bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting the NLRP3 inflammasome–IL-1β pathway in type 2 diabetes and obesity
Authors: Meier Daniel T. , de Paula Souza Joyce , Donath Marc Y. 
Published: November 2024

AbstractIncreased activity of the NACHT, LRR and PYD domains-containing protein 3 (NLRP3) inflammasome–IL-1β pathway is observed in obesity and contributes to the development of type 2 diabetes and its complications. In this review, we describe the pathological activation of IL-1β by metabolic stress, ageing and the microbiome and present data on the role of IL-1β in metabolism. We explore the physiological role of the IL-1β pathway in insulin secretion and the relationship between circulating levels of IL-1β and the development of diabetes and associated diseases. We highlight the paradoxical nature of IL-1β as both a friend and a foe in glucose regulation and provide details on clinical translation, including the glucose-lowering effects of IL-1 antagonism and its impact on disease modification. We also discuss the potential role of IL-1β in obesity, Alzheimer’s disease, fatigue, gonadal dysfunction and related disorders such as rheumatoid arthritis and gout. Finally, we address the safety of NLRP3 inhibition and IL-1 antagonists and the prospect of using this therapeutic approach for the treatment of type 2 diabetes and its comorbidities.
Graphical Abstract
On quaternionic bisectional curvature
Authors: Macia Oscar , Semmelmann Uwe , Weingart Gregor 
Published: November 2024

Abstract
In this article we study the concept of quaternionic bisectional curvature introduced by Chow and Yang in (J Differ Geom 29(2):361–372, 1989) for quaternion-Kähler manifolds. We show that non-negative quaternionic bisectional curvature is only realized for the quaternionic projective space

$$\mathbb {H}\textrm{P}^n$$

H

P
n

. We also show that all symmetric quaternion-Kähler manifolds different from

$$\mathbb {H}\textrm{P}^n$$

H

P
n

admit quaternionic lines of negative quaternionic bisectional curvature. In particular this implies that non-negative sectional curvature does not imply non-negative quaternionic bisectional curvature. Moreover we give a new and rather short proof of a classification result by A. Gray on compact Kähler manifolds of non-negative sectional curvature.
Predation rates on flatback turtle Natator depressus eggs and hatchlings at an island rookery
Authors: Avenant Casper , Fossette Sabrina , Whiting Scott , Hyndes Glenn A. 
Published: November 2024

AbstractPredation can significantly threaten the vulnerable egg and hatchling stages of sea turtles, yet for most populations this remains poorly quantified for use in conservation. We provided the first quantified predation rates of flatback turtle eggs and hatchlings at Thevenard Island, a medium-sized rookery on the northwest coast of Australia, with a focus on ghost crabs as potential predators. Burrow densities were used as proxy for ghost crab densities, while start- and end-of-season nest inventories and infrared videography were used to quantify egg and hatchling predation, respectively. Inventories of 27 nests suggested a mean hatching success of 74.2 ± 4.6% with zero predation of eggs, while videography at 17 nests indicated that 30.1 ± 8.1% of emerged hatchlings were predated, mainly by ghost crabs. Females selecting nest locations not easily accessible to ghost crabs, or the composition of flatback’s eggshells may explain the lack of egg predation. A 44.0% egg-to-surf survival rate was estimated, almost double the rate estimated for C. caretta on the Ningaloo coast (24.4%) using similar techniques. Further work is needed to understand if those predation rates are sustainable for recovering threatened species and if mitigation efforts tailored to each species and each life stage are needed.
Complications of Deep Venous Stenting and Their Management
Authors: Morris Rachael I. , Khan Taha , Black Stephen A. 
Published: November 2024

AbstractComplications after iliofemoral and inferior vena cava stenting are rare, and most can be managed effectively without significant long-term consequences for the patient. Nevertheless, the procedure is not without risk, and clinicians considering starting a venous practice must be aware of the range of complications that can occur, which range from minor access site bleeds to fatal arrhythmia from stent migration to the heart. Most complications can be avoided with appropriate patient selection, stent sizing, and careful access and deployment techniques.
Metabolic differentiation of brushtail possum populations resistant and susceptible to plant toxins revealed via differential gene expression
Authors: Carmelet-Rescan David , Morgan-Richards Mary , Trewick Steven A. 
Published: November 2024

Abstract
The Australian brushtail possum (Trichosurus vulpecula) is adapted to a wide range of food plants across its range and is exposed to numerous physiological challenges. Populations that are resistant to the plant toxin sodium fluoroacetate are of particular interest as this compound has been used since the 1940s for vertebrate pest management around the world. Candidate gene identification is an important first step in understanding how spatial populations have responded to local selection resulting in local physiological divergence. We employ differential gene expression of liver samples from wild-caught brushtail possums from toxin-resistant and toxin-susceptible populations to identify candidate genes that might be involved in metabolic pathways associated with toxin-resistance. This allowed us to identify genetic pathways involved in resistance to the plant toxin sodium fluoroacetate in Western Australian possums but not those originally from south eastern Australia. We identified differentially expressed genes in the liver that are associated with cell signalling, encapsulating structure, cell mobility, and tricarboxylic acid cycle. The gene expression differences detected indicate which metabolic pathways are most likely to be associated with sodium fluoroacetate resistance in these marsupials and we provide a comprehensive list of candidate genes and pathways to focus on for future studies.
Germline copy number variants and endometrial cancer risk
Authors: Stylianou Cassie E. , Wiggins George A. R. , Lau Vanessa L. , Dennis Joe , Shelling Andrew N. , Wilson Michelle , Sykes Peter , Amant Frederic , Annibali Daniela , De Wispelaere Wout , Easton Douglas F. , Fasching Peter A. , Glubb Dylan M. , Goode Ellen L. , Lambrechts Diether , Pharoah Paul D. P. , Scott Rodney J. , Tham Emma , Tomlinson Ian , Bolla Manjeet K. , Couch Fergus J. , Czene Kamila , Dörk Thilo , Dunning Alison M. , Fletcher Olivia , García-Closas Montserrat , Hoppe Reiner ,   ABCTB Investigators, Clarke Christine , Marsh Deborah , Scott Rodney , Baxter Robert , Yip Desmond , Carpenter Jane , Davis Alison , Pathmanathan Nirmala , Simpson Peter , Dinny Graham J , Sachchithananthan Mythily , Jernström Helena , Kaaks Rudolf , Michailidou Kyriaki , Obi Nadia , Southey Melissa C. , Stone Jennifer , Wang Qin , Spurdle Amanda B. , O’Mara Tracy A. , Pearson John , Walker Logan C. 
Published: November 2024

AbstractKnown risk loci for endometrial cancer explain approximately one third of familial endometrial cancer. However, the association of germline copy number variants (CNVs) with endometrial cancer risk remains relatively unknown. We conducted a genome-wide analysis of rare CNVs overlapping gene regions in 4115 endometrial cancer cases and 17,818 controls to identify functionally relevant variants associated with disease. We identified a 1.22-fold greater number of CNVs in DNA samples from cases compared to DNA samples from controls (p = 4.4 × 10–63). Under three models of putative CNV impact (deletion, duplication, and loss of function), genome-wide association studies identified 141 candidate gene loci associated (p < 0.01) with endometrial cancer risk. Pathway analysis of the candidate loci revealed an enrichment of genes involved in the 16p11.2 proximal deletion syndrome, driven by a large recurrent deletion (chr16:29,595,483-30,159,693) identified in 0.15% of endometrial cancer cases and 0.02% of control participants. Together, these data provide evidence that rare copy number variants have a role in endometrial cancer susceptibility and that the proximal 16p11.2 BP4-BP5 region contains 25 candidate risk gene(s) that warrant further analysis to better understand their role in human disease.
Increasing accuracy in predicting mode I fracture toughness of rock structures: a comparative analysis of the rock engineering system method
Authors: Fattahi Hadi , Ghaedi Hossein , Armaghani Danial Jahed 
Published: November 2024

AbstractThe investigation of crack initiation and expansion is vital for the stability of structures. The Mode I fracture toughness (KIc) of rocks is a key property used to predict crack propagation in tension and hydraulic fracturing. Various methods have been introduced to determine KIc, but results differ due to factors like sample dimensions, crack geometry, groove type, and loading conditions. The cracked chevron notched Brazilian disc (CCNBD) sample is commonly used in laboratory tests for its easy preparation. This study employs the rock engineering system (RES) technique to overcome the challenges of time-consuming and costly laboratory tests and the uncertainty in traditional methods (analytical, numerical, experimental, laboratory, regression). Using 88 CCNBD rock samples proposed by ISRM, input parameters include thickness of the disc specimen (B), uniaxial tensile strength (σt), initial crack length (α0), radius of the disc specimen (R), crack length (αB), and the length of the final crack (α1). The RES-based model used 70 data points (80% of the dataset) for development, and 18 data points (20%) for evaluation. Regression analysis compared the performance of the RES method, using statistical indicators such as squared correlation coefficient (R2), mean square error (MSE), and root mean square error (RMSE) to measure accuracy. The RES-based method outperformed other regression techniques, demonstrating significantly enhanced accuracy. This highlights the effectiveness and superior performance of the RES method in estimating fracture toughness, particularly for CCNBD samples, showcasing its potential as a robust analytical tool.
Subaxial cervical foraminal chondromas: case-based discussion on surgical management
Authors: Vandenbulcke Alberto , Sanjurjo Andrea , Rougemont Anne-Laure , Boudabbous Sana , Maduri Rodolfo 
Published: November 2024

AbstractCervical foraminal chondromas are benign lesions that may require surgical resection when symptomatic due to radicular and/or spinal cord compression. The aim of surgery is to achieve gross tumor removal while preserving neurological function and spine stability. The authors describe a case of subaxial foraminal chondroma with a systematic review of the literature on patients with cervical chondromas. In the reported case, the authors used a retrojugular approach to remove a C6-C7 right chondroma without the need for spinal stabilization. Literature review identified a total of 11 patients who underwent surgery for subaxial foraminal chondroma. The mean age at diagnosis is 33.6 years (range: 10–73). Most patients report neurological symptoms at the time of diagnosis. The most frequently involved vertebral level is C4-C5 (54.6%, 6/11). Preoperative foraminal enlargement is present in 63.6% (7/11) of patients. Surgical resection is performed via an anterior approach in 18.2% (2/11) of patients, with vertebral body resection and concomitant cervical instrumentation. The anterolateral approach is selected in 27.2% (3/11) of patients, and the posterior approach in 54.6% (6/11) of patients, with only one patient requiring both anterior and posterior instrumentation. The choice of surgical access for subaxial foraminal chondroma can be challenging due to the anatomical location of the tumor in relation to the cervical nerve roots and spinal cord. Accurate approach selection is key to achieving complete tumor removal while preserving cervical spine stability.
Volumetric Integrated Classification Index: An Integrated Voxel-Based Morphometry and Machine Learning Interpretable Biomarker for Post-Traumatic Stress Disorder
Authors: Jia Yulong , Yang Beining , Xin Haotian , Qi Qunya , Wang Yu , Lin Liyuan , Xie Yingying , Huang Chaoyang , Lu Jie , Qin Wen , Chen Nan 
Published: November 2024

AbstractPTSD is a complex mental health condition triggered by individuals’ traumatic experiences, with long-term and broad impacts on sufferers’ psychological health and quality of life. Despite decades of research providing partial understanding of the pathobiological aspects of PTSD, precise neurobiological markers and imaging indicators remain challenging to pinpoint. This study employed VBM analysis and machine learning algorithms to investigate structural brain changes in PTSD patients. Data were sourced ADNI-DoD database for PTSD cases and from the ADNI database for healthy controls. Various machine learning models, including SVM, RF, and LR, were utilized for classification. Additionally, the VICI was proposed to enhance model interpretability, incorporating SHAP analysis. The association between PTSD risk genes and VICI values was also explored through gene expression data analysis. Among the tested machine learning algorithms, RF emerged as the top performer, achieving high accuracy in classifying PTSD patients. Structural brain abnormalities in PTSD patients were predominantly observed in prefrontal areas compared to healthy controls. The proposed VICI demonstrated classification efficacy comparable to the optimized RF model, indicating its potential as a simplified diagnostic tool. Analysis of gene expression data revealed significant associations between PTSD risk genes and VICI values, implicating synaptic integrity and neural development regulation. This study reveals neuroimaging and genetic characteristics of PTSD, highlighting the potential of VBM analysis and machine learning models in diagnosis and prognosis. The VICI offers a promising approach to enhance model interpretability and guide clinical decision-making. These findings contribute to a better understanding of the pathophysiological mechanisms of PTSD and provide new avenues for future diagnosis and treatment.
Predicting nodal response to neoadjuvant treatment in breast cancer with core biopsy biomarkers of tumor microenvironment using data mining
Authors: Pislar Nina , Gasljevic Gorana , Matos Erika , Pilko Gasper , Zgajnar Janez , Perhavec Andraz 
Published: November 2024

Abstract

Purpose
To generate a model for predicting nodal response to neoadjuvant systemic treatment (NAST) in biopsy-proven node-positive breast cancer patients (cN+) that incorporates tumor microenvironment (TME) characteristics and could be used for planning the axillary surgical staging procedure.

Methods
Clinical and pathologic features were retrospectively collected for 437 patients. Core biopsy (CB) samples were reviewed for stromal content and tumor-infiltrating lymphocytes (TIL). Orange Datamining Toolbox was used for model generation and assessment.

Results
151/437 (34.6%) patients achieved nodal pCR (ypN0). The following 5 variables were included in the prediction model: ER, Her-2, grade, stroma content and TILs. After stratified tenfold cross-validation, the logistic regression algorithm achieved and area under the ROC curve (AUC) of 0.86 and F1 score of 0.72. Nomogram was used for visualization.

Conclusions
We developed a clinical tool to predict nodal pCR for cN+ patients after NAST that includes biomarkers of TME and achieves an AUC of 0.86 after tenfold cross-validation.
On Some Dynamics in Conceptual Spaces
Authors: Lisowski Piotr , Urban Roman 
Published: November 2024

AbstractIn this text, we consider Gärdenfors’ conceptual spaces that are separable Hilbert spaces. In particular, the results we obtained apply to finite-dimensional Euclidean spaces. Our main contribution can be formulated as a combination of the theory of opinion dynamics with the theory of conceptual spaces. This combination, in turn, leads us to propose a new model for the time evolution of conceptual spaces. To achieve this goal, we propose some extension of the multidimensional opinion dynamics model of Parsegov, Proskurnikov, Tempo and Friedkin to opinions with values in Hilbert spaces.
Accuracy and robustness of a plant-level cabbage yield prediction system generated by assimilating UAV-based remote sensing data into a crop simulation model
Authors: Yokoyama Yui , de Wit Allard , Matsui Tsutomu , Tanaka Takashi S. T. 
Published: November 2024

AbstractIn-season crop growth and yield prediction at high spatial resolution are essential for informing decision-making for precise crop management, logistics and market planning in horticultural crop production. This research aimed to establish a plant-level cabbage yield prediction system by assimilating the leaf area index (LAI) estimated from UAV imagery and a segmentation model into a crop simulation model, the WOrld FOod STudies (WOFOST). The data assimilation approach was applied for one cultivar in five fields and for another cultivar in three fields to assess the yield prediction accuracy and robustness. The results showed that the root mean square error (RMSE) in the prediction of cabbage yield ranged from 1,314 to 2,532 kg ha–1 (15.8–30.9% of the relative RMSE). Parameter optimisation via data assimilation revealed that the reduction factor in the gross assimilation rate was consistently attributed to a primary yield-limiting factor. This research further explored the effect of reducing the number of LAI observations on the data assimilation performance. The RMSE of yield was only 107 kg ha–1 higher in the four LAI observations obtained from the early to mid-growing season than for the nine LAI observations over the entire growing season for cultivar ‘TCA 422’. These results highlighted the great possibility of assimilating UAV-derived LAI data into crop simulation models for plant-level cabbage yield prediction even with LAI observations only in the early and mid-growing seasons.
Why do some retracted articles continue to get cited?
Authors: Schmidt Marion 
Published: November 2024

AbstractRetracted publications can still receive a substantial number of citations after the retraction. Little is known about the causes for this phenomenon and the nature of epistemic risk or harm in these retraction cases. Using this phenomenon also as an example for the broader question of how scholarly communities deal with uncertainty in the reception of publications, this case study aims to assess the epistemic contributions of retracted publications with continuous and decreasing citation impact and to relate these to the epistemic environments of the retracted papers and to reception patterns. Several parsing and natural language processing approaches are used, complemented, and validated by qualitative close reading. Specifically, (i) dissent and support are identified in citing and in co-cited publications; (ii) the concept terms of retracted publications are expanded by word embeddings and MeSH terms and traced in citation contexts; and finally (iii) rhetorical functions in citation contexts are identified based on keyword extraction. Empirical support and unresolved disputes are found almost exclusively in cases with continuous citations. Authors emphasize specific informational values in some cases with citations continuing after the retraction, while methodological and more general levels of claims prevail in others. Citations can be meaningfully examined by considering the weighing process between epistemic risks and informational value; persistent citation impact thus doesn’t necessarily indicate the perpetuation of epistemic harm.
The Finite Frame Property of Some Extensions of the Pure Logic of Necessitation
Authors: Kurahashi Taishi , Sato Yuta 
Published: November 2024

AbstractWe study the finite frame property of some extensions of Fitting, Marek, and Truszczyński’s pure logic of necessitation $$\textbf{N}$$
N
. For any natural numbers m, n, we introduce the logic $$\textbf{N}^+\textbf{A}_{m,n}$$

N
+

A

m
,
n

by adding the single axiom scheme $$\Box ^n \varphi \rightarrow \Box ^m \varphi $$

□
n

φ
→

□
m

φ

and the rule $$\dfrac{\lnot \Box \varphi }{\lnot \Box \Box \varphi }$$

¬
□
φ

¬
□
□
φ

($${\text {Ros}}^\Box $$

Ros

□

) into $$\textbf{N}$$
N
. We prove the finite frame property of $$\textbf{N}^+\textbf{A}_{m, n}$$

N
+

A

m
,
n

with respect to Fitting, Marek, and Truszczyński’s relational semantics. We also prove that for $$n \ge 2$$

n
≥
2

, the logic obtained by removing the rule $${\text {Ros}}^\Box $$

Ros

□

from $$\textbf{N}^+\textbf{A}_{0, n}$$

N
+

A

0
,
n

is incomplete with respect to that semantics.
Individual Giving in Ghana: A Self-Determination Theory Approach to Giving
Authors: Owusu-Ansah Matilda , Moyo Bhekinkosi 
Published: November 2024

AbstractThis study investigated individual charitable giving in Ghana. Given that comprehensive data on individual giving in Africa is limited, this study’s theory-based approach used quantitative and qualitative methods to identify demographic and psychographic factors influencing the donation of money, time, and other resources towards assisting individuals, organisations, and charitable causes. With a sample size of 741 participants, the study identified gender, household size, age, financial constraints, social norms, egoism, religion, and trust as influential factors shaping giving behaviour among Ghanaians. The study’s outcomes have theoretical significance and suggest that individuals previously unwilling or lacking the capacity to give can become generous in the appropriate social and environmental context. The findings hold significance for nurturing a culture of philanthropy and developing culturally relevant and impactful giving campaigns and policies in Africa.