bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing continuous spontaneous localization model with charged macromolecules
Authors: Lenler-Eriksen Emil , Drewsen Michael , Carlesso Matteo 
Published: November 2024

Abstract
In the last decade, a growing interest has been devoted to models of spontaneous collapse of the wavefunction, known also as collapse models. They coherently solve the well-known quantum measurement problem by suitably modifying the Schrödinger evolution. Quantum experiments are now finally within the reach of testing such models (and thus testing the limits of quantum theory). Here, we propose a method based on a two-ions confined in a linear Paul trap to possibly enhance the testing capabilities of such experiments. The combination of an atomic and a macromolecular ion provide a good match for the cooling of the motional degrees of freedom and a non-negligible insight in the collapse mechanism, respectively.
Electron attachment to CCl3COOH molecule and clusters
Authors: Kocábková Barbora , Schöpfer Gabriel , Ďurana Jozef , Rakovský Jozef , Poterya Viktoriya , Gatt Michael , Jank Dominik , Ončák Milan , Fárník Michal 
Published: November 2024

Abstract
Trichloroacetic acid (TCA) is an integral part of the atmosphere as well as a prototypical small polyhalogenated organic acid. Here, we investigate dissociative electron attachment (DEA) to the TCA molecule and small (TCA)
N
clusters combining cluster beam experiments with quantum chemical calculations exploiting genetic algorithm search and structure clustering. We report negative ion mass spectra at electron energies of 2 eV and 6.8 eV as well as energy dependent ion yields from 2 eV to 10 eV. The chlorine anion Cl− formation is by far the dominating channel at all energies in both isolated molecule and clusters. The calculations suggest that the C–Cl bond breaks spontaneously in the ground state of the transient negative anion. For a single molecule, about an order of magnitude less abundant CCl

2

−

,

CCl2COO−, and CCl3COO−ions are observed. These ions correspond to the HCl + CO2, HCl, and H abstraction reactions, respectively. In the cluster environment, the major cluster ion fragments after the Cl−ion correspond to the H abstraction, with other fragmentation pathways (HCl abstraction) being strongly suppressed or not observed at all (HCl + CO2). Our calculations substantiate the experimental observations and show how the hydrogen bond network efficiently controls the dissociation pathways in molecular clusters.
Non-Gaussian tails without stochastic inflation
Authors: Ballesteros Guillermo , Konstandin Thomas , Rodríguez Alejandro Pérez , Pierre Mathias , Rey Julián 
Published: November 2024

Abstract
We show, both analytically and
numerically,
that
non-Gaussian tails in the probability density function of curvature perturbations arise in ultra-slow-roll inflation from the δN formalism, without invoking stochastic inflation. Previously reported discrepancies between both approaches are a consequence of not correctly accounting for momentum perturbations. Once they are taken into account, both approaches agree to an excellent degree. The shape of the tail depends strongly on the phase space of inflation.
Impact of inhomogeneous diffusion on secondary cosmic ray and antiproton local spectra
Authors: Tovar-Pardo Álvaro , Luque Pedro De La Torre , Sánchez-Conde Miguel A. 
Published: November 2024

Abstract
Recent γ-ray and neutrino observations seem to favor the consideration of non-uniform diffusion of cosmic rays (CRs) throughout the Galaxy.
In this study, we investigate the consequences of spatially-dependent inhomogeneous propagation of CRs on the fluxes of secondary CRs and antiprotons detected at Earth. A comparison is made among different scenarios in search of potential features that may guide us toward favoring one over another in the near future. We also examine both the influence of inhomogeneous propagation in the production of secondary CRs from interactions with the gas, and the effects of this scenario on the local fluxes of antiprotons and light antinuclei produced as final products of dark matter annihilation. Our results indicate that the consideration of an inhomogeneous diffusion model could improve the compatibility of the predicted local antiproton flux with that of B, Be and Li, assuming only secondary origin of these particles. In addition, our model predicts a slightly harder local antiproton spectrum, making it more compatible with the high energy measurements of AMS-02.
Finally, no significant changes are expected in the predicted local flux of antiprotons and antinuclei produced from dark matter among the different considered propagation scenarios.
Shape/properties collaborative intelligent manufacturing of artificial bone scaffold: structural design and additive manufacturing process
Authors: Feng Pei , Liu Lingxi , Yang Feng , Min Rui , Wu Ping , Shuai Cijun 
Published: November 2024

Abstract
Artificial bone graft stands out for avoiding limited source of autograft as well as susceptibility to infection of allograft, which makes it a current research hotspot in the field of bone defect repair. However, traditional design and manufacturing method cannot fabricate bone scaffold that well mimics complicated bone-like shape with interconnected porous structure and multiple properties akin to human natural bone. Additive manufacturing, which can achieve implant’s tailored external contour and controllable fabrication of internal microporous structure, is able to form almost any shape of designed bone scaffold via layer-by-layer process. As additive manufacturing is promising in building artificial bone scaffold, only combining excellent structural design with appropriate additive manufacturing process can produce bone scaffold with ideal biological and mechanical properties. In this article, we sum up and analyze state of art design and additive manufacturing methods for bone scaffold to realize shape/properties collaborative intelligent manufacturing. Scaffold design can be mainly classified into design based on unit cells and whole structure, while basic additive manufacturing and 3D bioprinting are the recommended suitable additive manufacturing methods for bone scaffold fabrication. The challenges and future perspectives in additive manufactured bone scaffold are also discussed.
Bayesian optimization for state engineering of quantum gases
Authors: Müller Gabriel , Martínez-Lahuerta Víctor J , Sekulic Ivan , Burger Sven , Schneider Philipp-Immanuel , Gaaloul Naceur 
Published: November 2024

Abstract
State engineering of quantum objects is a central requirement for precision sensing and quantum computing implementations. When the quantum dynamics can be described by analytical solutions or simple approximation models, optimal state preparation protocols have been theoretically proposed and experimentally realized. For more complex systems such as interacting quantum gases, simplifying assumptions do not apply anymore and the optimization techniques become computationally impractical. Here, we propose Bayesian optimization based on multi-output Gaussian processes to learn the physical properties of a Bose–Einstein condensate within few simulations only. We evaluate its performance on an optimization study case of diabatically transporting the quantum gas while keeping it in its ground state. Within a few hundred executions, we reach a competitive performance to other protocols. While restricting this benchmark to the well known Thomas–Fermi approximation for straightforward comparisons, we expect a similar performance when employing more complex theoretical models, which would be computationally more challenging, rendering standard optimal control theory protocols impractical. This paves the way for efficient state engineering of complex quantum systems including mixtures of interacting gases or cold molecules.
MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures
Authors: Zhang Wenmin , Su Chen-Yang , Yoshiji Satoshi , Lu Tianyuan 
Published: November 2024

Abstract

Summary
Mendelian randomization is being utilized to assess causal effects of polygenic exposures, where many genetic instruments are subject to horizontal pleiotropy. Existing methods for detecting and correcting for horizontal pleiotropy have important assumptions that may not be fulfilled. Built upon the core gene hypothesis, we developed MR Corge for performing sensitivity analysis of Mendelian randomization. MR Corge identifies a small number of putative core instruments that are more likely to affect genes with a direct biological role in an exposure and obtains causal effect estimates based on these instruments, thereby reducing the risk of horizontal pleiotropy. Using positive and negative controls, we demonstrated that MR Corge estimates aligned with established biomedical knowledge and the results of randomized controlled trials. MR Corge may be widely applied to investigate polygenic exposure-outcome relationships.

Availability and implementation
An open-sourced R package is available at https://github.com/zhwm/MRCorge.
Labile sex allocation and sex ratio in the androdioecious barnacle Octolasmis unguisiformis
Authors: Wijayanti Hendry , Sawada Kota , Yasuda Keiko , Yusa Yoichi 
Published: November 2024

Abstract
Theoretical models predict that the sex allocation of hermaphrodites is affected by the number of individuals who can donate sperm to each other [mating group size (MGS)]. However, theory does not make clear predictions for solitary hermaphrodites (i.e. MGS = 1). Moreover, few empirical studies exist on the sex allocation of hermaphrodites coexisting with males (androdioecy). We studied male function (testis and seminal vesicle volumes), female function (ovary volume), sex allocation [male/(male + female functions)], and the male-to-hermaphrodite ratio in the androdioecious barnacle Octolasmis unguisiformis, with hermaphrodites carrying dwarf males. We analysed the effects of MGS on these traits separately for MGS 1 vs. 2 or larger (i.e., whether hermaphrodites are solitary or gregarious) and for MGS 2–4. The male function of mature hermaphrodites presented a positive relationship with MGS in both MGS 1 vs. 2 or larger and MGS 2–4, and female function presented a negative relationship with MGS when comparing MGS 1 vs. 2 or larger. Moreover, the sex allocation of hermaphrodites was positively related to MGS in the analyses of both MGS 1 vs. 2 or larger and MGS 2–4. Remarkably, we found many ‘hermaphrodites’ lacking sperm in MGS 1, suggesting that they are functional females. In addition, more dwarf males per hermaphrodite were present in small MGS. These results generally agreed with the theoretical predictions and revealed a highly plastic sexual system of this barnacle.
Risk of neurodevelopmental impairment in Swedish preterm children treated for necrotizing enterocolitis: retrospective cohort study
Authors: Brusselaers Nele , Simin Johanna , E. Lilja Helene 
Published: November 2024

Abstract

Background
As the survival of preterm infants has increased, the management of long-term complications, especially neurodevelopmental impairment, becomes increasingly important. The aim of this study was to investigate the risk of neurodevelopmental disorders in preterm babies receiving medical or surgical treatment for necrotizing enterocolitis, compared with other preterm babies and preterm babies who received abdominal surgery for other indications.

Methods
In this nationwide Swedish cohort study, including all liveborn preterm babies born between 1998 and 2019, the risk of attention deficit (and hyperactivity) disorder, autism spectrum disorders, cerebral palsy and intellectual disability was assessed by multivariable Cox regression, expressed as hazard ratios and 95% confidence intervals (c.i.).

Results
Of the surgically (n = 384) and medically (n = 709) treated preterm infants with necrotizing enterocolitis, neurodevelopmental disorders were present in 32% (HR 2.24, 95% c.i. 1.86 to 2.69) and 22% respectively (HR 1.40, 95% c.i. 1.19 to 1.65), compared with 21% (HR 1.63, 95% c.i. 1.40 to 1.91) in the abdominal surgery group (n = 844) and 13% (reference) among other preterm infants (n = 78 972). The highest relative increases were for intellectual disability (HR 3.60, 95% c.i. 2.65 to 4.89) in the surgical necrotizing enterocolitis group and abdominal surgery group (HR 2.84, 95% c.i. 2.12 to 3.80) compared with the control preterm group, and for cerebral palsy (respectively HR 2.74, 95% c.i. 2.04 to 3.68 and HR 2.54, 95% c.i. 1.87 to 3.44). Medically treated necrotizing enterocolitis was associated with autism (HR 1.67, 95% c.i. 1.34 to 2.08), without significant increases for the other specific outcomes. Both surgically treated groups were also strongly associated with both attention deficit (and hyperactivity) disorder and autism.

Conclusion
Surgically treated necrotizing enterocolitis, medically treated necrotizing enterocolitis and abdominal surgery for other indications in preterm infants were all associated with an increased risk of impaired neurodevelopmental outcomes, compared with other preterm infants.
In Response to the Editorial for the BJSW 54(4), Lived versus Living Experience by Dominic Watters
Authors: Cunningham Christopher 
Published: November 2024

Abstract
In applying the concept of living experience to widening participation in higher education, a process of ‘consumption’ that creates profit for powerholders is discussed—while championing social mobility, the widening participation agenda has done little to address the long-standing social and economic inequalities of British society. Yet, through this process, a ‘sector’ of higher education built upon neoliberal principles has been created. Pushing back against the systems of metrification that threaten education’s authenticity, I propose that powerholders apply ethnographic research methods to their decision-making processes.
Redefining pancreatic cancer management with tumor-agnostic precision medicine
Authors: Reddy Neha K , Subbiah Vivek 
Published: November 2024

Abstract
Precision oncology and tumor-agnostic drug development provide hope for enhancing outcomes among patients with pancreatic cancer. Tumor-agnostic therapies have emerged across various tumor types, driven by insights into shared biomarkers. In the case of pancreatic cancer, the prevalence of the KRAS gene mutation is noteworthy. However, there exist other actionable alterations, such as BRCA1/2 mutations and fusion genes (BRAF, FGFR2, RET, NTRK, NRG1, and ALK), which present potential targets for therapy. Notably, tumor-agnostic drugs have demonstrated efficacy in specific subsets of pancreatic cancer patients who harbor these genetic alterations. Despite the rarity of NTRK fusions in pancreatic cancer, larotrectinib and entrectinib have exhibited effectiveness in NTRK fusion-positive pancreatic cancers. Additionally, repotrectinib, a next-generation NTRK inhibitor, has shown promising activity in NTRK positive pancreatic cancer patients who have developed acquired resistance to previous NTRK inhibitors. Immune checkpoint inhibitors, such as pembrolizumab and dostarlimab, have proven to be effective in dMMR/MSI-H pancreatic cancers. Moreover, targeted therapies for BRAF V600, RET fusions, and HER2/neu overexpression have displayed promising results in specific subsets of pancreatic cancer patients. Emerging targets like NRG fusions, FGFR2 fusions, TP53 mutations, and KRAS G12C mutations present potential avenues for targeted therapy. Tumor-agnostic therapies have the potential to revolutionize pancreatic cancer treatment by focusing on specific genetic alterations. It is crucial to continue implementing comprehensive screening strategies that encompass the ability to detect all these tumor-agnostic biomarkers. This will be essential in identifying pancreatic cancer patients who may benefit from these therapies.
Oculomotor functional connectivity associated with motor sequence learning
Authors: Rubino Cristina , Andrushko Justin W , Rinat Shie , Harrison Adam T , Boyd Lara A 
Published: November 2024

Abstract
Acquisition of learned motor sequences involves saccades directed toward the goal to gather visual information prior to reaching. While goal-directed actions involve both eye and hand movements, the role of brain areas controlling saccades during motor sequence learning is still unclear. This study aimed to determine whether resting-state functional connectivity of oculomotor regions is associated with behavioral changes resulting from motor sequence learning. We investigated connectivity between oculomotor control regions and candidate regions involved in oculomotor control and motor sequence learning. Twenty adults had brain scans before 3 days of motor task practice and after a 24-hour retention test, which was used to assess sequence-specific learning. During testing, both saccades and reaches were tracked. Stronger connectivity in multiple oculomotor regions prior to motor task practice correlated with greater sequence-specific learning for both saccades and reaches. A more negative connectivity change involving oculomotor regions from pre- to post-training correlated with greater sequence-specific learning for both saccades and reaches. Overall, oculomotor functional connectivity was associated with the magnitude of behavioral change resulting from motor sequence learning, providing insight into the function of the oculomotor system during motor sequence learning.
miR-24-3p secreted as extracellular vesicle cargo by cardiomyocytes inhibits fibrosis in human cardiac microtissues
Authors: Senesi Giorgia , Lodrini Alessandra M , Mohammed Shafeeq , Mosole Simone , Hjortnaes Jesper , Veltrop Rogier J A , Kubat Bela , Ceresa Davide , Bolis Sara , Raimondi Andrea , Torre Tiziano , Malatesta Paolo , Goumans Marie-José , Paneni Francesco , Camici Giovanni G , Barile Lucio , Balbi Carolina , Vassalli Giuseppe 
Published: November 2024

Abstract

Aims
Cardiac fibrosis in response to injury leads to myocardial stiffness and heart failure. At the cellular level, fibrosis is triggered by the conversion of cardiac fibroblasts (CF) into extracellular matrix-producing myofibroblasts. miR-24-3p regulates this process in animal models. Here, we investigated whether miR-24-3p plays similar roles in human models.

Methods and results
Gain- and loss-of-function experiments were performed using human induced pluripotent stem cell-derived cardiomyocytes (hCM) and primary hCF under normoxic or ischaemia-simulating conditions. hCM-derived extracellular vesicles (EVs) were added to hCF. Similar experiments were performed using three-dimensional human cardiac microtissues and ex vivo cultured human cardiac slices. hCF transfection with miR-24-3p mimic prevented TGFβ1-mediated induction of FURIN, CCND1, and SMAD4—miR-24-3p target genes participating in TGFβ1-dependent fibrogenesis—regulating hCF-to-myofibroblast conversion. hCM secreted miR-24-3p as EV cargo. hCM-derived EVs modulated hCF activation. Ischaemia-simulating conditions induced miR-24-3p depletion in hCM-EVs and microtissues. Similarly, hypoxia down-regulated miR-24-3p in cardiac slices. Analyses of clinical samples revealed decreased miR-24-3p levels in circulating EVs in patients with acute myocardial infarction (AMI), compared with healthy subjects. Post-mortem RNAScope analysis showed miR-24-3p down-regulation in myocardium from patients with AMI, compared with patients who died from non-cardiac diseases. Berberine, a plant-derived agent with miR-24-3p-stimulatory activity, increased miR-24-3p contents in hCM-EVs, down-regulated FURIN, CCND1, and SMAD4, and inhibited fibrosis in cardiac microtissues.

Conclusion
These findings suggest that hCM may control hCF activation through miR-24-3p secreted as EV cargo. Ischaemia impairs this mechanism, favouring fibrosis.
At a Remove: The Curious State(lessness) of Migrant Mothering in Novels by Shumona Sinha and Nathacha Appanah
Authors: Lee Mark D 
Published: November 2024

Abstract
This article orchestrates a critical conversation between novels by contemporary French writers Shumona Sinha and Nathacha Appanah around the question of mothering, space, and migration. Whether mothers by choice, by default, or childless, the outwardly dissimilar women of the novels studied arrive at a shared poetic interrogation of a remove in migrant motherhood, culminating in a curious spectral statelessness. Rethinking this odd form of mothering at a distance, I identify the performance of a dispossession as both perilous and salutary. Finally, I articulate how this ghostly remove is reinscribed in Appanah’s remarks about how Sinha and she—as non-native, non-European writers of French—are disjointedly situated in French literature, which they re-imagine as a contested, stateless space for their literary expression.
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update
Authors: Cabas-Mora Gabriel , Daza Anamaría , Soto-García Nicole , Garrido Valentina , Alvarez Diego , Navarrete Marcelo , Sarmiento-Varón Lindybeth , Sepúlveda Yañez Julieta H , Davari Mehdi D , Cadet Frederic , Olivera-Nappa Álvaro , Uribe-Paredes Roberto , Medina-Ortiz David 
Published: November 2024

Abstract
In recent years, peptides have gained significant relevance due to their therapeutic properties. The surge in peptide production and synthesis has generated vast amounts of data, enabling the creation of comprehensive databases and information repositories. Advances in sequencing techniques and artificial intelligence have further accelerated the design of tailor-made peptides. However, leveraging these techniques requires versatile and continuously updated storage systems, along with tools that facilitate peptide research and the implementation of machine learning for predictive systems. This work introduces Peptipedia v2.0, one of the most comprehensive public repositories of peptides, supporting biotechnological research by simplifying peptide study and annotation. Peptipedia v2.0 has expanded its collection by over 45% with peptide sequences that have reported biological activities. The functional biological activity tree has been revised and enhanced, incorporating new categories such as cosmetic and dermatological activities, molecular binding, and antiageing properties. Utilizing protein language models and machine learning, more than 90 binary classification models have been trained, validated, and incorporated into Peptipedia v2.0. These models exhibit average sensitivities and specificities of 0.877±0.0530 and 0.873±0.054, respectively, facilitating the annotation of more than 3.6 million peptide sequences with unknown biological activities, also registered in Peptipedia v2.0. Additionally, Peptipedia v2.0 introduces description tools based on structural and ontological properties and user-friendly machine learning tools to facilitate the application of machine learning strategies to study peptide sequences.
Database URL: https://peptipedia.cl/
Move out of the land: certification and migration in China
Authors: Huangfu Bingyu , Gao Xuwen , Shi Xinjie , Jin Songqing 
Published: November 2024

Abstract
Motivated by the emphasis on securing property rights as an important tool for the efficient allocation of resources, including land and labour, we use three rounds of China Rural Household Panel Survey data to assess the impact of a land certification programme (LCP) on the labour and land allocation in rural China. We find that the LCP results in increased rural–urban migration, more active land rental markets, as well as higher household income and consumption in rural China. These effects vary with age and are larger for younger individuals and households with heads aged 50 years or younger. Improving property rights could be a central task for the Chinese government to tackle issues related to labour and land misallocation.