bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reverse engineering morphogenesis through Bayesian optimization of physics-based models
Authors: Kumar Nilay , Mim Mayesha Sahir , Dowling Alexander , Zartman Jeremiah J. 
Published: May 2024

AbstractMorphogenetic programs coordinate cell signaling and mechanical interactions to shape organs. In systems and synthetic biology, a key challenge is determining optimal cellular interactions for predicting organ shape, size, and function. Physics-based models defining the subcellular force distribution facilitate this, but it is challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the experimentally observed organ shapes. This integrative framework employs Gaussian Process Regression, a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that maintain the final organ shape. We calibrated and tested the method on Drosophila wing imaginal discs to study mechanisms that regulate epithelial processes ranging from development to cancer. The parameter estimation framework successfully infers the underlying changes in core parameters needed to match simulation data with imaging data of wing discs perturbed with collagenase. The computational pipeline identifies distinct parameter sets mimicking wild-type shapes. It enables a global sensitivity analysis to support the regulation of actomyosin contractility and basal ECM stiffness to generate and maintain the curved shape of the wing imaginal disc. The optimization framework, combined with experimental imaging, identified that Piezo, a mechanosensitive ion channel, impacts fold formation by regulating the apical-basal balance of actomyosin contractility and elasticity of ECM. This workflow is extensible toward reverse-engineering morphogenesis across organ systems and for real-time control of complex multicellular systems.
Initiating PeriCBD to probe perinatal influences on neurodevelopment during 3–10 years in China
Authors: Wang Yin-Shan , Su Xue-Ting , Ke Li , He Qing-Hua , Chang Da , Nie JingJing , Luo XinLi , Chen Fumei , Xu Jihong , Zhang Cai , Zhang Shudong , Zhang Shuyue , An Huiping , Guo Rui , Yue Suping , Duan Wen , Jia Shichao , Yang Sijia , Yu Yankun , Zhao Yang , Zhou Yang , Chen Li-Zhen , Fan Xue-Ru , Gao Peng , Lv Chenyu , Wu Ziyun , Zhao Yunyan , Quan Xi , Zhao Feng , Mu Yanchao , Yan Yu , Xu Wenchao , Liu Jie , Xing Lixia , Chen Xiaoqin , Wu Xiang , Zhao Lanfeng , Huang Zhijuan , Ren Yanzhou , Hao Hongyan , Li Hui , Wang Jing , Dong Qing , Chen Liyan , Huang Ruiwang , Liu Siman , Wang Yun , Dong Qi , Zuo Xi-Nian 
Published: May 2024

AbstractAdverse perinatal factors can interfere with the normal development of the brain, potentially resulting in long-term effects on the comprehensive development of children. Presently, the understanding of cognitive and neurodevelopmental processes under conditions of adverse perinatal factors is substantially limited. There is a critical need for an open resource that integrates various perinatal factors with the development of the brain and mental health to facilitate a deeper understanding of these developmental trajectories. In this Data Descriptor, we introduce a multicenter database containing information on perinatal factors that can potentially influence children’s brain-mind development, namely, periCBD, that combines neuroimaging and behavioural phenotypes with perinatal factors at county/region/central district hospitals. PeriCBD was designed to establish a platform for the investigation of individual differences in brain-mind development associated with perinatal factors among children aged 3–10 years. Ultimately, our goal is to help understand how different adverse perinatal factors specifically impact cognitive development and neurodevelopment. Herein, we provide a systematic overview of the data acquisition/cleaning/quality control/sharing, processes of periCBD.
Lactobacillus paracasei subsp. paracasei 2004 improves health and lifespan in Caenorhabditis elegans
Authors: Kishimoto Saya , Nono Masanori , Makizaki Yutaka , Tanaka Yoshiki , Ohno Hiroshi , Nishida Eisuke , Uno Masaharu 
Published: May 2024

AbstractRecent research has highlighted the importance of the gut microbiome in regulating aging, and probiotics are interventions that can promote gut health. In this study, we surveyed several novel lactic acid bacteria to examine their beneficial effect on organismal health and lifespan in C. elegans. We found that animals fed some lactic acid bacteria, including L. acidophilus 1244 and L. paracasei subsp. paracasei 2004, grew healthy. Supplementation with the lactic acid bacterial strains L. acidophilus 1244 or L. paracasei subsp. paracasei 2004 significantly improved health, including food consumption, motility, and resistance to oxidative stressor, hydrogen peroxide. Our RNA-seq analysis showed that supplementation with L. paracasei subsp. paracasei 2004 significantly increased the expression of daf-16, a C. elegans FoxO homolog, as well as genes related to the stress response. Furthermore, daf-16 deletion inhibited the longevity effect of L. paracasei subsp. paracasei 2004 supplementation. Our results suggest that L. paracasei subsp. paracasei 2004 improves health and lifespan in a DAF-16-dependent manner.
Assessment of induced allelopathy in crop-weed co-culture with rye-pigweed model
Authors: Mushtaq Waseem , Fauconnier Marie-Laure , de Clerck Caroline 
Published: May 2024

AbstractThis study evaluates induced allelopathy in a rye-pigweed model driven by rye’s (Secale cereale L.) allelopathic potential as a cover crop and pigweed’s (Amaranthus retroflexus L.) notoriety as a weed. The response of rye towards pigweed’s presence in terms of benzoxazinoids (BXs) provides valuable insight into induced allelopathy for crop improvement. In the 2 week plant stage, pigweed experiences a significant reduction in growth in rye’s presence, implying allelopathic effects. Rye exhibits increased seedling length and BXs upsurge in response to pigweed presence. These trends persist in the 4 week plant stage, emphasizing robust allelopathic effects and the importance of different co-culture arrangements. Germination experiments show rye’s ability to germinate in the presence of pigweed, while pigweed exhibits reduced germination with rye. High-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis identifies allelopathic compounds (BXs), 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) in rye. Rye significantly increases BX production in response to pigweed, age-dependently. Furthermore, pigweed plants are screened for possible BX uptake from the rhizosphere. Results suggest that allelopathy in rye-pigweed co-cultures is influenced by seed timing, and age-dependent dynamics of plants’ allelopathic compounds, providing a foundation for further investigations into chemical and ecological processes in crop-weed interactions.
Study on energy evolution and fractal characteristics of sandstone with different fracture dip angles under uniaxial compression
Authors: Tian Xin-yu , Zhao Fu-jun , Wang Wei-jun , Chen Biao , Ma Yu-jie , Fan Bao-jie 
Published: May 2024

AbstractIn order to investigate the failure modes and instability mechanism of fractured rock. Uniaxial compression tests were conducted on sandstone specimens with different dip angles. Based on rock energy dissipation theory and fractal theory, the energy evolution characteristics and fragmentation fractal characteristics in the process of deformation and failure of specimens were analyzed. The results show that the peak strength and elastic modulus of fractured rock mass are lower than those of intact samples, and both show an exponential increase with the increase of fracture dip angle. The energy evolution laws of different fracture specimens are roughly similar and can be classified into four stages based on the stress–strain curve: pressure-tight, elastic, plastic, and post-destructive. The total strain energy, elastic strain energy, and dissipated strain energy of the specimen at the peak stress point increased exponentially with crack inclination, and the dissipated strain energy and compressive strength conformed to a power function growth relationship. The distribution of the fragments after the failure of the fracture sample has fractal characteristics, and the fractal dimension increases with the increase of the fracture dip angle. In addition, the higher the compressive strength of the specimen, the greater the energy dissipation, the more serious the degree of fragmentation, and the greater the fractal dimension. The data fitting further shows that there is a power function relationship between the dissipated strain energy and the fractal dimension. The research results can provide a theoretical basis for the stability of rock mass engineering and structural deformation control.
A general quantum algorithm for numerical integration
Authors: Shu Guoqiang , Shan Zheng , Xu Jinchen , Zhao Jie , Wang Shuya 
Published: May 2024

AbstractQuantum algorithms have shown their superiority in many application fields. However, a general quantum algorithm for numerical integration, an indispensable tool for processing sophisticated science and engineering issues, is still missing. Here, we first proposed a quantum integration algorithm suitable for any continuous functions that can be approximated by polynomials. More impressively, the algorithm achieves quantum encoding of any integrable functions through polynomial approximation, then constructs a quantum oracle to mark the number of points in the integration area and finally converts the statistical results into the phase angle in the amplitude of the superposition state. The quantum algorithm introduced in this work exhibits quadratic acceleration over the classical integration algorithms by reducing computational complexity from O(N) to O(√N). Our work addresses the crucial impediments for improving the generality of quantum integration algorithm, which provides a meaningful guidance for expanding the superiority of quantum computing.
Domestication constrains the ability of dogs to convey emotions via facial expressions in comparison to their wolf ancestors
Authors: Hobkirk Elana R. , Twiss Sean D. 
Published: May 2024

AbstractDogs (Canis lupus familiaris) are the domestically bred descendant of wolves (Canis lupus). However, selective breeding has profoundly altered facial morphologies of dogs compared to their wolf ancestors. We demonstrate that these morphological differences limit the abilities of dogs to successfully produce the same affective facial expressions as wolves. We decoded facial movements of captive wolves during social interactions involving nine separate affective states. We used linear discriminant analyses to predict affective states based on combinations of facial movements. The resulting confusion matrix demonstrates that specific combinations of facial movements predict nine distinct affective states in wolves; the first assessment of this many affective facial expressions in wolves. However, comparative analyses with kennelled rescue dogs revealed reduced ability to predict affective states. Critically, there was a very low predictive power for specific affective states, with confusion occurring between negative and positive states, such as Friendly and Fear. We show that the varying facial morphologies of dogs (specifically non-wolf-like morphologies) limit their ability to produce the same range of affective facial expressions as wolves. Confusion among positive and negative states could be detrimental to human–dog interactions, although our analyses also suggest dogs likely use vocalisations to compensate for limitations in facial communication.
Identification of early coagulation changes associated with survival outcomes post severe burns from multiple perspectives
Authors: Huang Shengyu , Ma Qimin , Liao Xincheng , Yin Xi , Shen Tuo , Liu Xiaobin , Tang Wenbin , Wang Yusong , Wang Lei , Xin Haiming , Li Xiaoliang , Chang Liu , Chen Zhaohong , Liu Rui , Wu Choulang , Wang Deyun , Guo Guanghua , Zhu Feng 
Published: May 2024

AbstractCoagulation alterations manifest early after severe burns and are closely linked to mortality outcomes. Nevertheless, the precise characterization of coagulation changes associated with early mortality remains elusive. We examined alterations in indicators linked to mortality outcomes at both the transcriptomic and clinical characteristic levels. At the transcriptomic level, we pinpointed 28 differentially expressed coagulation-related genes (DECRGs) following burn injuries and endeavored to validate their causal relationships through Mendelian randomization. DECRGs tied to survival exhibit a significant association with neutrophil function, wherein the expression of CYP4F2 and P2RX1 serves as robust predictors of fatal outcomes. In terms of clinical indicators, early levels of D-dimer and alterations in serum calcium show a strong correlation with mortality outcomes. Coagulation depletion and fibrinolytic activation, stemming from the hyperactivation of coagulation pathways post-severe burns, are strongly linked to patient mortality. Monitoring these early coagulation markers with predictive value can effectively identify individuals necessitating priority critical care.
Large environmental changes reduce valence-dependent belief updating
Authors: Beron Juan Cruz , Solovey Guillermo , Ferrelli Ignacio A. , Pedreira María E. , Fernández Rodrigo S. 
Published: May 2024

AbstractWhen updating beliefs, humans tend to integrate more desirable information than undesirable information. In stable environments (low uncertainty and high predictability), this asymmetry favors motivation towards action and perceived self-efficacy. However, in changing environments (high uncertainty and low predictability), this process can lead to risk underestimation and increase unwanted costs. Here, we examine how people (n = 388) integrate threatening information during an abrupt environmental change (mandatory quarantine during the COVID-19 pandemic). Given that anxiety levels are associated with the magnitude of the updating belief asymmetry; we explore its relationship during this particular context. We report a significant reduction in asymmetrical belief updating during a large environmental change as individuals integrated desirable and undesirable information to the same extent. Moreover, this result was supported by computational modeling of the belief update task. However, we found that the reduction in asymmetrical belief updating was not homogeneous among people with different levels of Trait-anxiety. Individuals with higher levels of Trait-anxiety maintained a valence-dependent updating, as it occurs in stable environments. On the other hand, updating behavior was not associated with acute anxiety (State-Anxiety), health concerns (Health-Anxiety), or having positive expectations (Trait-Optimism). These results suggest that highly uncertain environments can generate adaptive changes in information integration. At the same time, it reveals the vulnerabilities of individuals with higher levels of anxiety to adapt the way they learn.
Common cold viruses circulating in children threaten wild chimpanzees through asymptomatic adult carriers
Authors: Weary Taylor E. , Pappas Tressa , Tusiime Patrick , Tuhaise Shamilah , Otali Emily , Emery Thompson Melissa , Ross Elizabeth , Gern James E. , Goldberg Tony L. 
Published: May 2024

AbstractReverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as “common cold” paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3–11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020–2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.
Genetic variations in ACE2 gene associated with metabolic syndrome in southern China: a case–control study
Authors: Pan Min , Yu Mingzhong , Zheng Suli , Luo Li , Zhang Jie , Wu Jianmin 
Published: May 2024

AbstractMetabolic syndrome (MetS) is closely related to cardiovascular and cerebrovascular diseases, and genetic predisposition is one of the main triggers for its development. To identify the susceptibility genes for MetS, we investigated the relationship between angiotensin-converting enzyme 2 (ACE2) single nucleotide polymorphisms (SNPs) and MetS in southern China. In total, 339 MetS patients and 398 non-MetS hospitalized patients were recruited. Four ACE2 polymorphisms (rs2074192, rs2106809, rs879922, and rs4646155) were genotyped using the polymerase chain reaction-ligase detection method and tested for their potential association with MetS and its related components. ACE2 rs2074192 and rs2106809 minor alleles conferred 2.485-fold and 3.313-fold greater risks of MetS in women. ACE2 rs2074192 and rs2106809 variants were risk factors for obesity, diabetes, and low–high-density lipoprotein cholesterolemia. However, in men, the ACE2 rs2074192 minor allele was associated with an approximately 0.525-fold reduction in MetS prevalence. Further comparing the components of MetS, ACE2 rs2074192 and rs2106809 variants reduced the risk of obesity and high triglyceride levels. In conclusion, ACE2 rs2074192 and rs2106809 SNPs were independently associated with MetS in a southern Chinese population and showed gender heterogeneity, which can be partially explained by obesity. Thus, these SNPs may be utilized as predictive biomarkers and molecular targets for MetS. A limitation of this study is that environmental and lifestyle differences, as well as genetic heterogeneity among different populations, were not considered in the analysis.
Amperometry approach curve profiling to understand the regulatory mechanisms governing the concentration of intestinal extracellular serotonin
Authors: Yeoman Mark S. , Fidalgo Sara , Marcelli Gianluca , Patel Bhavik Anil 
Published: May 2024

AbstractEnterochromaffin (EC) cells located within the intestinal mucosal epithelium release serotonin (5-HT) to regulate motility tones, barrier function and the immune system. Electroanalytical methodologies have been able to monitor steady state basal extracellular 5-HT levels but are unable to provide insight into how these levels are influenced by key regulatory processes such as release and uptake. We established a new measurement approach, amperometry approach curve profiling, which monitors the extracellular 5-HT level at different electrode–tissue (E–T) distances. Analysis of the current profile can provide information on contributions of regulatory components on the observed extracellular 5-HT level. Measurements were conducted from ex vivo murine ileum and colon using a boron-doped diamond (BDD) microelectrode. Amperometry approach curve profiling coupled with classical pharmacology demonstrated that extracellular 5-HT levels were significantly lower in the colon when compared to the ileum. This difference was due to a greater degree of activity of the 5-HT transporter (SERT) and a reduced amount of 5-HT released from colonic EC cells. The presence of an inhibitory 5-HT4autoreceptor was observed in the colon, where a 40% increase in extracellular 5-HT was the half maximal inhibitory concentration for activation of the autoreceptor. This novel electroanalytical approach allows estimates of release and re-uptake and their contribution to 5-HT extracellular concentration from intestinal tissue be obtained from a single series of measurements.
Agar-tragacanth/silk fibroin hydrogel containing Zn-based MOF as a novel nanobiocomposite with biological activity
Authors: Lalebeigi Farnaz , Kashtiaray Amir , Aghamirza Moghim Aliabadi Hooman , Moghadaskhou Fatemeh , Pajoum Zeinab , Nokandeh Seyede Mehrnoush , Mahdavi Mohammad , Eivazzadeh-Keihan Reza , Maleki Ali 
Published: May 2024

AbstractIn this study, a novel nanobiocomposite consisting of agar (Ag), tragacanth gum (TG), silk fibroin (SF), and MOF-5 was synthesized and extensively investigated by various analytical techniques and basic biological assays for potential biomedical applications. The performed Trypan blue dye exclusion assay indicated that the proliferation percentage of HEK293T cells was 71.19%, while the proliferation of cancer cells (K-562 and MCF-7) was significantly lower, at 10.74% and 3.33%. Furthermore, the Ag-TG hydrogel/SF/MOF-5 nanobiocomposite exhibited significant antimicrobial activity against bothE. coliandS. aureusstrains, with growth inhibition rates of 76.08% and 69.19% respectively. Additionally, the hemolytic index of fabricated nanobiocomposite was found approximately 19%. These findings suggest that the nanobiocomposite exhibits significant potential for application in cancer therapy and wound healing.