kath Jonas , Franke Clemens , Drosdek Vanessa , Du Weijie , Glaser Viktor , Fuster-Garcia Carla , Stein Maik , Zittel Tatiana , Schulenberg Sarah , Porter Caroline E. , Andersch Lena , Künkele Annette , Alcaniz Joshua , Hoffmann Jens , Abken Hinrich , Abou-el-Enein Mohamed , Pruß Axel , Suzuki Masataka , Cathomen Toni , Stripecke Renata , Volk Hans-Dieter , Reinke Petra , Schmueck-Henneresse Michael , Wagner Dimitrios L. 
Published: March 2024

Abstract
Chimeric antigen receptor (CAR)-redirected immune cells hold significant therapeutic potential for oncology, autoimmune diseases, transplant medicine, and infections. All approved CAR-T therapies rely on personalized manufacturing using undirected viral gene transfer, which results in nonphysiological regulation of CAR-signaling and limits their accessibility due to logistical challenges, high costs and biosafety requirements. Random gene transfer modalities pose a risk of malignant transformation by insertional mutagenesis. Here, we propose a novel approach utilizing CRISPR-Cas gene editing to redirect T cells and natural killer (NK) cells with CARs. By transferring shorter, truncated CAR-transgenes lacking a main activation domain into the human CD3ζ (CD247) gene, functional CAR fusion-genes are generated that exploit the endogenous CD3ζ gene as the CAR’s activation domain. Repurposing this T/NK-cell lineage gene facilitated physiological regulation of CAR expression and redirection of various immune cell types, including conventional T cells, TCRγ/δ T cells, regulatory T cells, and NK cells. In T cells, CD3ζ in-frame fusion eliminated TCR surface expression, reducing the risk of graft-versus-host disease in allogeneic off-the-shelf settings. CD3ζ-CD19-CAR-T cells exhibited comparable leukemia control to TCRα chain constant (TRAC)-replaced and lentivirus-transduced CAR-T cells in vivo. Tuning of CD3ζ-CAR-expression levels significantly improved the in vivo efficacy. Notably, CD3ζ gene editing enabled redirection of NK cells without impairing their canonical functions. Thus, CD3ζ gene editing is a promising platform for the development of allogeneic off-the-shelf cell therapies using redirected killer lymphocytes.
An international learning collaborative phase 2 trial for haploidentical bone marrow transplant in sickle cell disease
Authors: Kassim Adetola A. , de la Fuente Josu , Nur Erfan , Wilkerson Karina L. , Alahmari Ali D. , Seber Adriana , Bonfim Carmem , Simões Belinda Pinto , Alzahrani Mohsen , Eckrich Michael J. , Horn Biljana , Hanna Rabi , Dhedin Nathalie , Rangarajan Hemalatha G. , Gouveia Roseane Vasconcelos , Almohareb Fahad , Aljurf Mahmoud , Essa Mohammed , Alahmari Bader , Gatwood Katie , Connelly James A. , Dovern Elisabeth , Rodeghier Mark , DeBaun Michael R. 
Published: March 2024

Abstract
In the setting of a learning collaborative, we conducted an international multicenter phase 2 clinical trial testing the hypothesis that nonmyeloablative–related haploidentical bone marrow transplant (BMT) with thiotepa and posttransplant cyclophosphamide (PTCy) will result in 2-year event-free survival (no graft failure or death) of at least 80%. A total of 70 participants were evaluable based on the conditioning protocol. Graft failure occurred in 8 of 70 (11.4%) and only in participants aged &lt;18 years; all had autologous reconstitution. After a median follow-up of 2.4 years, the 2-year Kaplan-Meier–based probability of event-free survival was 82.6%. The 2-year overall survival was 94.1%, with no difference between children and adult participants. After excluding participants with graft failure (n = 8), participants with engraftment had median whole blood donor chimerism values at days +180 and +365 after transplant of 100% (n = 58), respectively, and 96.6% (57/59) were off immunosuppression 1 year after transplant. The 1-year grade 3 to 4 acute graft-versus-host disease (GVHD) rate was 10%, and the 2-year moderate–severe chronic GVHD rate was 10%. Five participants (7.1%) died from infectious complications. We demonstrate that nonmyeloablative haploidentical BMT with thiotepa and PTCy is a readily available curative therapy for most adults, even those with organ damage, compared to the more expensive myeloablative gene therapy and gene editing. Additional strategies are required for children to decrease graft failure rates. The trial was registered at www.clinicaltrials.gov as #NCT01850108.
Management of adult patients with CMML undergoing allo-HCT: recommendations from the EBMT PH&G Committee
Authors: Onida Francesco , Gagelmann Nico , Chalandon Yves , Kobbe Guido , Robin Marie , Symeonidis Argiris , de Witte Theo , Itzykson Raphael , Jentzsch Madlen , Platzbecker Uwe , Santini Valeria , Sanz Guillermo , Scheid Christof , Solary Eric , Valent Peter , Greco Raffaela , Sanchez-Ortega Isabel , Yakoub-Agha Ibrahim , Pleyer Lisa 
Published: March 2024

Abstract
Chronic myelomonocytic leukemia (CMML) is a heterogeneous disease presenting with either myeloproliferative or myelodysplastic features. Allogeneic hematopoietic cell transplantation (allo-HCT) remains the only potentially curative option, but the inherent toxicity of this procedure makes the decision to proceed to allo-HCT challenging, particularly because patients with CMML are mostly older and comorbid. Therefore, the decision between a nonintensive treatment approach and allo-HCT represents a delicate balance, especially because prospective randomized studies are lacking and retrospective data in the literature are conflicting. International consensus on the selection of patients and the ideal timing of allo-HCT, specifically in CMML, could not be reached in international recommendations published 6 years ago. Since then, new, CMML-specific data have been published. The European Society for Blood and Marrow Transplantation (EBMT) Practice Harmonization and Guidelines (PH&G) Committee assembled a panel of experts in the field to provide the first best practice recommendations on the role of allo-HCT specifically in CMML. Recommendations were based on the results of an international survey, a comprehensive review of the literature, and expert opinions on the subject, after structured discussion and circulation of recommendations. Algorithms for patient selection, timing of allo-HCT during the course of the disease, pretransplant strategies, allo-HCT modality, as well as posttransplant management for patients with CMML were outlined. The keynote message is, that once a patient has been identified as a transplant candidate, upfront transplantation without prior disease-modifying treatment is preferred to maximize chances of reaching allo-HCT whenever possible, irrespective of bone marrow blast counts.
Glyphosate lessons: is biodegradation of pesticides a harmless process for biodiversity?
Authors: Lozano Verónica Laura , Pizarro Haydée Norma 
Published: March 2024

AbstractThe historical perspective on the rapid biodegradation of pesticides as a mitigating factor in environmental risk assessment is reexamined through the example of glyphosate and its implications for freshwater biodiversity. Commonly employed standardized methods by national agencies for assessing the environmental risk of pesticides predominantly rely on single-species tests, overlooking the intricate nature of ecosystems. Glyphosate, one of the most widely used pesticides marketed for its purported rapid biodegradability, is often perceived as relatively innocuous. However, its degradation releases phosphorus into the environment, inducing a trophic state shift in water systems towards more eutrophic conditions, consequently affecting water quality. These findings highlight the cascading ecological repercussions of glyphosate biodegradation, driving the proliferation of specific aquatic organisms, such as picocyanobacteria and metaphyton, resulting in the alteration of ecosystem structure and dynamics. The study explores challenges posed by commercial pesticide formulations and investigates the consequences of pesticide interactions with specific anthropogenic factors. A case in point is the interaction of glyphosate with the invasive mussel Limnoperna fortunei, exacerbating the overall scenario. The ecological framework analyzed challenges the conventional notion that pesticide biodegradation is inherently a neutral or positive event. The results underscore the necessity of reassessing the role of biodegradation itself in environmental impact assessments for pesticides.
An analysis of published study designs in PubMed prisoner health abstracts from 1963 to 2023: a text mining study
Authors: Karystianis George , Lukmanjaya Wilson , Buchan Iain , Simpson Paul , Ginnivan Natasha , Nenadic Goran , Butler Tony 
Published: March 2024

Abstract
Background
The challenging nature of studies with incarcerated populations and other offender groups can impede the conduct of research, particularly that involving complex study designs such as randomised control trials and clinical interventions. Providing an overview of study designs employed in this area can offer insights into this issue and how research quality may impact on health and justice outcomes.

Methods
We used a rule-based approach to extract study designs from a sample of 34,481 PubMed abstracts related to epidemiological criminology published between 1963 and 2023. The results were compared against an accepted hierarchy of scientific evidence.

Results
We evaluated our method in a random sample of 100 PubMed abstracts. An F1-Score of 92.2% was returned. Of 34,481 study abstracts, almost 40.0% (13,671) had an extracted study design. The most common study design was observational (37.3%; 5101) while experimental research in the form of trials (randomised, non-randomised) was present in 16.9% (2319). Mapped against the current hierarchy of scientific evidence, 13.7% (1874) of extracted study designs could not be categorised. Among the remaining studies, most were observational (17.2%; 2343) followed by systematic reviews (10.5%; 1432) with randomised controlled trials accounting for 8.7% (1196) of studies and meta-analysis for 1.4% (190) of studies.

Conclusions
It is possible to extract epidemiological study designs from a large-scale PubMed sample computationally. However, the number of trials, systematic reviews, and meta-analysis is relatively small – just 1 in 5 articles. Despite an increase over time in the total number of articles, study design details in the abstracts were missing. Epidemiological criminology still lacks the experimental evidence needed to address the health needs of the marginalized and isolated population that is prisoners and offenders.
Predicting health outcomes with intensive longitudinal data collected by mobile health devices: a functional principal component regression approach
Authors: Yang Qing , Jiang Meilin , Li Cai , Luo Sheng , Crowley Matthew J. , Shaw Ryan J. 
Published: March 2024

AbstractBackgroundIntensive longitudinal data (ILD) collected in near real time by mobile health devices provide a new opportunity for monitoring chronic diseases, early disease risk prediction, and disease prevention in health research. Functional data analysis, specifically functional principal component analysis, has great potential to abstract trends in ILD but has not been used extensively in mobile health research.ObjectiveTo introduce functional principal component analysis (fPCA) and demonstrate its potential applicability in estimating trends in ILD collected by mobile heath devices, assessing longitudinal association between ILD and health outcomes, and predicting health outcomes.MethodsfPCA and scalar-to-function regression models were reviewed. A case study was used to illustrate the process of abstracting trends in intensively self-measured blood glucose using functional principal component analysis and then predicting future HbA1c values in patients with type 2 diabetes using a scalar-to-function regression model.ResultsBased on the scalar-to-function regression model results, there was a slightly increasing trend between daily blood glucose measures and HbA1c. 61% of variation in HbA1c could be predicted by the three preceding months’ blood glucose values measured before breakfast (P < 0.0001,$${R}_{adjusted}^{2}=0.61$$).ConclusionsFunctional data analysis, specifically fPCA, offers a unique tool to capture patterns in ILD collected by mobile health devices. It is particularly useful in assessing longitudinal dynamic association between repeated measures and outcomes, and can be easily integrated in prediction models to improve prediction precision.
Nonalcoholic fatty liver disease is an independent risk factor for ischemic stroke after revascularization in patients with Moyamoya disease: a prospective cohort study
Authors: Zhang Bojian , Li Junsheng , Zeng Chaofan , Tao Chuming , He Qiheng , Liu Chenglong , Zheng Zhiyao , Zhao Zhikang , Mou Siqi , Sun Wei , Wang Jia , Zhang Qian , Wang Rong , Zhang Yan , Ge Peicong , Zhang Dong 
Published: March 2024

Abstract
Background
The study aimed to investigate the association between nonalcoholic fatty liver disease (NAFLD) and ischemic stroke events after revascularization in patients with Moyamoya disease (MMD).

Methods
This study prospectively enrolled 275 MMD patients from September 2020 to December 2021. Patients with alcoholism and other liver diseases were excluded. NAFLD was confirmed by CT imaging or abdominal ultrasonography. Stroke events and modified Rankin Scale (mRS) scores at the latest follow-up were compared between the two groups.

Results
A total of 275 patients were enrolled in the study, among which 65 were diagnosed with NAFLD. Univariate logistic regression analysis showed that NAFLD (P = 0.029) was related to stroke events. Multivariate logistic regression analysis showed that NAFLD is a predictor of postoperative stroke in MMD patients (OR = 27.145, 95% CI = 2.031–362.81, P = 0.013). Kaplan-Meier analysis showed that compared with MMD patients with NAFLD, patients in the control group had a longer stroke-free time (P = 0.004). Univariate Cox analysis showed that NAFLD (P = 0.016) was associated with ischemic stroke during follow-up in patients with MMD. Multivariate Cox analysis showed that NAFLD was an independent risk factor for stroke in patients with MMD (HR = 10.815, 95% CI = 1.259–92.881, P = 0.030). Furthermore, fewer patients in the NAFLD group had good neurologic status (mRS score ≤ 2) than the control group (P = 0.005).

Conclusion
NAFLD was an independent risk factor for stroke in patients with MMD after revascularization and worse neurological function outcomes.
scRNA-seq analysis discovered suppression of immunomodulatory dependent inflammatory response in PMBCs exposed to silver nanoparticles
Authors: Perumalsamy Haribalan , Xiao Xiao , Kim Hyun-Yi , Yoon Tae-Hyun 
Published: March 2024

AbstractThe assessment of AgNPs toxicity in vitro and in vivo models are frequently conflicting and inaccurate. Nevertheless, single cell immunological responses in a heterogenous environment have received little attention. Therefore, in this study, we have performed in-depth analysis which clearly revealed cellular-metal ion association as well as specific immunological response. Our study didn’t show significant population differences in PMBC between control and AgNPs group implying no toxicological response. To confirm it further, deep profiling identified differences in subsets and differentially expressed genes (DEGs) of monocytes, B cells and T cells. Notably, monocyte subsets showed significant upregulation of metallothionein (MT) gene expression such as MT1G, MT1X, MT1E, MT1A, and MT1F. On the other hand, downregulation of pro-inflammatory genes such as IL1β and CCL3 in both CD16 + and CD16- monocyte subsets were observed. This result indicated that AgNPs association with monocyte subsets de-promoted inflammatory responsive genes suggesting no significant toxicity observed in AgNPs treated group. Other cell types such as B cells and T cells also showed negligible differences in their subsets suggesting no toxicity response. Further, AgNPs treated group showed upregulation of cell proliferation, ribosomal synthesis, downregulation of cytokine release, and T cell differentiation inhibition. Overall, our results conclude that treatment of AgNPs to PMBC cells didn’t display immunological related cytotoxicity response and thus motivate researchers to use them actively for biomedical applications.