bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streptococcus pneumoniae and influenza vaccination rates in oncological patients — data from Germany
Authors: Niederstein Emma , Underwood Journey , de Wit Maike , Reinwald Mark , Schwarzlose-Schwarck Sandra , Dammermann Werner , Deckert P. Markus , Kiderlen Til Ramón 
Published: November 2024

Abstract
Objectives
Due to disease- or therapy-associated immunosuppression, oncological patients suffer from significantly higher morbidity and mortality due to infections transmitted by respiratory pathogens such as Streptococcus pneumoniae and influenza virus. Although the German Standing Committee on Vaccination (STIKO) provides specific recommendations for vaccination against these pathogens, there is no data on vaccination rates in this high-risk population.

Methods
Data from the interventional EVO study were analyzed to provide information on vaccination rates against Streptococcus pneumoniae and influenza virus in oncological patients. Numbers presented in this publication summarize baseline and follow-up data of the control group; thus, data were not influenced by the intervention.

Results
Data of 370 patients were analyzed; 20.5% of patients were treated for hematological malignancies and 79.5% for solid cancer. 28.1% of patients had received vaccination against influenza and 32.2% against Streptococcus pneumoniae; for the latter only 7.3% according recommendations. While vaccination rates where even lower for patients with thoracic carcinoma (influenza 26.7% and Streptococcus pneumoniae 6.0% according to STIKO recommendations), rates in patients with multiple myeloma were remarkably higher (39.0% and 14.6%).

Conclusions
Despite strong recommendations to vaccinate and the clear clinical need to prevent infections in the vulnerable group of oncological patients, only the minority was vaccinated against Streptococcus pneumoniae or influenza, underlining the urgent need for better vaccination strategies in this high-risk population.
Energy barriers for boundary nucleation in a two-well model without gauge invariances
Authors: Tribuzio Antonio , Zemas Konstantinos 
Published: November 2024

Abstract
We study energy scaling laws for a simplified, singularly perturbed, double-well nucleation problem confined in a half-space, in the absence of gauge invariance and for an inclusion of fixed volume. Motivated by models for boundary nucleation of a single-phase martensite inside a parental phase of austenite, our main focus in this nonlocal isoperimetric problem is how the relationship between the rank-1 direction and the orientation of the half-space influences the energy scaling with respect to the fixed volume of the inclusion. Up to prefactors depending on this relative orientation, the scaling laws coincide with the corresponding ones for bulk nucleation (Knüpfer in Proc R Soc A Math Phys Eng Sci 467(2127): 695-717, 2011) for all rank-1 directions, but the ones normal to the confining hyperplane, where the scaling is as in a three-gradient problem in full space, resulting in a lower energy barrier (Rüland et al. J Nonlinear Sci 33(2): 25 2023).
Glioblastoma invasion patterns from a clinical perspective—a systematic review
Authors: Percuoco Veronica , Herlin Erica , Prada Francesco , Riva Marco , Pessina Federico , Staartjes Victor E. , Della Pepa Giuseppe Maria , Menna Grazia 
Published: November 2024

AbstractGlioblastoma (GBM) is the most common and aggressive primary brain tumor. Despite advances in treatment, mechanisms underlying GBM invasion remain incompletely understood. This systematic review synthesizes findings from laboratory and clinical studies to elucidate the molecular mechanisms driving GBM invasion and their implications for prognosis and therapy. This review adhered to PRISMA guidelines, conducting a comprehensive search of PubMed/Medline for studies published up to October 16, 2023. Inclusion criteria focused on studies investigating molecular mechanisms of GBM invasiveness with reported clinical outcomes (overall survival (OS) and progression-free survival (PFS). Exclusion criteria included systematic reviews, case reports, small case series, and studies limited to preclinical data. Risk of bias was assessed using the ROBINS-I tool. From 831 records, 21 studies (2198 patients) met the criteria. Key GBM invasion mechanisms included ECM degradation, vascular invasion, EMT, apoptotic regulation, cytoskeletal organization, and RNA sequencing. Vascular mechanisms were most studied. Bevacizumab resistance linked to poorer outcomes. EMT markers like TWIST and ECM degradation via MMPs such as CD147 correlated with decreased survival. Cytoskeletal and RNA studies highlighted the prognostic significance of tumor subtypes and microenvironmental interactions. This systematic review elucidates the molecular mechanisms underlying GBM invasiveness and their clinical implications. Integrating molecular profiling into routine clinical assessment may enhance prognostic accuracy and therapeutic efficacy, paving the way for personalized treatment strategies.
Development of hepatocellular carcinoma organoid model recapitulating HIF-1A metabolic signature
Authors: Khedr Mennatallah A. , Mohamed Zainab , El-Derby Azza M. , Soliman Malak M. , Edris Amira Abdel Fattah , Badr Eman , El-Badri Nagwa 
Published: November 2024

AbstractHypoxia is one of the main hallmarks of hepatocellular carcinoma (HCC) resulting from improper oxygenation and insufficient nourishment of the HCC microenvironment. The effect of hypoxia is mediated by hypoxia-inducible factor-1A (HIF-1A) via targeting various downstream pathways, including glycolysis, angiogenesis, and survival signaling. However, HCC cell lines in a 2-dimensional (2D) setting do not resemble the metabolic signature of HCC. Here we aim to overcome these limitations by developing an HCC organoid that recapitulates the HIF-1A metabolic shift. The enrichment analysis of the RNA-Seq data revealed that HIF-1A-driven glycolytic shift is of the significant pathways. The established organoid model, using xeno-free plasma-derived extracellular matrix (ECM) as a scaffold and nutritive biomatrix, maintained its structural integrity and viability for up to 14 days; the comparative analysis of the cobalt (II) chloride (CoCl2)-treated organoids to the untreated ones unveiled reduced size and proliferative capacity. Interestingly, our organoid model showed an elevated expression of HIF-1A and glycolysis enzymes compared to their counterparts in the CoCl2-treated organoids. HIF-1A molecular expression-translated biochemical signature is further assessed in our spontaneously growing organoids showing an increase in glucose uptake, intracellular pyruvate, extracellular lactate dehydrogenase expression, and extracellular lactate production, while hydrogen peroxide (H2O2), a marker for oxidative metabolism, is reduced. Our data confirmed the potency of the established organoid model to mimic the molecular and biochemical HIF-1A-driven metabolism, which validates its potential use as an in vitro HCC model. Our model naturally simulates hypoxic conditions and simultaneous HIF-1A-dependent glycolysis within HCC rather than using of CoCl2-induced hypoxic conditions.
Evidence and Computer Simulations in Public Health
Authors: Iranzo Valeriano , Pérez-González Saúl 
Published: November 2024

AbstractIn the last decades, the evidence-based approach has become dominant in the biomedical sciences. Its influence has extended from clinical practice to other areas such as drug regulation and public health. Nonetheless, given the limitations of the evidence-based framework, a more pluralist approach towards evidence has been demanded. In this sense, evidential pluralism holds that evidence of mechanisms should complement statistical evidence. This paper aims to explore and discuss the prospects of evidential pluralism in public health. First, we will analyse the evidential standards of the International Agency for Research on Cancer. Those standards are argued to be in line with the pluralist approach. Second, we will consider the main challenges for gathering evidence of mechanisms in public health. For that purpose, diverse types of evidence of mechanisms will be identified. And third, we will assess the role of agent-based models as mechanistic studies. Based on a case study, we will discuss whether agent-based models can provide evidence of mechanisms and mitigate the abovementioned challenges.
Evaluating the performance of intensity prediction equations for the Italian area
Authors: Antonucci Andrea , Lanzano Giovanni , Rovida Andrea , Sgobba Sara , D’Amico Vera , Gomez-Capera Augusto Antonio 
Published: November 2024

Abstract
In this study, we evaluate the performance of five recent Intensity Prediction Equations (IPEs) valid for Italy comparing their predictions with intensities documented at Italian localities. We build four different testing datasets using the data contained in the most recent versions of the Italian Parametric Earthquake Catalogue CPTI15 and Macroseismic Database DBMI15 and we estimate the residuals between observed and predicted intensity values for all the selected IPEs. The results are then analyzed using a measure-oriented approach to score each model according to the goodness of model prediction and a diagnostic-oriented approach to investigate the trend of the residuals as a function of the different variables. The results indicate the capability of all the tested IPEs to reproduce the average decay of macroseismic intensity in Italy although with a general underestimation of high-intensity values. In addition, an in-depth investigation of the spatial and temporal patterns of the event residual term, computed using the best predictive model, is carried out. Lastly, we provide some hints for the selection of calibration datasets for the development of future intensity attenuation models.
Reference gene selection for real-time qPCR in European flounder (Platichthys flesus) using organ-specific RNA-seq data
Authors: Pomianowski Konrad , Burzyński Artur 
Published: November 2024

Abstract
Background
The European flounder is readily chosen as an experimental subject and model in physiological and ecotoxicological studies mostly because of its adaptability to laboratory conditions. Many studies utilise a quantitative PCR (qPCR) approach to ascertain the expression of target genes under experimental conditions. Such an approach relies heavily on the selection of reference genes with stable expression. Yet certain housekeeping genes are commonly used in this role, often without due consideration of their overall expression patterns. Therefore, new approaches should be developed to identify stable reference genes for a given species and to expand the general pool of genes suitable for the reference in qPCR analysis.

Methods and results
Here RNA-seq data of nine flounder organs led to identify four candidate genes of the most stable expression. It was achieved by differential expression analysis and tritoconstrictor script. Specific primers were designed for the complete ORF as well as for qPCR analysis. RT-qPCR efficiencies were tested on ORF amplicon templates. Most of the genes tested showed good amplification in a wide range of template dilutions (107-101), with a correlation coefficient (R2) ranging from 0.991 to 0.998 and a consistent efficiency (E) (Sybr Green I staining and TaqMan molecular probe).

Conclusions
The proposed approach based on differential expression analysis and a new bioinformatic tool is an appropriate selection method of candidates for reference genes in qPCR. The proposed approach, combining differential expression analysis with a new bioinformatics tool, provides an effective method for selecting reference gene candidates for qPCR. As a result, we can propose four genes (polr2f, yif1a, sf3b6, uba52), each with a set of validated primers, as suitable for consideration as reference genes in qPCR analysis in European flounder, an emerging model species.
Concept on plug development in jacked open-ended piles in clay considering total stresses
Authors: Wiesenthal Philipp , Henke Sascha 
Published: November 2024

AbstractSoil plugging in open-ended piles is likely to occur in dense sandy soils which has been the subject of numerous scientific investigations. In contrast, the plugging behaviour in clayey soils is relatively unknown. In this paper an analytical approach to determine the soil plug resistance and its development during jacking in clayey soils is proposed. The new approach was developed using numerical simulations and was validated by back-calculating a field test from the literature. A total stress approach for the numerical simulations was chosen. The values calculated with the analytical formulas and the numerical solutions as well as the measurements from field tests are in very good agreement, given the high complexity of the interactions between pile and soil. Both the plug resistance and the plug height can be calculated during the jacking process. Further research is required to refine the proposed approach for soil plug resistance evaluation, as the proposed method is believed to enhance the understanding of occurring mechanisms.
A multi-center, multi-organ, multi-omic prediction model for treatment-induced severe oral mucositis in nasopharyngeal carcinoma
Authors: Nicol Alexander James , Lam Sai-Kit , Ching Jerry Chi Fung , Tam Victor Chi Wing , Teng Xinzhi , Zhang Jiang , Lee Francis Kar Ho , Wong Kenneth C. W. , Cai Jing , Lee Shara Wee Yee 
Published: November 2024

Abstract

Purpose
Oral mucositis (OM) is one of the most prevalent and crippling treatment-related toxicities experienced by nasopharyngeal carcinoma (NPC) patients receiving radiotherapy (RT), posing a tremendous adverse impact on quality of life. This multi-center study aimed to develop and externally validate a multi-omic prediction model for severe OM.

Methods
Four hundred and sixty-four histologically confirmed NPC patients were retrospectively recruited from two public hospitals in Hong Kong. Model development was conducted on one institution (n = 363), and the other was reserved for external validation (n = 101). Severe OM was defined as the occurrence of CTCAE grade 3 or higher OM during RT. Two predictive models were constructed: 1) conventional clinical and DVH features and 2) a multi-omic approach including clinical, radiomic and dosiomic features.

Results
The multi-omic model, consisting of chemotherapy status and radiomic and dosiomic features, outperformed the conventional model in internal and external validation, achieving AUC scores of 0.67 [95% CI: (0.61, 0.73)] and 0.65 [95% CI: (0.53, 0.77)], respectively, compared to the conventional model with 0.63 [95% CI: (0.56, 0.69)] and 0.56 [95% CI: (0.44, 0.67)], respectively. In multivariate analysis, only the multi-omic model signature was significantly correlated with severe OM in external validation (p = 0.017), demonstrating the independent predictive value of the multi-omic approach.

Conclusion
A multi-omic model with combined clinical, radiomic and dosiomic features achieved superior pre-treatment prediction of severe OM. Further exploration is warranted to facilitate improved clinical decision-making and enable more effective and personalized care for the prevention and management of OM in NPC patients.
Enhanced design of pCMViR-TSC plasmid vector for sustainably high cargo gene expression in mammalian cells
Authors: Sakaguchi Masakiyo , Kinoshita Rie , Tomonobu Nahoko , Sakaguchi Yoshihiko , Futami Junichiro , Yamauchi Akira , Murata Hitoshi , Yamamoto Ken-ichi , Takahashi Tetta , Gohara Yuma , Ochi Toshiki , Jiang Fan , Komalasari Ni Luh Gede Yoni , Chen Youyi , Ruma I Made Winarsa , Sumardika I Wayan , Zhou Jin , Honjo Tomoko , Kuribayashi Futoshi , Sagayama Kazumi , Toyooka Shinichi , Kondo Eisaku , Inoue Yusuke 
Published: November 2024

AbstractThe first-generation pCMViR-TSC, implemented through the promoter sandwich rule, yields 10- to 100-fold higher gene expression than the standard plasmid used with the CMV (cytomegalovirus) or CAG promoter. However, the vector’s shortcomings limit its utility to transient expression only, as it is not suitable for establishing stable transformants in mammalian cells. To overcome this weakness, we here introduce the improved plasmid vector pSAKA-4B, derived from pCMViR-TSC as a second-generation chromosome-insertable vector. This vector facilitates the linear entry of the expression unit into the TTAA site of DNA universally with transposase assistance. The vector is helpful for the indefinite expression of our target gene. The new vector system is proven here to be efficient in establishing stable transformants with a high likelihood of positive clones that exhibit significantly elevated expression levels of the delivered foreign gene. This system, alongside the first-generation vector, is therefore instrumental for diverse basic research endeavors concerning genes, proteins, cells, and animals, and potentially for clinical applications such as gene therapy.
Know Thyself, Improve Thyself: Personalized LLMs for Self-Knowledge and Moral Enhancement
Authors: Giubilini Alberto , Porsdam Mann Sebastian , Voinea Cristina , Earp Brian , Savulescu Julian 
Published: November 2024

AbstractIn this paper, we suggest that personalized LLMs trained on information written by or otherwise pertaining to an individual could serve as artificial moral advisors (AMAs) that account for the dynamic nature of personal morality. These LLM-based AMAs would harness users’ past and present data to infer and make explicit their sometimes-shifting values and preferences, thereby fostering self-knowledge. Further, these systems may also assist in processes of self-creation, by helping users reflect on the kind of person they want to be and the actions and goals necessary for so becoming. The feasibility of LLMs providing such personalized moral insights remains uncertain pending further technical development. Nevertheless, we argue that this approach addresses limitations in existing AMA proposals reliant on either predetermined values or introspective self-knowledge.
Justifying Our Credences in the Trustworthiness of AI Systems: A Reliabilistic Approach
Authors: Ferrario Andrea 
Published: November 2024

AbstractWe address an open problem in the philosophy of artificial intelligence (AI): how to justify the epistemic attitudes we have towards the trustworthiness of AI systems. The problem is important, as providing reasons to believe that AI systems are worthy of trust is key to appropriately rely on these systems in human-AI interactions. In our approach, we consider the trustworthiness of an AI as a time-relative, composite property of the system with two distinct facets. One is the actual trustworthiness of the AI and the other is the perceived trustworthiness of the system as assessed by its users while interacting with it. We show that credences, namely, beliefs we hold with a degree of confidence, are the appropriate attitude for capturing the facets of the trustworthiness of an AI over time. Then, we introduce a reliabilistic account providing justification to the credences in the trustworthiness of AI, which we derive from Tang’s probabilistic theory of justified credence. Our account stipulates that a credence in the trustworthiness of an AI system is justified if and only if it is caused by an assessment process that tends to result in a high proportion of credences for which the actual and perceived trustworthiness of the AI are calibrated. This approach informs research on the ethics of AI and human-AI interactions by providing actionable recommendations on how to measure the reliability of the process through which users perceive the trustworthiness of the system, investigating its calibration to the actual levels of trustworthiness of the AI as well as users’ appropriate reliance on the system.
Pattern of psychedelic substance use: a comparison between populations in Spain and South America using the Psychedelic Use Scale (PUS)
Authors: Rojas-Hernández Jaime , Borkel Lucas F. , Quintana-Hernández Domingo J. , del Pino Ángelo Santana , Henríquez-Hernández Luis Alberto 
Published: November 2024

AbstractPsychedelic use has increased in the last decade. However, it is unclear whether the cultural background of the consumers exerts any influence. The aim of the present study was to determine the pattern of psychedelic use in Spain and Spanish-speaking populations in South America and compare these consumption patterns to understand the use of these substances in two culturally distinct populations. The Psychedelic Use Scale (PUS) was administered via the Google Surveys platform between September and November 2022. 735 participants were selected using a non-probability purposive sampling technique. The study received ethics approval from the local ethics committee. Psilocybin was the most used substance. MDMA was more frequently consumed in the Spanish population (78.5 vs. 37.1%), while mescaline was more commonly used among participants from South America (31.9 vs. 24.0%), mainly among males (P < 0.05). Among the Spanish population, MDMA was the most commonly combined psychedelic; for the South American population, LSD was the substance most frequently combined, highlighting the predominant recreational use of this substance. DMT predicted the most adverse effects during consumption, whereas MDMA predicted the most adverse effects after consumption. Age was as a risk factor for the development of adverse effects, with a significant increase in risk observed in individuals under 30 years of age (OR = 2.01, CI95% 1.1–3.6). In conclusion, the pattern of psychedelic substance use differed between both populations, highlighting the necessity for comprehensive studies. This is especially crucial in light of the social shifts stemming from the ongoing psychedelic renaissance.
In Search of the Lost Link: The Fascinating Platinum Host Rock of Chocó, Colombia
Authors: Salazar Gabriel , Salazar Susana , Ochoa Andrés , Bedoya Álvaro 
Published: November 2024

AbstractIn Colombia, after nearly 500 years of the quest for the platinum source rock, a remarkable discovery of a fossiliferous limestone with gold and platinum now resides under the watch of the Geological Survey’s Museum in Medellín, registered as RS 2.2.1.1.3. Platinum group minerals, long sought after in Colombia’s placer deposits since the 19th century, typically found in the form of nuggets, have received special attention due to the missing link that exists between authigenesis in mafic/ultramafic rocks to detrital alluvium associations. Consequently, this finding unveils an entirely new environment hosting platinum. In this article, we delve into the historical context and the heritage value of a sample boasting $$\sim $$
∼
200-300 g/ton of platinum and $$\sim $$
∼
30 g/ton of gold found by atomic absorption spectroscopy, embedded in a dolomitized biosparite. Various analyses, encompassing X-ray diffraction, micropetrographic characterization, and scanning electron microscopy coupled with energy-dispersive spectroscopy, were performed on the sample. The sample baffled experts due to its unassuming sedimentary rock appearance and the unusual circumstances of its arrival at the museum. Hence, it stands as one of those uncommon scientific curiosities with an unforeseen origin, accessible only through a stroke of chance and an unbiased perspective regarding its origin. Beyond its historical and geological significance, this specimen, safeguarded within the museum’s collection, encourages education and awareness regarding geosites, advocating for the preservation of one of the planet’s most biologically diverse regions, where platinum was first discovered.