bluuebunny/crossref_metadata_2025_split huggingface dataset:
NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysis
Authors: Agrawal Ankit , Thomann Stefan , Basu Sukanya , Grün Dominic 
Published: December 2024

AbstractCell states are modulated by intrinsic driving forces such as gene expression noise and extrinsic signals from the tissue microenvironment. The distinction between intrinsic and extrinsic cell state determinants is essential for understanding the regulation of cell fate in tissues during development, homeostasis and disease. The rapidly growing availability of single-cell resolution spatial transcriptomics makes it possible to meet this challenge. However, available computational methods to infer topological tissue domains, spatially variable genes, or ligand-receptor interactions are limited in their capacity to capture cell state changes driven by crosstalk between individual cell types within the same niche. We present NiCo, a computational framework for integrating single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing reference data to infer the influence of the spatial niche on the cell state. By applying NiCo to mouse embryogenesis, adult small intestine and liver data, we demonstrate the ability to predict novel niche interactions that govern cell state variation underlying tissue development and homeostasis. In particular, NiCo predicts a feedback mechanism between Kupffer cells and neighboring stellate cells dampening stellate cell activation in the normal liver. NiCo provides a powerful tool to elucidate tissue architecture and to identify drivers of cellular states in local niches.
Insights into self-evaluated stress, anxiety, and depression among dental students
Authors: Rotaru Doina Iulia , Chisnoiu Radu Marcel , Bolboacă Sorana D. , Gileru Edith Ana , Chisnoiu Andrea Maria , Delean Ada Gabriela 
Published: December 2024

AbstractStress, anxiety, and depression have a negative impact on students’ learning and academic performances. In our longitudinal study conducted on dental students from Cluj-Napoca and Oradea, the most representative university centers in north-west of Romania, we evaluated the prevalence and effect of exams on stress, anxiety, and depression, in association with socio-demographic factors. The students self-administered the DASS-21R questionnaire at the beginning of the academic year 2022–2023, before the Christmas holiday, during the winter session, and after the winter session. Students from Cluj-Napoca had higher stress scores at the beginning of the academic year compared to those from Oradea (6.8% vs. 3.7%, P-value < 0.05), especially the females and students with no previous university graduations. Anxiety and depression were significantly more frequently reported by students who study in Cluj-Napoca compared to those who study in Oradea (anxiety 37% vs. 28.2%, P-value < 0.05; depression 17% vs. 11%, P-value < 0.05). We did not observe any significant differences in DASS-21R scores regarding summer jobs, foreign language knowledge, or monthly income. Our results support the needs for interventions regarding stress, anxiety, and depression implemented from the very beginning of university studies and, along with strategies for stress prevention and management of these conditions.
Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain
Authors: Jagadeesh Jaiganesh , Vembar Shruthi Sridhar 
Published: December 2024

Abstract
The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. First discovered in archaea, this protein domain has evolved from RNA- to DNA-binding, with a concomitant expansion in the range of cellular processes that it regulates. Despite its widespread presence, the full extent of its sequence, structural, and functional diversity remains unexplored. In this study, we employed iterative searches in PSI-BLAST to identify 15,161 unique Alba domain-containing proteins from the NCBI non-redundant protein database. Sequence similarity network (SSN) analysis clustered them into 13 distinct subgroups, including the archaeal Alba and eukaryotic Rpp20/Pop7 and Rpp25/Pop6 groups, as well as novel fungal and Plasmodium-specific Albas. Sequence and structural conservation analysis of the subgroups indicated high preservation of the dimer interface, with Alba domains from unicellular eukaryotes notably exhibiting structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms.
Neural network representations of multiphase Equations of State
Authors: Kevrekidis George A. , Serino Daniel A. , Kaltenborn M. Alexander R. , Gammel J. Tinka , Burby Joshua W. , Klasky Marc L. 
Published: December 2024

AbstractEquations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general Equation of State model are adherence to the Laws of Thermodynamics, incorporation of phase transitions, and multiscale accuracy. Analytic models that adhere to all three are hard to develop and cumbersome to work with, often resulting in sacrificing one of these elements for the sake of efficiency. In this work, two deep-learning methods are proposed that provably satisfy the first and second conditions on a large-enough region of thermodynamic variable space. The first is based on learning the generating function (thermodynamic potential) while the second is based on structure-preserving, symplectic neural networks, respectively allowing modifications near or on phase transition regions. They can be used either “from scratch” to learn a full Equation of State, or in conjunction with a pre-existing consistent model, functioning as a modification that better adheres to experimental data. We formulate the theory and provide several computational examples to justify both approaches, highlighting their advantages and shortcomings.
Superdiffusion of energetic particles at shocks: A Lévy flight model for acceleration
Authors: Aerdker Sophie , Merten Lukas , Effenberger Frederic , Fichtner Horst , Becker Tjus Julia 
Published: December 2024

Context. In the heliosphere, power-law particle distributions are observed, for example, upstream of interplanetary shocks, which can result from superdiffusive transport. This non-Gaussian transport regime may be due to intermittent magnetic field structures. Recently, we have shown that a Lévy flight model reproduces the observed features at shocks: power-law distributions upstream of the shock and enhanced intensities at the shock.
Aims. In this work, we extend the Lévy flight model to study the impact of superdiffusive transport on particle acceleration at shocks. We compared the acceleration timescale and spectral slope to Gaussian diffusion and a Lévy walk model.
Methods. We solved the fractional transport equation by sampling the number density with the corresponding stochastic differential equation that is driven by an alpha-stable Lévy distribution. For both Gaussian and superdiffusive transport, we used a modified version of the cosmic ray propagation framework CRPropa 3.2.
Results. We obtained the number density and energy spectra for constant and energy-dependent anomalous diffusion, and we find, compared to the case of Gaussian diffusion, harder energy spectra at the shock as well as faster acceleration. The spectral slope is even harder than predicted for Lévy walks.
Conclusions Lévy flight models of superdiffusive transport lead to observed features in the heliosphere. We further show that superdiffusive transport impacts the acceleration process by changing the probability of escaping the shock. The flexibility of the Lévy flight model allows for further studies in the future that can take the shock geometry and magnetic field structure into account.
Retroverted Uterus in the First Trimester and Associated Pregnancy Outcomes
Authors: Schneider Emily R. , Kantorowska Agata , Clough Joanna M. , Miller Erin L. , Kobara Emmanuella , Brite Jasmine , Akerman Meredith L. , Kinzler Wendy L. , Suhag Anju , Chavez Martin R. , Rekawek Patricia 
Published: December 2024

Objective This study aimed to investigate if retroverted (RV) uterus noted on nuchal translucency (NT) ultrasound is associated with second-trimester pregnancy loss and other adverse pregnancy outcomes.
Study Design This was a retrospective cohort study of patients with RV uterus documented on NT ultrasound at a single academic medical center from October 2019 to March 2023. Subjects were identified using a query for “retroverted” uterine position within an obstetric ultrasound imaging program. For each RV case, two anteverted (AV) subjects were selected for comparison. Patients with multiple gestation, Mullerian anomalies, or fetal aneuploidy were excluded. Maternal demographics, obstetric, and neonatal outcomes were obtained by chart review. Fisher's exact test and Mann–Whitney test were used for categorical and continuous variables, respectively, with p-value <0.05 denoting significance. Multivariable logistic regression was used to adjust for possible confounding variables.
Results Analysis included 249 patients—83 RV and 166 AV. RV patients were more likely to identify as Caucasian (71.1 vs. 49.4%, p = 0.001), have private insurance (80.7 vs. 59.4%, p = 0.001), lower body mass index (25.4 ± 5.1 vs 29.1 ± 7.2, p < 0.001), and conceive by in vitro fertilization (IVF, 11 vs. 3%, p = 0.018). Most RV subjects (98%) had a resolution of retroversion by the second trimester. There was no difference in second-trimester pregnancy loss (0 vs. 1.2%, p = 0.55). After adjusting for race and IVF, RV subjects were four times more likely to have first-trimester vaginal bleeding (16.9 vs. 4.2%, odds ratio = 4.1, p = 0.0056). No other differences in adverse outcomes were observed.
Conclusion Persistent RV uterus in the first trimester is associated with increased risk of first-trimester vaginal bleeding. However, rates of pregnancy loss were similar between groups, providing valuable information for patient counseling. Significantly more RV subjects conceived by IVF, highlighting the need for further study in this population.
Key Points
Contralateral Expansion of Hemorrhagic Contusion in Patients Undergoing Decompressive Craniectomy: A Series of Two Patients
Authors: Gupta Pragya , Shukla Ashutosh , Ranjan Nitish , Singh Mayank , Maurya Ved Prakash 
Published: December 2024

AbstractContralateral formation and expansion of hemorrhagic contusion is a significant and rare complication following decompressive craniectomy. Decompressive craniectomy is an important surgical tool for management of raised intracranial hypertension secondary to various pathologies including trauma. These uncommon events are reported in the literature along substantive explanations and theories. We present two cases of road traffic accident (RTA) who following decompressive craniectomy developed expansion of contralateral hematoma. In this article, we are focus on the appearance and expansion of contralateral intraparenchymal contusion following decompressive craniectomy with a deep dive into the existing literature.
Multilingualism from the perspective of the medieval Islamic vision of language
Authors: Salvaggio Federico 
Published: December 2024

AbstractArabic holds a cardinal position within Islamic civilisation, where it enjoys the status of sacred language for its direct connection to the Revelation and for the role attributed to it by the Revelation itself. However, not only does the Qur’an mention the existence of other languages and put them in relation with different divine messages, but also the providential nature of language diversity is explicitly maintained by the Holy Book of Islam. This theology of multilingualism represented the theoretical and symbolic framework within which the premodern Islamic world conceptualized language diversity. By looking at the works of philosophers, historians, poets, and religious masters from different parts of the Islamic world, we will try to understand how premodern authors viewed multilingualism, explained the existence of different languages, and accordingly engaged in plurilingual practices. Plurilingual practices provided the fertile ground on which various vernaculars, often bereft of any former written tradition (let alone literary prestige), could be transformed into full-fledged literary languages and become part of the wide Islamic language family. This process of incorporation of the multiple languages, encountered by the Islamic civilisation in its expansion, gave rise, throughout the Islamic world, to complex multilingual societies where individuals were frequently plurilingual and able to accommodate language diversity in flexible, creative, and, as reflected in literary productions, even aesthetic ways. In some cases, like the Andalusian context, such linguistic incorporation even involved romance vernaculars with significant consequences for their destiny as future modern European literary languages.
Transcriptomic analysis of luteal tissue supports the earlier onset of luteolysis in heifers with diminished ovarian reserve
Authors: Kaps Martim , Snider Alexandria P. , Quail Lacey K. , Miles Jeremy R. , Perry George A. , Cushman Robert A. 
Published: December 2024

Context Antral follicle count (AFC) is reflective of ovarian reserve and linked to reproductive performance in mammalian females. We previously demonstrated earlier upregulation of endometrial oxytocin receptor transcription in heifers with low AFC, indicating an earlier onset of luteolysis. Aims We aimed to support the earlier onset of luteolysis in non-pregnant heifers with a low number of antral ovarian follicles (Open Low AFC) and hypothesized a reduced abundance of luteinizing hormone/choriogonadotropin receptor (LH/CG-R) and increased abundance of thrombospondin-1 (THBS1) in luteal tissue of those heifers. We further investigated if classical interferon stimulated genes (ISGs) are already upregulated in response to conceptus-derived interferon tau. Methods For 4 years, 10 heifers with the highest (High AFC) and 10 heifers with the lowest AFC (Low AFC) of the population (n = 120/year) were selected, synchronized and inseminated. On day 15 or 16 after insemination, reproductive tracts were collected, and pregnancy status was determined. Corpora lutea were isolated, weighed and underwent transcriptomic analysis. Key results Transcript abundance of LH/CG-R was lower in Open Low AFC heifers compared to all other subgroups. Transcript abundance of THBS1 was upregulated in Open vs Pregnant heifers and showed greater abundance in Low vs High AFC heifers. Luteal weights and abundance of ISGs did not differ between heifers of differing AFC groups or pregnancy status. Conclusions The patterns of luteal LH/CG-R and THBS1 abundance support the concept of earlier onset of luteolysis in Open heifers with diminished AFC. Implications This may result in a shorter window for maternal recognition of pregnancy and contribute to inferior reproductive performance.
Capturing power in diplomatic language use
Authors: House Juliane , Kádár Dániel Z. , Todorović Tadej , Klemenčič Matjaž , Hazemali David , Onič Tomaž , Plemenitaš Katja 
Published: December 2024

Abstract
In this study we capture power dynamics in diplomacy from a pragmatic angle, by examining a closed-door diplomatic
mediatory negotiation and its aftermath. We first analyse the transcript of a mediation session between representatives of Slovenia and
Croatia and a European Economic Community (EEC) delegation during the breakup of Yugoslavia. While the EEC representatives officially acted
as mediators, they had earlier secretly agreed with the Yugoslav side to keep Yugoslavia intact. Second, we examine the transcript of a
meeting between Slovenian politicians shortly after the mediation session. Studying these two datasets helps us to capture how power
manifests itself in the mediatory negotiation studied, and how it is judged by the powerless afterwards. Focusing on language behaviour in
the two datasets provides insight into the presence of power in a diplomatic situation where it should in theory not be played out. We use
speech acts to analyse our data.
Theoretical analysis of a fractional-order nipah virus transmission system with sensitivity and cost-effectiveness analysis
Authors: Barman Snehasis , Jana Soovoojeet , Majee Suvankar , Kar T K 
Published: December 2024

Abstract
Nipah virus is a newly discovered infectious illness in a crowded world. It has a deadly impact on both the human and animal populations. Controlling the disease will need a deeper understanding of the route of transmission. To better explain how the illness behaves, an epidemic system consisting of eight separate compartments has been devised based on the actual Requirement, which uses a set of fractional-order differential equations. With the assistance of the next-generation matrix method, the basic reproduction numbers for humans (

R

0

m

) and animals (

R

0

a

) are determined. Depending upon the numerical quantity of

R

0

m

,

R

0

a

, the feasibility and existence requirements of the system at the equilibria are investigated. Also, we observe that the system displays two transcritical bifurcations: one occurs at

R

0

a

=
1

for any value of

R

0

m

and the second one occurs at

R

0

m

=
1

for

R

0

a

<
1

. Additionally, we looked at optimal control strategies by considering treatment and media as two dynamic control variables. Two ratios are computed to evaluate the cost-effectiveness of all feasible control measures: the incremental cost-effectiveness ratio and the infected averted ratio. Moreover, the impact of system parameters on disease transmission is determined by performing the sensitivity analysis.
Modeling marburg virus control with limited hospital beds: a fractional approach
Authors: Soni Kaushal , Kumar Sinha Arvind 
Published: December 2024

Abstract
The Marburg virus is a serious global health threat due to its high mortality rate and rapid transmission. Effective control measures, such as hospital beds, are vital but often limited by inadequate healthcare resources. This study aims to address this challenge by developing a fractional-order epidemic model for Marburg virus, which considers the effects of limited hospital beds on transmission dynamics. We present a model to provide a more accurate understanding of Marburg virus transmission patterns and prevalence incorporating the memory effect through a fractional-order approach. The study explores the impact of constrained healthcare resources on virus progression and calculates the basic reproduction number using the next-generation matrix technique. Further analysis of the model’s global dynamics is conducted using reproduction numbers, the Lyapunov functional approach, and the Routh-Hurwitz criterion, shedding light on how hospital bed availability influences disease progression.We also apply Hyers-Ulam stability criterion to find the stability of the model and obtain numerical solutions through a fractional Lagrange two-step interpolation method. The fractional-order Marburg virus model, by accounting for memory effects, offers a more nuanced understanding of the disease dynamics compared to classical models. Our results demonstrate that increasing hospital bed availability significantly reduces Marburg virus infection rates. This approach highlights the value of fractional calculus in epidemiological modeling, offering significant insights into optimal control measures and strategies to improve public health outcomes during Marburg virus outbreaks.
Scale-dependent chirality as a smoking gun for Abelian gauge fields during inflation
Authors: Özsoy Ogan , Papageorgiou Alexandros , Fasiello Matteo 
Published: December 2024

Abstract
Axion-inflation models are a compelling candidate as a mechanism behind the accelerated expansion in the early universe in light of the possibility to embed them in higher dimensional UV complete theories and the exciting prospect of testing them with next-generation cosmological probes. Adding an Abelian gauge sector to axion-inflation models makes for a rich, interesting, phenomenology spanning from primordial black holes to gravitational waves (GWs). Several recent studies employ an approximate analytic (Gaussian) template to characterize the effect of gauge field production on cosmological perturbations. In this work we go beyond such approximation and numerically study particle production and the ensuing scalar and tensor spectra. We find a significant deviation from results based on log-normally distributed vector field excitations. As an important phenomenological application of the improved method, we study the expected chirality and spectral index of the sourced GW background at scales relevant for current and next-generation GW detectors. One striking feature is that of a scale-dependent chirality. We derive a consistency relation between these two observables that can serve as an important tool in identifying key signatures of multi-field dynamics in axion inflation.
Constraining small-scale primordial magnetic fields from the abundance of primordial black holes
Authors: Kushwaha Ashu , Suyama Teruaki 
Published: December 2024

Abstract
The presence of magnetic fields in the early universe affects the cosmological processes,
leading to the distinct signature, which allows constraining their properties and the genesis
mechanisms. In this study, we revisit the method to constrain the amplitude of the magnetic fields
on small scales in the radiation-dominated era from the abundance of primordial black holes.
Constraints in the previous work were based on the fact that the density perturbations sourced by
stronger magnetic fields become large enough to gravitationally collapse to form PBHs. However, we
demonstrate that this picture is incomplete because magnetic fields also increase the threshold
value of the density contrast required for PBH formation. The increase in threshold density
contrast is more pronounced on smaller scales, and in extreme cases, it might even prevent PBH
production despite the presence of significant magnetic field. Taking into account the relevant
physical effects on the magnetized overdense region, we establish an upper-limit on the amplitude
of comoving magnetic fields, approximately 0.13-0.15 μG at a scale of 1017
Mpc-1. Additionally, we compare our constraints with various small-scale probes.
Propagation characteristics of nonplanar electron acoustic waves in nonthermal plasma
Authors: Ullah Shakir , Al-Shomar S M , Affan Hira , Fathy Naglaa , Mahmoud Safwat A , Attia Mohamed S 
Published: December 2024

Abstract
Nonplanar electron acoustic waves (NEAWs) with double spectral index-distributed hot electrons are studied under the two-temperature electrons model in a collisionless unmagnetized plasma. Using this model, the Korteweg–de Vries (KdV) equation is derived in nonplanar geometry. On the basis of the solutions of KdV equation, alterations of velocity, width, and amplitude of acoustic waves having various plasma factors are investigated. Nonlinear and dispersion coefficients obtained rely on double spectral index parameters r and q, and particle density α. The combined influence of these factors significantly alters the features of electron acoustic waves in nonplanar geometry. This study is expected to contribute to the understanding of nonlinear principles that underlie nonplanar electrostatic waves in laboratory plasmas as well as in space.