bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Definition of RNA Age Related to RNA Sequence Changes
Authors: Xu Zhongneng , Asakawa Shuichi 
Published: December 2024

ABSTRACTRibonucleic acid (RNA) undergoes dynamic changes in its structure and function under various intracellular and extracellular conditions over time. However, there is a lack of research on the concept of the RNA age to describe its diverse fates. This study proposes a definition of RNA age to address this issue. RNA age was defined as a sequence of numbers wherein the elements in the sequence were the nucleotide ages of the ribonucleotide residues in the RNA. Mean nucleotide age was used to represent RNA age. This definition describes the temporal properties of RNAs that have undergone diverse life histories and reflects the dynamic state of each ribonucleotide residue, which can be expressed mathematically. Notably, events (including base insertions, base deletions, and base substitutions) are likely to cause RNA to become younger or older when using mean nucleotide ages to represent the RNA age. Although information, including the presence of added markers in RNA, chemical modification structure of the RNA, and the excision of introns in the mRNA in cells, may provide a basis for identifying RNA age, little is known about determining the RNA age of extracellular RNA in the wild. Nonetheless, we believe that RNA age has an important relationship with the diverse biological properties of RNA under intracellular and extracellular conditions. Therefore, our proposed definition of RNA age offers new perspectives for studying dynamic changes in RNA function, RNA aging, ancient RNA, environmental RNA, and the ages of other biomolecules.
Religion and Faith-Based Organizations in Brazil’s Social Policies
Authors: Segatto Catarina Ianni 
Published: December 2024

AbstractIn Latin America, the prominence of the Catholic Church dates back to colonization in the 1500s. Most countries are still majoritarian Catholic, but there was a shift in its monopoly with the Evangelicals’ growth. This chapter discusses the intersections between religious and social policies in Brazil and the centrality of faith-based organizations in the country by analyzing their role in shaping poverty and family issues in social policies.
Future Challenges Facing Third Sector Research
Authors: Alves Mario Aquino , Bassi Andrea , Cordery Carolyn 
Published: December 2024

AbstractThe realm of societal advancement is multifaceted, involving a balance of public and private attention. Yet, nestled within this framework lies the Third Sector, a constantly evolving and dynamic entity. Comprising non-profit organizations, charities, voluntary groups, and social enterprises, the Third Sector is crucial in fostering social change, community empowerment, and humanitarian efforts. To comprehend the forthcoming hurdles that Third Sector research must overcome, it is essential to delve into its historical origins, scholarly underpinnings, research infrastructure, and emerging trends that shape its trajectory.
Commentary on Part I - Theory of the Third Sector
Authors: Young Dennis R. 
Published: December 2024

AbstractIn this book, my distinguished colleagues have taken on the daunting task of summarizing the development of theory of the Third Sector over the past half century and suggesting how this body of theory can usefully be extended and modified to address the changing character of the contemporary third sector. In this chapter, I critique their work, by pointing out misconceptions about early economic theory of the sector, noting that this theory also helps explain the behavior as well as existence of nonprofit organizations, highlighting where early economic theory of the sector continues to be relevant, questioning the efficacy of social origins theory, and arguing that an expanded theory should encompass the phenomenon of social enterprise.
In Search of a Positive, Historical and Experimentalist Definition of Civil Society
Authors: Andion Carolina 
Published: December 2024

AbstractDefinitions are not only conceptual constructs, they emerge from practice, investigations and academic discourses what are embedded in history, institutional frames, political cultures and social realities. This observation makes even more sense when we discuss civil society, an interdisciplinary field whose demarcation change in time throughout theoretical debate in multiple disciplines and definitions assumes different contours in every country and social reality in which it operates. In this sense, we observe the importance of broadening definitions, in order to consider the plurality of types and ecologies of civil society world while. With this in mind, this chapter sets out to (re) discuss the definitions of civil society in social and political sciences. To this end, we begin by problematizing the classical conceptualizations of civil society, showing the similarities in the meanings historically attributed to this concept and highlighting a “positive” definition of civil society conceived more recently and its consequences, exploring the challenges on civil society definitions nowadays. Positivity here does not express a judgment in the sense of being “good” or “better” than others, but rather it centers on exploring the particularities of the phenomenon, defining it based on what civil society is and characterizing it, rather than solely by what it is not (negative) or how it complements or differs. Given this genealogy of the concept and the development of the debate on civil society, we argue to consider definitions and conceptualizations that are more open to the multiple organizational configurations, forms of action and patterns of social-state interactions that have been built up in civil societies historically and coexist in the fields of practice. With the trajectory, changes and challenges of this concept in mind we defend a research agenda that reinforces the coproduction of definitions for civil societies that are less normative and “modelling” and more experimental, capable of supporting investigations and empirical research that help advance the understanding of this complex, interdisciplinary and multifaceted phenomenon that is extremely relevant to strengthening democracy, social justice and sustainability.
Consistency conditions for O-plane unsmearing from second-order perturbation theory
Authors: Emelin Maxim 
Published: December 2024

Abstract
Scale-separated AdS compactifications of string theory can be constructed at the two-derivative supergravity level in the presence of smeared orientifold planes. The unsmearing corrections are known to leading order in the large volume, weak coupling limit. However, first-order perturbative approximations of non-linear problems can often produce spurious solutions, which are only weeded out by additional consistency conditions imposed at higher orders. In this work, we revisit the unsmearing procedure and present consistency conditions obtained from the second order warp factor and dilaton equations. This requires proper treatment of the near-source singularities. The resulting conditions appear as integral constraints on various non-linear combinations of the first order corrections, which we argue can generally be satisfied by appropriate choice of integration constants of the leading-order solutions. This provides a non-trivial consistency check for the perturbative unsmearing procedure and supports the existence of scale-separated AdS vacua in string theory.
ETS-NOCV description of chemical bonding: from covalent bonds to non-covalent interactions
Authors: Kukułka Mercedes , Żurowska Olga , Mitoraj Mariusz , Michalak Artur 
Published: December 2024

Abstract

Context
The interpretation of ETS-NOCV for typical covalent and dative-covalent chemical bonds is presented and compared with that for halogen bonds. Possible tuning of the strength of halogen bonding is considered, first by applying an electric field (modeled by the point charges or the electric field vector), and then by constructing a model transition-metal complex with enhanced strength of halogen bonding. For all the systems, the ETS-NOCV picture is supplemented by the analysis of the deformation in molecular electrostatic potential (ΔMEP). The results demonstrate important characteristic features of the analysis based on NOCV: (i) this approach is based on pairs of orbitals with antibonding and bonding character and, thus, allows us to “extract” the “diatomic-like” picture of chemical bonding; (ii) the NOCV-pair contributions to the deformation density often correspond to donation (AB) and back-donation (AB) of electron density between the fragments. The results for halogen bonding demonstrate that it is possible to tune their strength by an electric field in the molecular environment; the halogen-bond energy can reach the order of magnitude typical of dative-covalent bonds. However, the nature of halogen bonds still differs from that of dative-covalent interactions, as the accumulation of electron density between fragments is of significantly lower magnitude. The main effect of the electric field is an increase in the polarization of the fragments, which is clearly manifested by the deformation in the MEP.

Methods
All calculations were performed using the ADF/AMS package. The BLYP exchange–correlation functional was employed with Grimme’s dispersion correction (D3 version) and Becke-Johnson damping, using TZP basis sets. The deformation in the MEP was determined as

$$\Delta V\left(r\right)={V}^{AB}\left(r\right)- {V}^{A}\left(r\right)- {V}^{B}\left(r\right),$$

Δ
V

r

=

V

AB

r

-

V

A

r

-

V

B

r

,

with the same fragment definition as in the ETS-NOCV method.
Cone Beam Computed Tomography Image-Quality Improvement Using “One-Shot” Super-resolution
Authors: Tsuji Takumasa , Yoshida Soichiro , Hommyo Mitsuki , Oyama Asuka , Kumagai Shinobu , Shiraishi Kenshiro , Kotoku Jun’ichi 
Published: December 2024

AbstractCone beam computed tomography (CBCT) images are convenient representations for obtaining information about patients’ internal organs, but their lower image quality than those of treatment planning CT images constitutes an important shortcoming. Several proposed CBCT image-quality improvement methods based on deep learning require large amounts of training data. Our newly developed model using a super-resolution method, “one-shot” super-resolution (OSSR) based on the “zero-shot” super-resolution method, requires only small amounts of training data to improve CBCT image quality using only the target CBCT image and the paired treatment planning CT image. For this study, pelvic CBCT images and treatment planning CT images of 30 prostate cancer patients were used. We calculated the root mean squared error (RMSE), peak signal-to-noise ratio (PSNR), and structural similarity (SSIM) to evaluate image-quality improvement and normalized mutual information (NMI) as a quantitative evaluation of positional accuracy. Our proposed method can improve CBCT image quality without requiring large amounts of training data. After applying our proposed method, the resulting RMSE, PSNR, SSIM, and NMI between the CBCT images and the treatment planning CT images were as much as 0.86, 1.05, 1.03, and 1.31 times better than those obtained without using our proposed method. By comparison, CycleGAN exhibited values of 0.91, 1.03, 1.02, and 1.16. The proposed method achieved performance equivalent to that of CycleGAN, which requires images from approximately 30 patients for training. Findings demonstrated improvement of CBCT image quality using only the target CBCT images and the paired treatment planning CT images.
Agricultural innovations for sustainability? Diverse pathways and plural perspectives on rice seeds in Odisha, India
Authors: Arora Saurabh , Narayanarao Bhuvana , Mittal Nimisha , Vadekkal Rasheed Sulaiman 
Published: December 2024

AbstractWe focus on alternative innovation pathways for addressing agricultural sustainability challenges in Odisha, India. The first pathway that we term as industrial, is focused on breeding new seed varieties in modern laboratories and test fields, ostensibly for climate resilience. It is driven by public scientific institutions and private corporations. The second pathway that we call agroecological, is grounded in saving and sharing of diverse local varieties, largely by Indigenous (Adivasi) smallholders and their allies in civil society. Using the pathways’ descriptions as bases, we present perspectives of different professional groups who appraise how effectively each pathway addresses a range of sustainability issues. While all participants appraise the agroecological pathway to be clearly better performing for addressing agricultural biodiversity and cultural uses of rice, appraisals for issues of the economy, seed accessibility, stress tolerance, and nutrition diverged from each other. An overall picture in support of one pathway did not emerge. Embracing such ambiguities and uncertainties associated with appraisals, we argue for balancing political support between diverse pathways. Greater support for structurally marginalised agroecological pathways may be crucial to meet sustainability goals. This support can include the restitution of lands and other socio-ecological resources for marginalised pathways as well as guaranteeing autonomy of Adivasi (Indigenous) communities among whom the pathways thrive.
Generative AI model privacy: a survey
Authors: Liu Yihao , Huang Jinhe , Li Yanjie , Wang Dong , Xiao Bin 
Published: December 2024

AbstractThe rapid progress of generative AI models has yielded substantial breakthroughs in AI, facilitating the generation of realistic synthetic data across various modalities. However, these advancements also introduce significant privacy risks, as the models may inadvertently expose sensitive information from their training data. Currently, there is no comprehensive survey work investigating privacy issues, e.g., attacking and defending privacy in generative AI models. We strive to identify existing attack techniques and mitigation strategies and to offer a summary of the current research landscape. Our survey encompasses a wide array of generative AI models, including language models, Generative Adversarial Networks, diffusion models, and their multi-modal counterparts. It indicates the critical need for continued research and development in privacy-preserving techniques for generative AI models. Furthermore, we offer insights into the challenges and discuss the open problems in the intersection of privacy and generative AI models.
Melatonin ameliorates inflammation and improves outcomes of ischemia/reperfusion injury in patients undergoing coronary artery bypass grafting surgery: a randomized placebo-controlled study
Authors: Casper Eman Ahmed , Wakeel Lamia El , Sabri Nagwa A. , Khorshid Ramy , Gamal Mohamed A. , Fahmy Sarah F. 
Published: December 2024

Abstract
To investigate the protective role of high dose melatonin concerning myocardial I/R injury and inflammation in patients undergoing on-pump coronary artery bypass grafting (CABG) surgery by evaluating IR/inflammatory biomarkers and clinical outcomes. This was a prospective; randomized; single-blinded placebo-controlled study conducted at cardio-thoracic surgery department of the Academy of the Cardiovascular and Thoracic Surgery, Ain Shams University. Eligible patients were randomly allocated to; melatonin-treated group (MTG) or placebo-treated group (PTG). The MTG (n = 17) received 60 mg/day melatonin capsules daily starting 5 days before surgery in addition to the standard of care. PTG (n = 17) received placebo also 5 days before surgery plus standard of care. The levels of nuclear factor kappa beta (NF-κb) (primary outcome), tumor necrosis factor (TNF-α), cardiac troponins I, and IL-6 levels were all assessed for both groups at five time points: baseline before melatonin or placebo administration (T0), before cross-clamp application(T1), 5 min after cross-clamp removal(T2), 6 h after cross-clamp removal(T3) and 24 h after cross-clamp removal(T4). Blood pressure was assessed at baseline, pre-operative and 24-hours post-operative. The Quality of recovery-40 score (QOR-40) was assessed for both groups on day 4 after surgery. TNF-α levels decreased in the MTG at T1(p = 0.034) versus PTG. At T2(p = 0.005), and T3(p = 0.04), TNF-α significantly increased in PTG versus MTG. Troponins significantly increased in PTG at T3 (p = 0.04) versus MTG. NF-κB levels declined at T1 (p = 0.013) and T2 (p = 0.0001) in MTG compared to PTG. IL-6 significantly increased in PTG versus MTG at T3 (p = 0.04). The QOR-40 score significantly decreased in MTG versus PTG. MTG had statistically significant decrease in DBP compared to the placebo group (p = 0.024). MTG had a statistically significant shorter intubation time than did the placebo group (p = 0.03). Melatonin 60 mg was well-tolerated without any reported side effects. Our findings suggested that melatonin could ameliorate myocardial I/R injury after on-pump CABG and that this outcome was essentially correlated to its antiapoptotic and anti-inflammatory effects. Trial registration: ClinicalTrials.gov registration number NCT05552586, 9/2022.
Prevalence of SPOP and IDH Gene Mutations in Prostate Cancer in a Jordanian Population
Authors: Alorjani Mohammed S. , Al Bashir Samir , Al-Zaareer Basmah , Al-Khatib Sohaib , Al-Zoubi Raed M. , Al-Trad Bahaa , AbuAlarja Manal , Alzu’bi Ayman , Al-Hamad Mohammad , Al-Batayneh Khalid , Al-Zoubi Mazhar S. 
Published: December 2024

AbstractSpeckle-type POZ (SPOP) is described as an essential tumor suppressor factor in gastric cancer, colorectal cancer, and prostate cancer (PCa). SPOP gene mutations were reported in primary human PCa. Isocitrate dehydrogenase-1 (IDH1) oncogene mutations were detected in gliomas, acute myeloid leukemia, some benign and malignant cartilaginous tumors, and only 1% of PCa. This study aimed to investigate the prevalence of mutations of SPOP and IDH1 genes in PCa in the Jordanian population. One hundred formalin-fixed paraffin-embedded tissue samples were collected from patients diagnosed with prostate adenocarcinoma. The obtained specimens were subjected to genomic DNA extraction, PCR amplification, and direct sequencing of exons 4, 5, 6, and 7 of the SPOP gene and exon 6 of the IDH1 gene. SPOP gene mutations were found in 17% of PCa cases, while no mutation was detected in the screened exon 6 of the IDH1 gene. Clinicopathological data demonstrated a strong correlation between prostate-specific antigen (PSA) levels and both Gleason score (GS) and the International Society of Urological Pathology (ISUP) grade group (GG). There was no significant correlation between PSA levels and age (p = 0.816) nor there were significant associations for SPOP mutational status with age (p = 0.659), PSA levels (p = 0.395), GS (p = 0.259), and ISUP GG (p = 0.424) in the tested population. The study found a strong correlation between PSA levels and both GS and ISUP GG. It also identified a high frequency (17%) of SPOP gene mutations in Jordanian Arab PCa patients, mainly in exon 7. No IDH1 mutations were detected in exon 6.
A hidden barrier surface complementary to the zero velocity surface in the circular restricted three-body problem
Authors: Oshima Kenta 
Published: December 2024

AbstractThe zero velocity surface has been one of the most fundamental structures in many dynamical systems. It plays the role of a barrier placing bounds on the motion and separating the regions of possible and impossible motion. The present paper identifies another barrier surface in addition to the zero velocity surface in the circular restricted three-body problem. We highlight the feature of the new surface in bounding trajectories complementary to that of the zero velocity surface.
Depression Symptoms are Associated with Frequency of Cognitive Distortions in Psychotherapy Transcripts
Authors: Lalk Christopher , Steinbrenner Tobias , Pena Juan S. , Kania Weronika , Schaffrath Jana , Eberhardt Steffen , Schwartz Brian , Lutz Wolfgang , Rubel Julian 
Published: December 2024

Abstract
Background
Based on previous work on the identification of cognitive distortions in language data, we aim to predict patient depression symptoms by identifying cognitive distortions in their psychotherapy transcripts. Further, using explainable AI we want to create a machine learning model that can be used to identify important distortions, allowing us to assess the most important distortions across the whole dataset and for individual patients.

Methods
We identified 14 cognitive distortions by modifying lists of representative n-grams created by Bathina et al. (Nat Hum Behav 5(4):458–466, 2021, https://doi.org/10.1038/s41562-021-01050-7). Based on these n-grams, the relative frequency of the distortions was calculated across 552 transcripts of 124 patients and employed to predict patient depression symptoms. Further, we joined all distortions in an exploratory explainable AI model, combining various machine learning algorithms in a nested cross-validation framework for the prediction of depression symptoms.

Results
Depression severity and occurrence were predicted by the distortions personalizing ($$r=.13)$$

r
=
.
13
)

, dichotomous thinking ($$r=.11)$$

r
=
.
11
)

, and overgeneralizing ($$r=.10)$$

r
=
.
10
)

, while occurrence was additionally predicted by mental filtering. The joined machine learning model achieved a moderate performance of $$r=.29$$

r
=
.
29

. Using explainable AI, we identified the distortions with the highest feature impact in the combined model (i.e., dichotomous reasoning, minimization, personalizing, mindreading, and mental filtering) and were able to explain the prediction for individual transcripts.

Conclusions
This approach illustrates how language-based measures can identify relevant processes that predict depression symptoms. This may improve our understanding of the effects of cognitive distortions and may be utilized to create feedback to therapists. Limitations prevail due to small effect sizes and the exploratory approach of this study.
Sand tiger shark Carcharias taurus mating season in the northwest Atlantic Ocean inferred from wound healing dynamics
Authors: Wyffels Jennifer T. , Riter Joshua , Price Carol S. , Poelzl Kate , Young Brenda , Handsel Tim , Edsberg Laura E. 
Published: December 2024

AbstractAll sharks and rays reproduce using internal fertilization. This necessitates males and females to be coupled tightly during copulation, and as a result, bite wounds associated with mating occur. The appearance of these bite wounds can be used to gauge the timeframe of mating activity without direct observation of copulation. A wound staging system was developed for the sand tiger shark Carcharias taurus through longitudinal observations of an aquarium-housed female that sustained a full-thickness mating wound, an injury that extends through the epidermis, dermis, and hypodermis, exposing underlying muscle. Four wound stages were established: (1) full-thickness, (2) healing, (3) closure, and (4) scar revision. The female’s stage 1 (full thickness) wound transitioned to stage 2 (healing) 2 weeks post-injury. Stage 3 (wound closure) was observed 3–6 weeks post-injury and stage 4 (scar revision) followed and persisted for the duration of the study, 35 weeks post-injury. The staging system was used to characterize the incidence, severity, and etiology of wounds for in situ sharks aggregating at North Carolina shipwreck sites from digital images contributed to the Spot A Shark USA database. There was a significant association between wound stage and its location or zone on the body as well as season of the year for males and females. Mating wounds on females corroborate a late spring and early summer mating season. The presence of stages 1 and 2 mating wounds on sand tiger sharks in North Carolina suggests the area is used for mating while females with stages 3 and 4 mating wounds provide evidence that the area also serves as gestation habitat for this species. This research highlights minimally invasive methodology that leverages citizen science divers to further characterize the reproductive life history of sand tiger sharks.