bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneous folding landscapes and predetermined breaking points within a protein family
Authors: Pechmann Sebastian 
Published: November 2024

AbstractThe accurate prediction of protein structures with artificial intelligence has been a spectacular success. Yet, how proteins fold into their native structures inside the cell remains incompletely understood. Of particular interest is to rationalize how proteins interact with the protein homeostasis network, an organism specific set of protein folding and quality control enzymes. Failure of protein homeostasis leads to widespread misfolding and aggregation, and thus neurodegeneration. Here, I present a comparative analysis of the folding of 16 single‐domain proteins from the same organism across a protein family, the Saccharomyces cerevisiae small GTPases. Using computational modeling to directly probe protein folding dynamics, this work shows how near identical structures from the same folding environment can exhibit heterogeneous folding landscapes. Remarkably, yeast small GTPases are found to unfold along different pathways either via the N‐ or C‐terminus initiated by structure‐encoded predetermined breaking points. Degrons as recognition signals for ubiquitin‐dependent degradation were systematically absent from the initial unfolding sites, as if to protect from too rapid degradation upon spontaneous unfolding or before completion of the folding. The presented results highlight a direct coordination of folding pathway and protein homeostasis interaction signals across a protein family. A deeper understanding of the interdependence of proteins with their folding environment will help to rationalize and combat diseases linked to protein misfolding and dysregulation. More generally, this work underlines the importance of understanding protein folding in the cellular context, and highlights valuable constraints towards a systems‐level understanding of protein homeostasis.
Low‐dimensional neural ordinary differential equations accounting for inter‐individual variability implemented in Monolix and NONMEM
Authors: Bräm Dominic Stefan , Steiert Bernhard , Pfister Marc , Steffens Britta , Koch Gilbert 
Published: November 2024

AbstractNeural ordinary differential equations (NODEs) are an emerging machine learning (ML) method to model pharmacometric (PMX) data. Combining mechanism‐based components to describe “known parts” and neural networks to learn “unknown parts” is a promising ML‐based PMX approach. In this work, the implementation of low‐dimensional NODEs in two widely applied PMX software packages (Monolix and NONMEM) is explained. Inter‐individual variability is introduced to NODEs and proposals for the practical implementation of NODEs in such software are presented. The potential of such implementations is shown on various demonstrational datasets available in the Monolix model library, including pharmacokinetic (PK), pharmacodynamic (PD), target‐mediated drug disposition (TMDD), and survival analyses. All datasets were fitted with NODEs in Monolix and NONMEM and showed comparable results to classical modeling approaches. Model codes for demonstrated PK, PKPD, TMDD applications are made available, allowing a reproducible and straight‐forward implementation of NODEs in available PMX software packages.
(Re)membering Home(lands): Generative Analysis of Human Displacement in Children's Literature
Authors: Strekalova‐Hughes Ekaterina , Peterman Nora , Minaya Richard 
Published: November 2024

AbstractChildren's literature is a powerful pedagogical tool within culturally sustaining literacy classrooms. Drawing from generative metanarrative theory of human displacement, culturally sustaining pedagogies, and critical refugee studies, this research investigates how representations of home(lands) in 30 acclaimed picturebooks about children who experienced displacement could affirm critically informed history and cultivate cultural sustenance. We analyze the narrative structures of time space (chronotope) within and across these stories, as well as the substance therein, identifying troubling generic patterns. We propose strategies for remembering home(lands) through acts of collective imagining.
Understanding an exceptional Afropollis‐dominated flora in the middle Cretaceous palaeotropics of the southern Tethys
Authors: El Atfy Haytham , Coiffard Clément , El Beialy Salah Y. , Doyle James A. 
Published: November 2024

AbstractAfropollis is a common element in Cretaceous low‐latitude palynofloras ranging from the Barremian to the Cenomanian. Despite an abundant fossil record, its affinities are still elusive. Nine Afropollis‐rich subsurface samples from the Cenomanian Bahariya Formation in the northern part of the Western Desert of Egypt were palynologically analysed, and the palynoflora was compared with previously published material. The geographical distribution of Afropollis‐yielding strata was compared with known macrofloras. The Bahariya material yielded a distinct palynomorph assemblage dominated by an unusually high frequency of Afropollis jardinus, reaching up to 60.7% of the total palynomorph count. The dominance of A. jardinus may be ecologically related to a near‐coastal lacustrine or lagoonal environment. Its association with two kinds of macrofloras suggests that the plants producing A. jardinus may have been part of a tropical azonal vegetation type, either aquatic or mangrove‐like.
Mining and the Formation of Modern Geology
Authors: Felten Sebastian 
Published: November 2024

AbstractMining mineral resources and knowing the Earth are historically entwined activities. This connex of practical and theoretical interest in the Earth has long been noted by historians of science. This historiographical chapter uses Vaccari and Morello’s survey as a starting point. It revisits the idea that an eighteenth-century conjuncture of mining and scholarship brought about modern geology, tracing some strands of this narrative into the period of institutional entrenchment and global diffusion in the nineteenth century. It surveys canonical and recent works in the history of geology. Section 2 situates the interaction of mining and geology in a broader debate on practical and theoretical knowledge in the Scientific and Industrial Revolution. Sections 3, 4, 5, and 6 describe four ways in which historians have found mining (including other forms of earthwork like digging canals or quarrying) to have shaped the modern earth sciences. Section 7 points to a new avenue for research about the interface between mining and science: the impact of specifically bureaucratic knowledge production on modern geology during its formation. The Conclusion asks how the interaction between mining and science was shaped, or even constituted, by social mechanisms of inclusion and exclusion based on class/status, gender, and race.
Stochastic Fluids with Transport Noise: Approximating Diffusion from Data Using SVD and Ensemble Forecast Back-Propagation
Authors: Woodfield James 
Published: November 2024

AbstractWe introduce and test methods for the calibration of the diffusion term in Stochastic Partial Differential Equations (SPDEs) describing fluids. We take two approaches, one uses ideas from the singular value decomposition and the Biot-Savart law. The other backpropagates through an ensemble forecast, with respect to diffusion parameters, to minimise a probabilistic ensemble forecasting metric. We describe the approaches in the specific context of solutions to SPDEs describing the evolution of fluid particles, sometimes called inviscid vortex methods. The methods are tested in an idealised setting in which the reference data is a known realisation of the parameterised SPDE, and also using a forecast verification metric known as the Continuous Rank Probability Score (CRPS).
An imperative study of the angular observables in $$ {\Lambda}_b\to {\Lambda}_c^{+}\left(\to \Lambda {\pi}^{+}\right){\ell}^{-}{\overline{\nu}}_{\ell } $$ decay and probing the footprint of new physics
Authors: Nandi Soumitra , Sahoo Shantanu , Sain Ria 
Published: November 2024

Abstract
We study the four-fold angular distribution of the semileptonic $$ {\Lambda}_b\to {\Lambda}_c^{+}\left(\to \Lambda {\pi}^{+}\right){\ell}^{-}{\overline{\nu}}_{\ell } $$

Λ
b

→

Λ
c
+

→
Λ

π
+

ℓ
−

ν
¯

ℓ

decay and find out analytical expressions for various asymmetric and angular observables in the standard model (SM) and the relevant new physics (NP) scenarios. Using the available inputs on the form factors from the lattice, we predict the values with uncertainties of all these observables in the SM. We have considered NP effects only in $$ b\to c{\tau}^{-}{\overline{\nu}}_{\tau } $$
b
→
c

τ
−

ν
¯

τ

transitions, and constrain the Wilson coefficients of the model-independent beyond the SM operators from the available data on B → D(*)ℓνℓ and $$ {\Lambda}_b\to {\Lambda}_c^{+}{\ell}^{-}{\overline{\nu}}_{\ell } $$

Λ
b

→

Λ
c
+

ℓ
−

ν
¯

ℓ

decays. In this study, we focus on analysing the contributions to these decays in one- and two-operator scenarios. Furthermore, we test the new physics sensitivities (one or two-operator scenarios) of the different angular and asymmetric observables in $$ {\Lambda}_b\to {\Lambda}_c^{+}\left(\to \Lambda {\pi}^{+}\right){\tau}^{-}{\overline{\nu}}_{\tau } $$

Λ
b

→

Λ
c
+

→
Λ

π
+

τ
−

ν
¯

τ

decays and discuss the phenomenology. We observe that it will be possible to distinguish the different NP effects from one another by measuring these observables.
Totally Symmetric Self-Complementary Plane Partition Matrices and Related Polytopes
Authors: Holmlund Vincent , Striker Jessica 
Published: November 2024

AbstractPlane partitions in the totally symmetric self-complementary symmetry class (TSSCPPs) are known to be equinumerous with $$n\times n$$

n
×
n

alternating sign matrices, but no explicit bijection is known. In this paper, we give a bijection from these plane partitions to $$\{0,1,-1\}$$

{
0
,
1
,
-
1
}

-matrices we call magog matrices, some of which are alternating sign matrices. We explore enumerative properties of these matrices related to natural statistics such as inversion number and number of negative ones. We then investigate the polytope defined as their convex hull. We show that all the magog matrices are extreme and give a partial inequality description. Finally, we define another TSSCPP polytope as the convex hull of TSSCPP boolean triangles and determine its dimension, inequalities, vertices, and facets.
Emerging socioeconomic correlates of loneliness. Evidence from the Barcelona Health Survey 2021
Authors: Mangot-Sala Lluís , Bartoll-Roca Xavier , Sánchez-Ledesma Esther , Cortés-Albaladejo Mònica , Liefbroer Aart C. , Pérez Katherine 
Published: November 2024

Abstract
Purpose
Recent evidence shows that loneliness is associated with socioeconomic factors. However, studies often focus on traditional socioeconomic indicators (income, occupation, educational level) only, disregarding other important socioeconomic determinants, such as job insecurity, housing conditions or material deprivation. Therefore, we analyse the association of a broad range of socioeconomic indicators with loneliness. Moreover, we investigate potential age and gender differences in this relationship.

Methods
We used cross-sectional data from the Barcelona Health Survey 2021, representative of the population of Barcelona (Spain). Individuals over the age of 14 were selected (n = 3,337). The outcome was a loneliness score based on 4 items of the UCLA scale. Loneliness was regressed on a series of sociodemographic and emerging socioeconomic correlates. Linear regression models were fitted, and potential age and gender moderation effects were tested by means of two-way interactions.

Results
Job insecurity and precarity-related factors, such as having a temporary job or working without a contract, material deprivation and financial difficulties, as well as poor housing conditions and facing housing insecurity were associated with increased loneliness levels. While the association between loneliness and precarity-related factors is stronger among younger individuals, material deprivation is associated with increased loneliness among older workers and women.

Conclusion
Beyond sociodemographic individual characteristics, socioeconomic factors are strongly associated with loneliness levels in the population. Findings support the relevance of broadening the scope of socioeconomic indicators, assessing both material conditions as well as perceived insecurity.
Quantitative distribution of essential elements and non-essential metals in breast cancer tissues by LA-ICP-TOF–MS
Authors: Escudero-Cernuda Sara , Clases David , Eiro Noemi , González Luis O. , Fraile María , Vizoso Francisco J. , Fernández-Sánchez María Luisa , Gonzalez de Vega Raquel 
Published: November 2024

AbstractBreast cancer (BC) is the leading cause of cancer death among women worldwide, making the discovery and quantification of new biomarkers essential for improving diagnostic and preventive strategies to limit dissemination and improve prognosis. Essential trace metals such as Fe, Cu, and Zn may play critical roles in the pathophysiology of both benign and malignant breast tumors. However, due to the high metabolic activity and reduced element selectivity of cancer cells, also non-essential elements may be taken up and may even be implicated with disease progression. This study investigates the spatial distribution and concentrations of both essential and non-essential elements in breast tissues, assessing their potential for diagnostic applications. Laser ablation (LA)–inductively coupled plasma–mass spectrometry (ICP-MS) with a time-of-flight (ToF) mass analyzer (LA-ICP-ToF–MS) was used to inquire the distribution of almost all elements across the periodic table and their abundance in metastatic (n = 11), non-metastatic (n = 7), and healthy (n = 4) breast tissues. Quantification was achieved using gelatine-based standards for external calibration to quantitatively map various elements. Overall, the Fe, Cu, Zn, Sr, and Ba levels were significantly increased in tumor samples with Sr and Ba showing strong correlation, likely due to their similar chemistry. Comparison of calibrated LA-ICP-ToF–MS data with a histologic staining demonstrated the possibility to clearly differentiate between various tissue types and structures in breast tissues such as tumor niche and stroma. The levels of the studied elements were significantly higher in the tumor niche areas compared to the stroma, and for Fe, a significant accumulation was observed in the tumor niche areas from the metastatic patient group relative to the levels found in the same areas of the non-metastatic group.
Graphical Abstract
LA-ICP-ToF–MS was used to quantitatively map the biodistribution of essential and non-essential elements in metastatic and non-metastatic breast cancer tissues.
$$\varvec{\Gamma }$$-Convergence and Stochastic Homogenization of Second-Order Singular Perturbation Models for Phase Transitions
Authors: Donnarumma Antonio Flavio 
Published: November 2024

Abstract
We study the effective behavior of random, heterogeneous, anisotropic, second-order phase transitions energies that arise in the study of pattern formations in physical–chemical systems. Specifically, we study the asymptotic behavior, as

$$\varepsilon $$

ε

goes to zero, of random heterogeneous anisotropic functionals in which the second-order perturbation competes not only with a double well potential but also with a possibly negative contribution given by the first-order term. We prove that, under suitable growth conditions and under a stationarity assumption, the functionals

$$\Gamma $$

Γ

-converge almost surely to a surface energy whose density is independent of the space variable. Furthermore, we show that the limit surface density can be described via a suitable cell formula and is deterministic when ergodicity is assumed.
Challenges in the terminology of second-degree atrioventricular block
Authors: Barold S. Serge , Israel Carsten W. , Herweg Bengt 
Published: November 2024

AbstractThe terminology of second-degree atrioventricular block has evolved over time, thereby creating some confusion and misinterpretations. Strict adherence to standard terminology and the appropriate use of eponyms are important to avoid diagnostic errors.
Persistent pulmonary hypertension in children after apparent resolution of ultrasound-defined pulmonary hypertension associated with bronchopulmonary dysplasia
Authors: Takeoka Mami , Sawada Hirofumi , Mitani Yoshihide , Ohashi Hiroyuki , Yodoya Noriko , Ohya Kazunobu , Tsuboya Naoki , Harada Tomoya , Hirayama Masahiro 
Published: November 2024

Abstract
To evaluate pulmonary hemodynamics in patients who had been followed up for bronchopulmonary dysplasia (BPD)-associated pulmonary hypertension (PH) in the mid-term by right heart catheterization (RHC). A retrospective study was conducted among 56 patients who were born at a gestational age < 28 weeks during 2018–2020, and the consecutive patients complicated by BPD and ultrasound-defined PH (n = 10, 18%), of whom 7 patients were treated with sildenafil, were examined by RHC in the mid-term follow-up (median age: 25 months [IQR: 19–32]). Ultrasound study at RHC showed improvement in PH as represented by left ventricular end-systolic eccentricity index (median [IQR], 1.05 [IQR: 1.03–1.06] vs. 1.18 [IQR: 1.15–1.33]), pulmonary artery acceleration time (PAAT) (mean ± SD, 97.3 ± 18.2 vs. 55.2 ± 10.1) and a ratio of PAAT to right ventricular ejection time (0.35 ± 0.05 vs. 0.25 ± 0.04) compared with those at 40 weeks of postmenstrual age (PMA) (p < 0.05, respectively). RHC (mean pulmonary artery [PA] pressure: 21 [19–22] mmHg; pulmonary vascular resistance index [PVRi]: 2.63 [1.95–2.94] Wood Units·m2) revealed that 5 infants (50%) had mild PH (21–24 mmHg) and reduced peripheral PAs by pulmonary wedge angiography. The presence of emphysema on chest CT at 40 weeks of PMA and moderate/marked reduction of contrast filling in peripheral PAs on angiography were correlated with increased PVRi (p < 0.05, respectively).

Conclusion: We observed that even after apparent resolution of ultrasound-defined PH, half of patients had catheterization-defined PH and vasculopathy at 2 years of age. These findings warrant long-term follow-up studies of BPD-associated PH.

What is Known:
• Pulmonary hypertension (PH) is associated with increased mortality in infants with bronchopulmonary dysplasia
(BPD). Mortality in patients with BPD-associated PH predominantly occurs within the first 6 months of life and most
patients who survive beyond 6 months show resolution of PH on echocardiography by 2 to 3 years of age.
What is New:
• Even after the resolution of echocardiography-derived PH in infants with BPD-associated PH in the mid-term, the majority of such patients have abnormal pulmonary vasculature with PH or mildly elevated pulmonary artery pressure on right heart catheterization (RHC), indicating that echocardiography is insufficient and RHC may be
necessary to follow up this population of patients.
In vitro fertilization and long-term child health and development: nationwide birth cohort study in Japan
Authors: Matsumoto Naomi , Mitsui Takashi , Kadowaki Tomoka , Mitsuhashi Toshiharu , Hirota Tomoya , Masuyama Hisashi , Yorifuji Takashi 
Published: November 2024

Abstract
The aim of this study is to compare long-term health outcomes between IVF-conceived children and non-IVF-conceived children in Japan, in the context of strong recommendation for single embryo transfer. Using data from a nationwide birth cohort linked with perinatal database, this study analyzed 2140 children born in Japan in May 2010. It compared child health and development outcomes up to 9 years of age between IVF-conceived and non-IVF-conceived children (binary exposure). A Poisson regression with robust variance to estimate the risk ratios for the association between IVF and various long-term child health and developmental outcomes. After adjusting for confounding factors, no significant differences were observed between IVF-conceived and naturally conceived children for most outcomes, including hospitalization, obesity, and developmental milestones. IVF-conceived children showed a slightly lower risk of attention problems at 8 years (adjusted Risk Ratio [aRR]: 0.73, 95% CI: 0.53–1.00). In subgroup analyses, IVF-conceived term children and singletons demonstrated reduced risk of cognitive delays at 5.5 years (aRR: 0.31, 95% CI: 0.10–0.96 and aRR: 0.37, 95% CI: 0.14–0.98, respectively).

Conclusion: In this Japanese cohort, IVF conception was not associated with adverse long-term health or developmental outcomes. These findings provide reassurance about the safety of IVF, particularly in the context of single embryo transfer policies. Further research is needed to explore specific IVF protocols and subgroups.

What is known:
• Long-term health and developmental outcomes of IVF-conceived children remain inconsistent across studies and populations, despite the widespread use of this technology.

What is new:
• A nationwide population-based cohort study in Japan did not show adverse effects of IVF on long-term child health and development through age 9.
• These findings provide reassurance about the safety of IVF, while indicating the need for careful monitoring in specific subgroups such as preterm and multiple births.
In vivo assessment of pediatric kidney function using multi-parametric and multi-nuclear functional magnetic resonance imaging: challenges, perspectives, and clinical applications
Authors: De Mul Aurélie , Schleef Maxime , Filler Guido , McIntyre Christopher , Lemoine Sandrine 
Published: November 2024

AbstractThe conventional methods for assessing kidney function, such as glomerular filtration rate and microalbuminuria, provide only partial insight into kidney function. Multi-parametric and multi-nuclear functional resonance magnetic imaging (MRI) techniques are innovative approaches to unraveling kidney physiology. Multi-parametric MRI includes various sequences to evaluate kidney perfusion, tissue oxygenation, and microstructure characterization, including fibrosis—a key pathological event in acute and chronic kidney disease and in transplant patients—without the need for invasive kidney biopsy. Multi-nuclear MRI detects nuclei other than protons. 23Na MRI enables visualization of the corticomedullary gradient and assessment of tissue sodium storage, which can be particularly relevant for personalized medicine in salt-wasting tubular disorders. Meanwhile, 31P-MRS measures intracellular phosphate and ATP variations, providing insights into oxidative metabolism in the muscle during exercise and recovery. This technique can be useful for detecting subclinical ischemia in chronic kidney disease and in tubulopathies with kidney phosphate wasting. These techniques are non-invasive and do not involve radiation exposure, making them especially suitable for longitudinal and serial assessments. They enable in vivo evaluation of kidney function on a whole-organ basis within a short acquisition time and with the ability to distinguish between medullary and cortical compartments. Therefore, they offer considerable potential for pediatric patients. In this review, we provide a brief overview of the main imaging techniques, summarize available literature data on both adult and pediatric populations, and examine the perspectives and challenges associated with multi-parametric and multi-nuclear MRI.
Graphical Abstract