bluuebunny/crossref_metadata_2025_split huggingface dataset:
Male infertility is associated with differential DNA methylation signatures of the imprinted gene GNAS and the non-imprinted gene CEP41
Authors: Ozkocer Suheyla Esra , Guler Ismail , Ugras Dikmen Asiye , Bozkurt Nuray , Varol Nuray , Konac Ece 
Published: July 2024

Abstract
Purpose
To investigate whether the DNA methylation profiles of GNAS(20q13.32), MEST(7q32.2), MESTIT1(7q32.2), IGF2(11p15.5), H19 (7q32.2), and CEP41(7q32.2) genes are related to the transcriptomic and epigenomic etiology of male infertility.

Methods
The DNA methylation levels of spermatozoa were obtained from fertile (n = 30), oligozoospermic (n = 30), and men with normal sperm count (n = 30). The methylation status of each CpG site was categorized as hypermethylated or hypomethylated. Expression levels of target gene transcripts were determined using real-time PCR.

Results
The oligozoospermia showed a higher frequency of hypermethylation at GNASAS 1st, 3rd, and 5th CpG dinucleotides (66.7%, 73.3%, 73.3%) compared to the fertile group (33.3%, 33.3%, 40%, respectively). The normal sperm count exhibited a higher frequency of hypermethylation at the 3rd CpG of CEP41 (46.7%) than the fertile group (16.7%). Normal sperm count was predicted by CEP41 hypermethylation (OR = 1.750, 95%CI 1.038–2.950) and hypermethylation of both CEP41 and GNASAS (OR = 2.389, 95%CI 1.137–5.021). Oligozoospermia was predicted solely by GNASAS hypermethylation (OR = 2.460, 95%CI 1.315–4.603). In sperms with decreased IGF2 expression in the fertile group, we observed hypomethylation in the 2nd CpG of IGF2 antisense (IFG2AS), and hypermethylation in the 1st, 2nd, and 4th CpGs of H19. No significant relationship was found between IGF2 expression and methylation status of IGF2AS and H19 in infertile groups.

Conclusion
The disappearance of the relationship between IGF2 expression and IGF2AS and H19 methylations in the infertile group provides new information regarding the disruption of epigenetic programming during spermatogenesis. A better understanding of sperm GNASAS and CEP41 hypermethylation could advance innovative diagnostic markers for male infertility.
The Relationship Between Psychological Pain, Spiritual Well-Being, and Social Support in Turkish Women Undergoing Therapeutic or Elective Abortion
Authors: Yılmaz Figen Alp , Avci Dilek 
Published: July 2024

Abstract
This study was conducted to determine the relationship between psychological pain, spiritual well-being, and social support among Turkish women undergoing therapeutic or elective abortion. The cross-sectional study was conducted with 342 women who were hospitalized in the gynecology and obstetrics service of a city hospital between March 2021 and December 2022 in Turkey. The mean psychological pain, spiritual well-being and perceived social support scores of women undergoing therapeutic/elective abortion were 26.96 ± 11.21, 110.72 ± 13.09 and 64.09 ± 15.62, respectively. There were a significant negative correlation between psychological pain with spiritual well-being and social support. According to linear regression analysis, spiritual well-being, social support, age, employment status, economic level, history of abortion, number of abortion, current abortion type, and gestational week were statistically significant predictive factors of psychological pain. Therefore, healthcare providers can provide individualized psychosocial-spiritual care and counseling services that decrease psychological pain in women after therapeutic or elective abortion.
Causal relationship between multiple sclerosis and primary Sjögren’s syndrome: a two-sample mendelian randomization study
Authors: Shen Jie , Ye Qiao , Luo Fang , Yu Tianhang , Miao Jinli , Wang Wenmin , Yuan Hui 
Published: July 2024

AbstractThis study aims to investigate the causal relationship between primary Sjögren’s syndrome (SS) and multiple sclerosis (MS) using a two-sample Mendelian randomization (MR) analysis to provide insights into their common mechanisms and implications for therapeutic strategies. We utilized data from Genome-Wide Association Studies (GWAS) for primary SS (1,290 cases and 213,145 controls) and MS (4,888 cases and 10,395 controls), restricted to European ancestry. Instrumental variables (IVs) were selected based on genetic variants associated with primary SS. The primary MR method was Inverse Variance Weighted (IVW), supplemented by MR Egger, Weighted Median, Simple Mode, and Weighted Mode algorithms to assess the bidirectional causal relationships between MS and primary SS. Sensitivity analyses, including MR-PRESSO and leave-one-out analysis, were conducted to ensure the robustness of our findings. After excluding SNPs with pleiotropic effects, 42 and 5 SNPs were identified as robust IVs for primary SS and MS, respectively. Our analysis revealed a significant protective effect of MS on primary SS, with IVW showing an OR of 0.896 (95% CI: 0.841–0.954, P = 0.001). No significant heterogeneity or horizontal pleiotropy was detected, supporting the reliability of the results. Our findings suggest a potential protective effect of MS against primary SS, indicating a negative causal association between these two autoimmune diseases. This adds valuable genetic evidence to the understanding of the complex interplay between primary SS and MS, offering new avenues for research and therapeutic interventions.
Wave propagation at nano-scale in coupled transport phenomena: application to thermoelectricity
Authors: Di Domenico M. , Carlomagno I. , Sellitto A. 
Published: July 2024

AbstractThe analysis of coupled transport phenomena is one of the most outstanding aspects of non-equilibrium thermodynamics. In this paper the attention is put on thermoelectricity, i.e., the coupling of heat and electricity. We propose a theoretical model which goes beyond the usual relations employed at macro-scale to describe thermoelectric effects. It introduces the non-local effects which should be taken into account in view of the possible applications of thermoelectric effects at nano-scale. The proposed model is here employed to investigate how non-local effects may influence the propagation of waves.
Toward a Responsible Fairness Analysis: From Binary to Multiclass and Multigroup Assessment in Graph Neural Network-Based User Modeling Tasks
Authors: Purificato Erasmo , Boratto Ludovico , De Luca Ernesto William 
Published: July 2024

AbstractUser modeling is a key topic in many applications, mainly social networks and information retrieval systems. To assess the effectiveness of a user modeling approach, its capability to classify personal characteristics (e.g., the gender, age, or consumption grade of the users) is evaluated. Due to the fact that some of the attributes to predict are multiclass (e.g., age usually encompasses multiple ranges), assessing fairness in user modeling becomes a challenge since most of the related metrics work with binary attributes. As a workaround, the original multiclass attributes are usually binarized to meet standard fairness metrics definitions where both the target class and sensitive attribute (such as gender or age) are binary. However, this alters the original conditions, and fairness is evaluated on classes that differ from those used in the classification. In this article, we extend the definitions of four existing fairness metrics (related to disparate impact and disparate mistreatment) from binary to multiclass scenarios, considering different settings where either the target class or the sensitive attribute includes more than two groups. Our work endeavors to bridge the gap between formal definitions and real use cases in bias detection. The results of the experiments, conducted on four real-world datasets by leveraging two state-of-the-art graph neural network-based models for user modeling, show that the proposed generalization of fairness metrics can lead to a more effective and fine-grained comprehension of disadvantaged sensitive groups and, in some cases, to a better analysis of machine learning models originally deemed to be fair. The source code and the preprocessed datasets are available at the following link: https://github.com/erasmopurif/toward-responsible-fairness-analysis.
The Logical Perspective in Pragma-dialectics
Authors: Marraud Hubert 
Published: July 2024

AbstractI argue that the logical perspective—the study of arguments as products—is not well integrated into pragma-dialectics. I show that the Validity Rule and the Argumentation Scheme Rule, despite being procedural rules, are, in a certain sense, “logical” rules. Subsequently, I distinguish and review three successive periods in the development of the logical dimension of pragma-dialectics: conventionalist, inferentialist and dualist, to reveal that none of them is completely satisfactory. I contend that, given the assumptions and conceptual apparatus of pragma-dialectics, the integration of the logical perspective, and especially of a suitable account of counterargumentation, requires the adoption of a conception of logic as a theory of reasons, as opposed to the traditional conception of logic as a theory of inferences. Understanding logic as a theory of the dialogical construction of reasons enables us to approach the study of the relationships between arguments and the weighing of opposing arguments.
Total nitrogen and phosphorus loads in surface runoff from urban land use (city of Lublin) under climate change
Authors: Szalińska Ewa , Jarosińska Elżbieta , Orlińska-Woźniak Paulina , Jakusik Ewa , Warzecha Wiktoria , Ogar Wioletta , Wilk Paweł 
Published: July 2024

AbstractAn expansion of impervious surfaces in urban areas leads to increases of nutrient loads discharged with the surface runoff to receivers. A study of a different density of urban development impact on total nitrogen (TN) and phosphorus (TP) loads from the city of Lublin (eastern Poland) with the use of the SWAT (Soil & Water Assessment Tool) model was performed. To distinguish between areas with high and low density of urban development (UHD and ULD), a special analysis of hydrological parameters has been proposed. Moreover, to investigate the impact of climate change, four variant scenarios were taken into account, combining the RCP (representative concentration pathway) 4.5 and 8.5 forecasts and the adopted time horizons (2026–2035 and 2046–2055). The results showed a much higher share of TN and TP from UHD compared to ULD (86%—32 022 kg/year and 89%—2574 kg/year, respectively). In addition, the variant scenarios showed that the forecasted increase in precipitation and temperature will result in increased loads of nutrients from UHD and ULD up to 30%. Furthermore, the current increase of inhabitant number, due to the Ukrainian war migration and the common tendency to convert agricultural land to residential areas, could contribute to further expansion of UHD and ULD areas and an additional increase of nutrient loads.
Graphical abstract
Hidden Transformation of Authoritarian Regionalism: Tracing Organizations’ Functions Through Officials’ Biographies
Authors: Libman Alexander 
Published: July 2024

AbstractAuthoritarian regionalism constitutes a challenging topic for empirical research due to a substantial gap between official mandates and the actual practices of regional organizations (ROs). While formally most authoritarian ROs “download” the global script of regionalism and imitate the European Union, in practice, they are used by their member states for different purposes than economic integration—in particular, to legitimize the nondemocratic regimes. At the same time, there are also examples of authoritarian ROs that go beyond simple autocracy-sustaining rhetoric and have actual policy implications. This paper argues that the differences between authoritarian ROs can be better observed if one looks not at the official mandates but at the background of their key officials. Using the case of post-Soviet Eurasia with its proliferation of authoritarian ROs, I show that a look at the biographies of officials clearly reveals the existence of two generations of ROs—one with primarily symbolic importance and one with actual economic integration ambitions.
Optimizing construction supplier selection in conflict-affected regions: a hybrid multi-criteria framework
Authors: Hallak Jamil 
Published: July 2024

AbstractConflicts and wars profoundly impact infrastructure, exacerbating the adversity already caused by natural disasters. Therefore, it is imperative that the reconstruction process be both effective and efficient to expedite a return to normalcy. This study aims to enhance the efficacy of reconstruction efforts through improved construction supplier evaluation and selection. It introduces an innovative hybrid multi-objective decision-making model that integrates a broad spectrum of economic, technical, and humanitarian criteria. The model is designed to optimally select and assign construction suppliers in regions affected by human and natural conflicts and crises. Fifteen criteria have been incorporated into the evaluation process to validate its effectiveness and maximize its contribution to local communities. This methodology streamlines decision-making and enhances transparency in conflict zones, aligning with the interests of all stakeholders. The study incorporates advanced methodologies, including Fuzzy Goal Programming (F-GP), Geographic Information System (GIS)-based Risk Assessment, and Fuzzy Analytic Hierarchy Process (F-AHP), leveraging real-world data and a case study. Additionally, a sensitivity analysis examines the impact of varying inputs on the model's output. The findings attest to the model's utility in conflict-affected regions and its potential applicability in stable settings.
Dose–response relationship between serum N-glycan markers and liver fibrosis in chronic hepatitis B
Authors: Zhang Chi , Liu Yiqi , Wang Lin , Liu Xueen , Chen Cuiying , Zhang Junli , Zhang Chao , Wang Guiqiang , Zhuang Hui , Zhao Hong ,   China HepB-Related Fibrosis Assessment Research Group, Cao Li-Hua , Zhang Zhan-Qing , Zhao Wei-Feng , Shang Qing-Hua , Zhang Da-Zhi , Ma An-Lin , Xie Qing , Gui Hong-Lian , Zhang Guo , Liu Ying-Xia , Shang Jia , Xie Shin-Bin , Li Jun , Zhang Xu-Qing , Zou Zhi-Qiang , Chen Yu-Ping , Zhang Zong , Zhang Ming-Xiang , Cheng Jun , Zhang Fu-Chun , Huang Li-Hua , Li Jia-Bin , Meng Qing-Hua , Yu Hai-Bin , Mi Yu-Qiang , Peng Yan-Zhong , Wang Zhi-Jin , Chen Li-Ming , Meng Fan-Ping , Ren Wan-Hua , Bai Lang , Zeng Yi-Lan , Fan Rong , Lou Xian-Zhi , Liang Wei-Feng 
Published: July 2024

Abstract
Background
Evaluation of liver fibrosis played a monumental role in the diagnosis and monitoring of chronic hepatitis B (CHB). We aimed to explore the value of serum N-glycan markers in liver fibrosis.

Methods
This multi-center (33 hospitals) study recruited 760 treatment-naïve CHB patients who underwent liver biopsy. Serum N-glycan markers were analyzed by DNA sequencer-assisted fluorophore-assisted with capillary electrophoresis (DSA-FACE) technology. First, we explore the relationship between 12 serum N-glycan markers and the fibrosis stage. Then, we developed a Px score for diagnosing significant fibrosis using the LASSO regression. Next, we compared the diagnostic performances between Px, LSM, APRI, and FIB-4. Finally, we explored the relationships between glycosyltransferase gene and liver fibrosis with RNA-transcriptome sequencing.

Results
We included 622 CHB participants: male-dominated (69.6%); median age 42.0 (IQR 34.0–50.0); 287 with normal ALT; 73.0% with significant fibrosis. P5(NA2), P8(NA3), and P10(NA4) were opposite to the degree of fibrosis, while other profiles (except for P0[NGA2]) increased with the degree of fibrosis. Seven profiles (P1[NGA2F], P2[NGA2FB], P3[NG1A2F], P4[NG1A2F], P7[NA2FB], P8[NA3], and P9[NA3Fb]) were selected into Px score. Px score was associated with an increased risk of significant fibrosis (for per Px score increase, the risk of significant fibrosis was increased by 3.54 times (OR = 4.54 [2.63–7.82]) in the fully-adjusted generalized linear model. p for trend was <0.001. The diagnostic performance of the Px score was superior to others. Glycosyltransferase genes were overexpressed in liver fibrosis, and glycosylation and glycosyltransferase-related pathways were significantly enriched.

Conclusions
Serum N-glycan markers were positively correlated with liver fibrosis. Px score had good performance in distinguishing significant fibrosis.
1H, 13C and 15N assignment of self-complemented MrkA protein antigen from Klebsiella pneumoniae
Authors: Monaci Valentina , Gasperini Gianmarco , Banci Lucia , Micoli Francesca , Cantini Francesca 
Published: July 2024

AbstractKlebsiella pneumoniae (Kp) poses an escalating threat to public health, particularly given its association with nosocomial infections and its emergence as a leading cause of neonatal sepsis, particularly in low- and middle-income countries (LMICs). Host cell adherence and biofilm formation of Kp is mediated by type 1 and type 3 fimbriae whose major fimbrial subunits are encoded by the fimA and mrkA genes, respectively. In this study, we focus on MrkA subunit, which is a 20 KDa protein whose 3D molecular structure remains elusive. We applied solution NMR to characterize a recombinant version of MrkA in which the donor strand segment situated at the protein’s N-terminus is relocated to the C-terminus, preceded by a hexaglycine linker. This construct yields a self-complemented variant of MrkA. Remarkably, the self-complemented MrkA monomer loses its capacity to interact with other monomers and to extend into fimbriae structures. Here, we report the nearly complete assignment of the 13C,15N labelled self-complemented MrkA monomer. Furthermore, an examination of its internal mobility unveiled that relaxation parameters are predominantly uniform across the polypeptide sequence, except for the glycine-rich region within loop 176–181. These data pave the way to a comprehensive structural elucidation of the MrkA monomer and to structurally map the molecular interaction regions between MrkA and antigen-induced antibodies.
Development Pathways and the Political Economy of Maladaptation: The Case of Bioenergy as a Climate Strategy in Brazil
Authors: Rodriguez Morales Jorge Ernesto 
Published: July 2024

AbstractAlthough it is well known that large-scale bioenergy expansion erodes different environmental, social, and economic dimensions of sustainable development, in countries like Brazil, bioenergy is institutionalized as a flagship climate strategy aimed to cut down CO2 emissions in transport. These trade-offs have serious implications for climate change governance and sustainable development; however, conventional approaches have not yet properly explained this seeming paradox. This article addresses this gap from a critical development pathways approach to bioenergy as a maladaptive strategy in Brazil. I propose an analytical framework to observe how different ideas, interests, and institutions interplay in the historical institutionalization of bioenergy as a climate strategy. The analysis shows that bioenergy institutionalization has been driven by the endemic economic crisis in the sugar sector and governmental interests associated with security and developmental imperatives. The unsustainable co-evolution of development pathways and bioenergy, marked by deforestation, land colonization, and agricultural expansion, has narrowed the adaptation space in agriculture, gearing current climate policy towards path-dependent maladaptive strategies like bioenergy. Paradoxically, framing bioenergy as a climate strategy has been useful to justify more expansive policies in favor of the sugarcane industry, and to greenwash the Brazilian climate policy in the international arena of climate governance.
Connecting Mindfulness Practice to Generative Semiotic Activity—Self-Other Referent in Umwelt and Semiosphere
Authors: Morioka Masayoshi 
Published: July 2024

Abstract
In this comment paper on von Fircks (2023a), I would like to focus on four issues and offer some reflections on them: first, what is happening in the process of a new I arising through mindfulness meditation practice? I would like to supplement the dialogue between Buber and Rogers in 1957 on the dynamism of I and Me, which is the basis of Mead's theory of self formation, in which I and Me separate, discover and meet a new self. The second, is that meditation, which at first glance appears to be an internal meditation practice and a personal activity, leads to a semiotic mediated social process. The Tao and early Buddhist ideas that form the background to the experiential process of mindfulness meditation will be reviewed, and the significance of people experiencing the interdependence of non-human nature and the environment through the practice will be discussed. Third, connecting this to the idea of Umwelt (Uexküll) and the semiosphere (Lotman), an attempt is made to extend the otherness as a collating body of self formation to Umwelt. Fourth, mindfulness meditation focuses attention on the breath. In relation to Mead's focus on the environment under the skin, i.e. corporeality, I will supplement the psychological meaning of cultivating the body's sense of interoception through the sensing of repetitive movements of tension and relaxation. Through the above, what kind of semiotic mediating function does mindfulness meditation have in relation to the construction of the new I, and how does it lead to the creation of social meaning? We would like to discuss these points.

Clinical Trial Registration
The article does not contain any studies with clinical trial. This, clinical Trial registration is not applicable.
From self-criticism to self-compassion: exploring the mediating role of two emotion dysregulation variables in their relationship to depressive symptoms
Authors: Vidal Joana , Ciudad-Fernández Víctor , Navarrete Jaime , Soler Joaquim , Schmidt Carlos , Molinari Guadalupe , Cebolla Ausiàs 
Published: July 2024

AbstractSelf-criticism has been considered as a transdiagnostic dimension that contributes to the development of several mental health difficulties. Moreover, there is a significant association between self-criticism and emotion regulation difficulties. Of special interest are two variables, related to emotion dysregulation, that have garnered significant attention in recent years: emotional overproduction and the perseveration of negative emotions. By contrast, increased self-compassion has been proposed as a protective mechanism of mental health symptoms, specifically depression. The present study used Structural Equation Modeling (SEM) to investigate the relationship between self-criticism, self-compassion, and depressive symptoms, while considering emotional overproduction and perseveration of negative emotions as mediating variables. A cross-sectional design was used. The sample consisted of 453 participants who completed measures of self-criticism, self-compassion, depressive symptoms, emotional overproduction, and perseveration of negative emotions. Results indicate that emotional overproduction mediates the relationship between self-criticism and depressive symptoms. Additionally, both emotional overproduction and the perseveration of negative emotions mediate the negative association between self-compassion and depressive symptoms. Therefore, developing self-compassion may diminish the negative impact of self-criticism on depressive symptoms through these two variables. In conclusion, this study deepens our understanding of the mechanism by which self-compassion can mitigate mental health problems such as depressive symptoms.