bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Authors: Lou Jingzhi , Liang Weiwen , Cao Lirong , Hu Inchi , Zhao Shi , Chen Zigui , Chan Renee Wan Yi , Cheung Peter Pak Hang , Zheng Hong , Liu Caiqi , Li Qi , Chong Marc Ka Chun , Zhang Yexian , Yeoh Eng-kiong , Chan Paul Kay-Sheung , Zee Benny Chung Ying , Mok Chris Ka Pun , Wang Maggie Haitian 
Published: March 2024

AbstractInfluenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolution and select representative virus for influenza vaccine. The method involves modelling site-wise mutation fitness. Informed by virus genome and population sero-positivity, we calibrate transition time of mutations and project the fitness landscape to future time, based on which beth-1 selects the optimal vaccine strain. In season-to-season prediction in historical data for the influenza A pH1N1 and H3N2 viruses, beth-1 demonstrates superior genetic matching compared to existing approaches. In prospective validations, the model shows superior or non-inferior genetic matching and neutralization against circulating virus in mice immunization experiments compared to the current vaccine. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus through capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response.
Direct visualization of stacking-selective self-intercalation in epitaxial Nb1+xSe2 films
Authors: Wang Hongguang , Zhang Jiawei , Shen Chen , Yang Chao , Küster Kathrin , Deuschle Julia , Starke Ulrich , Zhang Hongbin , Isobe Masahiko , Huang Dennis , van Aken Peter A. , Takagi Hidenori 
Published: March 2024

AbstractTwo-dimensional (2D) van der Waals (vdW) materials offer rich tuning opportunities generated by different stacking configurations or by introducing intercalants into the vdW gaps. Current knowledge of the interplay between stacking polytypes and intercalation often relies on macroscopically averaged probes, which fail to pinpoint the exact atomic position and chemical state of the intercalants in real space. Here, by using atomic-resolution electron energy-loss spectroscopy in a scanning transmission electron microscope, we visualize a stacking-selective self-intercalation phenomenon in thin films of the transition-metal dichalcogenide (TMDC) Nb1+xSe2. We observe robust contrasts between 180°-stacked layers with large amounts of Nb intercalants inside their vdW gaps and 0°-stacked layers with little detectable intercalants inside their vdW gaps, coexisting on the atomic scale. First-principles calculations suggest that the films lie at the boundary of a phase transition from 0° to 180° stacking when the intercalant concentration x exceeds ~0.25, which we could attain in our films due to specific kinetic pathways. Our results offer not only renewed mechanistic insights into stacking and intercalation, but also open up prospects for engineering the functionality of TMDCs via stacking-selective self-intercalation.
Facile Cu–MOF-derived Co3O4 mesoporous-structure as a cooperative catalyst for the reduction nitroarenes and dyes
Authors: Malmir Masoume , Heravi Majid M. , Shafiei Toran Poshti Elham 
Published: March 2024

AbstractThe present study describes the environmentally friendly and cost-effective synthesis of magnetic, mesoporous structure-Co3O4 nanoparticles (m-Co3O4) utilizing almond peel as a biotemplate. This straightforward method yields a material with high surface area, as confirmed by various characterization techniques. Subsequently, the utilization of m-Co3O4, graphene oxide (GO), Cu(II)acetate (Cu), and asparagine enabled the successful synthesis of a novel magnetic MOF, namely GO–Cu–ASP–m-Co3O4 MOF. This catalyst revealed remarkable stability that could be easily recovered using a magnet for consecutive use without any significant decline in activity for eight cycles in nitro compound reduction and organic dye degradation reactions. Consequently, GO–Cu–ASP-m-Co3O4 MOF holds immense potential as a catalyst for reduction reactions, particularly in the production of valuable amines with high industrial value, as well as for the elimination of toxic-water pollutants such as organic dyes.
High-resolution co-seismic fault offsets of the 2023 Türkiye earthquake ruptures using satellite imagery
Authors: Provost Floriane , Karabacak Volkan , Malet Jean-Philippe , Van der Woerd Jérôme , Meghraoui Mustapha , Masson Frédéric , Ferry Matthieu , Michéa David , Pointal Elisabeth 
Published: March 2024

AbstractOn February 6, 2023, southern Türkiye was struck by two large earthquakes at 01:17 UTC (Mw=7.8, Pazarcık, Kahramanmaraş) and 10:30 UTC (Mw = 7.6, Elbistan, Kahramanmaraş), causing severe damage at the complex junction of the Dead Sea Fault (DSF), the Cyprus Arc and the East Anatolian Fault Zone (EAFZ). The ruptures propagated along several known strands of the southwestern termination of the EAFZ, the main Pazarcık and Karasu valley faults, and the Çardak-Sürgü fault. Here we present the high-resolution mapping of the entire coseismic surface rupture and an estimate of the rupture width, total and on-fault offset, and diffuse deformation obtained a few days to three months after the two mainshocks. The mapping is derived from image correlation of Sentinel-2 optical satellite imagery and validated with offset measurements collected on the ground. We find that the ruptures extend over lengths of 310 km and 140 km for the Mw 7.8 and Mw 7.6 mainshocks, respectively. The maximum offsets reach 7.5 ± 0.8 m and 8.7 ± 0.8 m near the epicenters of the Mw 7.8 and Mw 7.6 events, respectively. We propose a segmentation of the two ruptures based on these observations, and further discuss the location of the potential supershear rupture. The use of optical image correlation, complemented by field investigations along earthquake faults, provides new insights into seismic hazard assessment.
Investment by maternal grandmother buffers children against the impacts of adverse early life experiences
Authors: Helle Samuli , Tanskanen Antti O. , Coall David A. , Perry Gretchen , Daly Martin , Danielsbacka Mirkka 
Published: March 2024

AbstractExogenous shocks during sensitive periods of development can have long-lasting effects on adult phenotypes including behavior, survival and reproduction. Cooperative breeding, such as grandparental care in humans and some other mammal species, is believed to have evolved partly in order to cope with challenging environments. Nevertheless, studies addressing whether grandparental investment can buffer the development of grandchildren from multiple adversities early in life are few and have provided mixed results, perhaps owing to difficulties drawing causal inferences from non-experimental data. Using population-based data of English and Welsh adolescents (sample size ranging from 817 to 1197), we examined whether grandparental investment reduces emotional and behavioral problems in children resulting from facing multiple adverse early life experiences (AELEs), by employing instrumental variable regression in a Bayesian structural equation modeling framework to better justify causal interpretations of the results. When children had faced multiple AELEs, the investment of maternal grandmothers reduced, but could not fully erase, their emotional and behavioral problems. No such result was observed in the case of the investment of other grandparent types. These findings indicate that in adverse environmental conditions the investment of maternal grandmothers can improve child wellbeing.
A number sense as an emergent property of the manipulating brain
Authors: Kondapaneni Neehar , Perona Pietro 
Published: March 2024

AbstractThe ability to understand and manipulate numbers and quantities emerges during childhood, but the mechanism through which humans acquire and develop this ability is still poorly understood. We explore this question through a model, assuming that the learner is able to pick up and place small objects from, and to, locations of its choosing, and will spontaneously engage in such undirected manipulation. We further assume that the learner’s visual system will monitor the changing arrangements of objects in the scene and will learn to predict the effects of each action by comparing perception with a supervisory signal from the motor system. We model perception using standard deep networks for feature extraction and classification. Our main finding is that, from learning the task of action prediction, an unexpected image representation emerges exhibiting regularities that foreshadow the perception and representation of numbers and quantity. These include distinct categories for zero and the first few natural numbers, a strict ordering of the numbers, and a one-dimensional signal that correlates with numerical quantity. As a result, our model acquires the ability to estimatenumerosity, i.e. the number of objects in the scene, as well assubitization, i.e. the ability to recognize at a glance the exact number of objects in small scenes. Remarkably, subitization and numerosity estimation extrapolate to scenes containing many objects, far beyond the three objects used during training. We conclude that important aspects of a facility with numbers and quantities may be learned with supervision from a simple pre-training task. Our observations suggest that cross-modal learning is a powerful learning mechanism that may be harnessed in artificial intelligence.
Evaluation of indicators of acute emotional states in dogs
Authors: Flint Hannah E. , Weller Jennifer E. , Parry-Howells Nia , Ellerby Zack W. , McKay Stephanie L. , King Tammie 
Published: March 2024

AbstractA complete assessment of animal welfare requires not just an understanding of negative emotional states, such as fear and anxiety, but also of positive states, such as calmness and happiness. However, few studies have identified accurate and reliable indicators of positive emotional states in dogs. This study aimed to identify parameters that may serve as indicators of short-term emotional states in dogs. Using a cross-over design, 60 dogs living at a research facility were exposed to six different 10-min scenarios expected to elicit responses varying in emotional valence and arousal. A range of behavioural and physiological parameters were collected and their relationship to anticipated emotional valence and arousal was analysed using linear and logistic mixed models. Cortisol, adrenocorticotropic hormone, heart rate variability, panting, whining, and body shake all demonstrated significant differences based on arousal levels, but only within negative valence scenarios. Scores from a qualitative behavioural assessment (QBA) were associated with both emotional valence and arousal and were considered the best indicator of positive valence. Activity, ear temperature, and sitting were associated with positive high arousal, although this may have been influenced by differing levels of movement induced during these scenarios. Meanwhile, heart rate, secretory immunoglobulin A, standing and lying all showed similar changes associated with arousal for both positive and negative valence scenarios. This study provides a critical first step towards identifying evidence-based indicators of short-term emotional states in dogs, while highlighting considerations that should be made when employing these parameters, including the influence of coder bias, food provision, exercise, and external temperature. Overall, it is recommended future dog emotion and welfare research use a combination of parameters including indicators of both emotional valence and arousal.
Identification of a novel LDLR p.Glu179Met variant in Thai families with familial hypercholesterolemia and response to treatment with PCSK9 inhibitor
Authors: Pussadhamma Burabha , Wongvipaporn Chaiyasith , Wutthimanop Atthakorn , Nuinoon Manit , Porntadavity Sureerut , Jeenduang Nutjaree 
Published: March 2024

AbstractFamilial hypercholesterolemia (FH) is a genetic disease characterized by elevated LDL-C levels. In this study, two FH probands and 9 family members from two families from northeastern Thailand were tested for LDLR, APOB, and PCSK9 variants by whole-exome sequencing, PCR-HRM, and Sanger sequencing. In silico analysis of LDLR was performed to analyse its structure‒function relationship. A novel variant of LDLR (c.535_536delinsAT, p.Glu179Met) was detected in proband 1 and proband 2 in homozygous and heterozygous forms, respectively. A total of 6 of 9 family members were heterozygous for LDLR p.Glu179Met variant. Compared with proband 2, proband 1 had higher baseline TC and LDL-C levels and a poorer response to lipid-lowering therapy combined with a PCSK9 inhibitor. Multiple sequence alignment showed that LDLR p.Glu179Met was located in a fully conserved region. Homology modelling demonstrated that LDLR p.Glu179Met variant lost one H-bond and a negative charge. In conclusion, a novel LDLR p.Glu179Met variant was identified for the first time in Thai FH patients. This was also the first report of homozygous FH patient in Thailand. Our findings may expand the knowledge of FH-causing variants in Thai population, which is beneficial for cascade screening, genetic counselling, and FH management to prevent coronary artery disease.
The effect of cognitive reappraisal and early-life maternal care on neuroendocrine stress responses
Authors: Bentele Ulrike U. , Klink Elea S. C. , Benz Annika B. E. , Meier Maria , Gaertner Raphaela J. , Denk Bernadette F. , Dimitroff Stephanie J. , Unternaehrer Eva , Pruessner Jens C. 
Published: March 2024

AbstractEarly-life adversity (ELA) is related to profound dysregulation of the hypothalamic–pituitary–adrenal (HPA) axis, reflected in both, blunted or exaggerated cortisol stress responses in adulthood. Emotion regulation strategies such as cognitive reappraisal might contribute to this inconsistent finding. Here, we investigate an interaction of early-life maternal care (MC), where low MC represents a form of ELA, and instructed emotion regulation on cortisol responses to acute stress. Ninety-three healthy young women were assigned to a low (n = 33) or high (n = 60) MC group, based on self-reported early-life MC. In the laboratory, participants received regulation instructions, asking to cognitively reappraise (reappraisal group, n = 45) or to focus on senses (control group, n = 48) during subsequent stress exposure, induced by the Trier Social Stress Test. Salivary cortisol and subjective stress levels were measured repeatedly throughout the experiment. Multilevel model analyses confirmed a MC by emotion regulation interaction effect on cortisol trajectories, while controlling for hormonal status. Individuals with low MC in the control compared with the reappraisal group showed increased cortisol responses; individuals with high MC did not differ. These results highlight the significance of emotion regulation for HPA axis stress regulation following ELA exposure. They provide methodological and health implications, indicating emotion regulation as a promising target of treatment interventions for individuals with a history of ELA.
Single nuclei transcriptomics of the in situ human limbal stem cell niche
Authors: Davidson Kathryn C. , Sung Minkyung , Brown Karl D. , Contet Julian , Belluschi Serena , Hamel Regan , Moreno-Moral Aida , dos Santos Rodrigo L. , Gough Julian , Polo Jose M. , Daniell Mark , Parfitt Geraint J. 
Published: March 2024

AbstractThe corneal epithelium acts as a barrier to pathogens entering the eye; corneal epithelial cells are continuously renewed by uni-potent, quiescent limbal stem cells (LSCs) located at the limbus, where the cornea transitions to conjunctiva. There has yet to be a consensus on LSC markers and their transcriptome profile is not fully understood, which may be due to using cadaveric tissue without an intact stem cell niche for transcriptomics. In this study, we addressed this problem by using single nuclei RNA sequencing (snRNAseq) on healthy human limbal tissue that was immediately snap-frozen after excision from patients undergoing cataract surgery. We identified the quiescent LSCs as a sub-population of corneal epithelial cells with a low level of total transcript counts. Moreover, TP63, KRT15, CXCL14, and ITGβ4 were found to be highly expressed in LSCs and transiently amplifying cells (TACs), which constitute the corneal epithelial progenitor populations at the limbus. The surface markers SLC6A6 and ITGβ4 could be used to enrich human corneal epithelial cell progenitors, which were also found to specifically express the putative limbal progenitor cell markers MMP10 and AC093496.1.
MCU-independent Ca2+ uptake mediates mitochondrial Ca2+ overload and necrotic cell death in a mouse model of Duchenne muscular dystrophy
Authors: Bround Michael J. , Abay Eaman , Huo Jiuzhou , Havens Julian R. , York Allen J. , Bers Donald M. , Molkentin Jeffery D. 
Published: March 2024

AbstractMitochondrial Ca2+ overload can mediate mitochondria-dependent cell death, a major contributor to several human diseases. Indeed, Duchenne muscular dystrophy (MD) is driven by dysfunctional Ca2+ influx across the sarcolemma that causes mitochondrial Ca2+ overload, organelle rupture, and muscle necrosis. The mitochondrial Ca2+ uniporter (MCU) complex is the primary characterized mechanism for acute mitochondrial Ca2+ uptake. One strategy for preventing mitochondrial Ca2+ overload is deletion of the Mcu gene, the pore forming subunit of the MCU-complex. Conversely, enhanced MCU-complex Ca2+ uptake is achieved by deleting the inhibitory Mcub gene. Here we show that myofiber-specific Mcu deletion was not protective in a mouse model of Duchenne MD. Specifically, Mcu gene deletion did not reduce muscle histopathology, did not improve muscle function, and did not prevent mitochondrial Ca2+ overload. Moreover, myofiber specific Mcub gene deletion did not augment Duchenne MD muscle pathology. Interestingly, we observed MCU-independent Ca2+ uptake in dystrophic mitochondria that was sufficient to drive mitochondrial permeability transition pore (MPTP) activation and skeletal muscle necrosis, and this same type of activity was observed in heart, liver, and brain mitochondria. These results demonstrate that mitochondria possess an uncharacterized MCU-independent Ca2+ uptake mechanism that is sufficient to drive MPTP-dependent necrosis in MD in vivo.
Experimental realization of entangled coherent states in two-dimensional harmonic oscillators of a trapped ion
Authors: Jeon Honggi , Kang Jiyong , Kim Jaeun , Choi Wonhyeong , Kim Kyunghye , Kim Taehyun 
Published: March 2024

AbstractEntangled coherent states play pivotal roles in various fields such as quantum computation, quantum communication, and quantum sensing. We experimentally demonstrate the generation of entangled coherent states with the two-dimensional motion of a trapped ion system. Using Raman transitions with appropriate detunings, we simultaneously drive the red and blue sidebands of the two transverse axes of a single trapped ion and observe multi-periodic entanglement and disentanglement of its spin and two-dimensional motion. Then, by measuring the spin state, we herald entangled coherent states of the transverse motions of the trapped ion and observe the corresponding modulation in the parity of the phonon distribution of one of the harmonic oscillators. Lastly, we trap two ions in a linear chain and realize Mølmer–Sørensen gate using two-dimensional motion.
Polyphenol consumption and Nonalcoholic fatty liver disease risk in adults
Authors: Rahimlou Mehran , Baghdadi Ghazal , Khodi Ali , Rahimi Zahra , Saki Nader , Banaei Jahromi Nasrin , Cheraghian Bahman , Tavasolian Ronia , Hosseini Seyed Ahmad 
Published: March 2024

AbstractIn this cross-sectional investigation, the primary objective was to explore the correlation between the consumption of polyphenols and the likelihood of non-alcoholic fatty liver disease (NAFLD) in the adult population participating in the Hoveyzeh cohort. Data from the Hoveyzeh cohort study, part of the Persian Cohort Study, involving 10,009 adults aged 35–70, were analyzed. Exclusions were made for missing data, extreme energy intake, and liver cancer patients. Dietary habits were assessed using a food frequency questionnaire, and polyphenol intake was calculated using the Phenol Explorer database. Logistic regression analyses, adjusted for confounders, were performed to assess the relationship between polyphenol subclasses (total polyphenols, total flavonoids, phenolic acid, and lignin) and NAFLD. Among 9894 participants, those in the highest quintile of total polyphenol (OR 0.65, CI 0.5–0.84; P = 0.007), phenolic acid (OR 0.67, CI 0.52–0.86; P < 0.001), and lignin intake (OR 0.69, CI 0.52–0.87; P = 0.001) demonstrated lower odds of NAFLD compared to the lowest quintile, even after adjusting for confounding factors. However, no significant association was found between total flavonoid intake and NAFLD (OR 1.26, CI 0.96–1.67; P = 0.47). Subgroup analysis indicated a significant inverse association between total polyphenols and NAFLD in women (OR 0.64, CI 0.42–0.93; P = 0.001). Higher intake of total polyphenols, phenolic acid, and lignin was associated with reduced odds of NAFLD among adults in the Hoveyzeh cohort. This suggests that dietary patterns rich in these polyphenols may play a role in mitigating the risk of NAFLD. Further interventional and longitudinal studies are needed to validate these findings and explore potential preventive strategies involving polyphenol-rich diets.
Investigation on three-dimensional printed prosthetics leg sockets coated with different reinforcement materials: analysis on mechanical strength and microstructural
Authors: Ramlee Muhammad Hanif , Ammarullah Muhammad Imam , Mohd Sukri Nurelisya Suraya , Faidzul Hassan Nur Syafiqah , Baharuddin Muhammad Hanif , Abdul Kadir Mohammed Rafiq 
Published: March 2024

AbstractPrevious research has primarily focused on pre-processing parameters such as design, material selection, and printing techniques to improve the strength of 3D-printed prosthetic leg sockets. However, these methods fail to address the major challenges that arise post-printing, namely failures at the distal end of the socket and susceptibility to shear failure. Addressing this gap, the study aims to enhance the mechanical properties of 3D-printed prosthetic leg sockets through post-processing techniques. Fifteen PLA + prosthetic leg sockets are fabricated and reinforced with four materials: carbon fiber, carbon-Kevlar fiber, fiberglass, and cement. Mechanical and microstructural properties of the sockets are evaluated through axial compression testing and scanning electron microscopy (SEM). Results highlight superior attributes of cement-reinforced sockets, exhibiting significantly higher yield strength (up to 89.57% more than counterparts) and higher Young’s modulus (up to 76.15% greater). SEM reveals correlations between microstructural properties and socket strength. These findings deepen the comprehension of 3D-printed prosthetic leg socket post-processing, presenting optimization prospects. Future research can focus on refining fabrication techniques, exploring alternative reinforcement materials, and investigating the long-term durability and functionality of post-processed 3D-printed prosthetic leg sockets.