bluuebunny/crossref_metadata_2025_split huggingface dataset:
UPF1 plays critical roles in early B cell development
Authors: Iwai Noriki , Akaki Kotaro , Hia Fabian , Li Wei , Yoshinaga Masanori , Mino Takashi , Takeuchi Osamu 
Published: July 2024

AbstractThe ATP-dependent RNA helicase UPF1 plays a crucial role in various mRNA degradation pathways, most importantly in nonsense-mediated mRNA decay (NMD). Here, we show that UPF1 is upregulated during the early stages of B cell development and is important for early B cell development in the bone marrow. B-cell-specific Upf1 deletion in mice severely impedes the early to late LPre-B cell transition, in which VH-DHJH recombination occurs at the Igh gene. Furthermore, UPF1 is indispensable for VH-DHJH recombination, without affecting DH-JH recombination. Intriguingly, the genetic pre-arrangement of the Igh gene rescues the differentiation defect in early LPre-B cells under Upf1 deficient conditions. However, differentiation is blocked again following Ig light chain recombination, leading to a failure in development into immature B cells. Notably, UPF1 interacts with and regulates the expression of genes involved in immune responses, cell cycle control, NMD, and the unfolded protein response in B cells. Collectively, our findings underscore the critical roles of UPF1 during the early LPre-B cell stage and beyond, thus orchestrating B cell development.
The mycobacterial glycoside hydrolase LamH enables capsular arabinomannan release and stimulates growth
Authors: Franklin Aaron , Salgueiro Vivian C. , Layton Abigail J. , Sullivan Rudi , Mize Todd , Vázquez-Iniesta Lucía , Benedict Samuel T. , Gurcha Sudagar S. , Anso Itxaso , Besra Gurdyal S. , Banzhaf Manuel , Lovering Andrew L. , Williams Spencer J. , Guerin Marcelo E. , Scott Nichollas E. , Prados-Rosales Rafael , Lowe Elisabeth C. , Moynihan Patrick J. 
Published: July 2024

AbstractMycobacterial glycolipids are important cell envelope structures that drive host-pathogen interactions. Arguably, the most important are lipoarabinomannan (LAM) and its precursor, lipomannan (LM), which are trafficked from the bacterium to the host via unknown mechanisms. Arabinomannan is thought to be a capsular derivative of these molecules, lacking a lipid anchor. However, the mechanism by which this material is generated has yet to be elucidated. Here, we describe the identification of a glycoside hydrolase family 76 enzyme that we term LamH (Rv0365c in Mycobacterium tuberculosis) which specifically cleaves α−1,6-mannoside linkages within LM and LAM, driving its export to the capsule releasing its phosphatidyl-myo-inositol mannoside lipid anchor. Unexpectedly, we found that the catalytic activity of this enzyme is important for efficient exit from stationary phase cultures, potentially implicating arabinomannan as a signal for growth phase transition. Finally, we demonstrate that LamH is important for M. tuberculosis survival in macrophages.
Piezoelectricity in chalcogenide perovskites
Authors: Abir Sk Shamim Hasan , Sharma Shyam , Sharma Prince , Karla Surya , Balasubramanian Ganesh , Samuel Johnson , Koratkar Nikhil 
Published: July 2024

AbstractPiezoelectric materials show potential to harvest the ubiquitous, abundant, and renewable energy associated with mechanical vibrations. However, the best performing piezoelectric materials typically contain lead which is a carcinogen. Such lead-containing materials are hazardous and are being increasingly curtailed by environmental regulations. In this study, we report that the lead-free chalcogenide perovskite family of materials exhibits piezoelectricity. First-principles calculations indicate that even though these materials are centrosymmetric, they are readily polarizable when deformed. The reason for this is shown to be a loosely packed unit cell, containing a significant volume of vacant space. This allows for an extended displacement of the ions, enabling symmetry reduction, and resulting in an enhanced displacement-mediated dipole moment. Piezoresponse force microscopy performed on BaZrS3 confirmed that the material is piezoelectric. Composites of BaZrS3 particles dispersed in polycaprolactone were developed to harvest energy from human body motion for the purposes of powering electrochemical and electronic devices.
Mechanisms underlying the therapeutic effects of Gang Huo Qing wen granules in the treatment of influenza based on network pharmacology, molecular docking and molecular dynamics
Authors: Wu Wenyu , Lan Wanning , Jiao Xin , Shao Axue , Wu Peng , Wang Kai , Zhan Shaofeng 
Published: July 2024

AbstractInfluenza (Flu) is a severe health, medical, and economic problem, but no medication that has excellent outcomes and lowers the occurrence of these problems is now available. GanghuoQingwenGranules (GHQWG) is a common Chinese herbal formula for the treatment of influenza (flu). However, its methods of action remain unknown. We used network pharmacology, molecular docking, and molecular dynamics simulation techniques to investigate the pharmacological mechanism of GHQWG in flu. TCMSP and various types of literature were used to obtain active molecules and targets of GHQWG. Flu-related targets were found in the Online Mendelian Inheritance in Man (OMIM) database, the DisFeNET database, the Therapeutic Target Database (TTD), and the DrugBank database. To screen the key targets, a protein–protein interaction (PPI) network was constructed. DAVID was used to analyze GO and KEGG pathway enrichment. Target tissue and organ distribution was assessed. Molecular docking was used to evaluate interactions between possible targets and active molecules. For the ideal core protein–compound complexes obtained using molecular docking, a molecular dynamics simulation was performed. In total, 90 active molecules and 312 GHQWG targets were discovered. The PPI network's topology highlighted six key targets. GHQWG's effects are mediated via genes involved in inflammation, apoptosis, and oxidative stress, as well as the TNF and IL-17 signaling pathways, according to GO and KEGG pathway enrichment analysis. Molecular docking and molecular dynamics simulations demonstrated that the active compounds and tested targets had strong binding capabilities. This analysis accurately predicts the effective components, possible targets, and pathways involved in GHQWG flu treatment. We proposed a novel study strategy for future studies on the molecular processes of GHQWG in flu treatment. Furthermore, the possible active components provide a dependable source for flu drug screening.
Speckle statistics as a tool to distinguish collective behaviors of Zebrafish shoals
Authors: de Souza Adauto J. F. , Romaguera Antonio. R. de C. , Vasconcelos João V. A. , Negreiros-Neto Luis G. , de Oliveira Viviane M. , Cadena Pabyton G. , Barbosa Anderson L. R. , Lyra Marcelo L. 
Published: July 2024

AbstractZebrafish have become an important model animal for studying the emergence of collective behavior in nature. Here, we show how to properly analyze the polarization statistics to distinguish shoal regimes. In analogy with the statistical properties of optical speckles, we show that exponential and Rayleigh distributions emerge in shoals with many fish with uncorrelated velocity directions. In the opposite limit of just two fish, the polarization distribution peaks at high polarity, with the average value being a decreasing function of the shoal’s size, even in the absence of correlations. We also perform a set of experiments unveiling two shoaling regimes. Large shoals behave as small domains with strong intra-domain and weak inter-domain correlations. A strongly correlated regime develops for small shoals. The reported polarization statistical features shall guide future automated neuroscience, pharmacological, toxicological, and embryogenesis-motivated experiments aiming to explore the collective behavior of fish shoals.
Osteoporosis, spinal degenerative disorders, and their association with low back pain, activities of daily living, and physical performance in a general population
Authors: Iwata Shoei , Hashizume Hiroshi , Yoshimura Noriko , Oka Hiroyuki , Iwahashi Hiroki , Ishimoto Yuyu , Nagata Keiji , Teraguchi Masatoshi , Kagotani Ryohei , Sasaki Takahide , Tanaka Sakae , Yoshida Munehito , Yamada Hiroshi 
Published: July 2024

AbstractOsteoporosis, vertebral fractures, and spinal degenerative diseases are common conditions that often coexist in older adults. This study aimed to determine the factors influencing low back pain and its impact on activities of daily living (ADL) and physical performance in older individuals with multiple comorbidities. This cross-sectional study was part of a large-scale population-based cohort study in Japan, involving 1009 participants who underwent spinal magnetic resonance imaging (MRI) to assess cervical cord compression, radiographic lumbar spinal stenosis, and lumbar disc degeneration. Vertebral fractures in the thoracolumbar spine were evaluated using sagittal MRI with a semi-quantitative method. Bone mineral density was measured using dual-energy X-ray absorptiometry. Low back pain, Oswestry Disability Index (ODI), and physical performance tests, such as one-leg standing time, five times chair-stand time, maximum walking speed, and maximum step length, were assessed. Using clinical conditions as objective variables and image evaluation parameters as explanatory variables, multiple regression analysis showed that vertebral fractures were significantly associated with low back pain and ODI. Vertebral fractures and osteoporosis significantly impacted physical performance, whereas osteoporosis alone did not affect low back pain or ODI. Our findings contribute to new insights into low back pain and its impact on ADL and physical performance.
Co-regulatory network analysis of the main secondary metabolite (SM) biosynthesis in Crocus sativus L.
Authors: Eshaghi Mahsa , Rashidi-Monfared Sajad 
Published: July 2024

AbstractSaffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.
High-gain far-detuned nonlinear frequency conversion in a few-mode graded-index optical fiber
Authors: Stefańska Karolina , Béjot Pierre , Fatome Julien , Millot Guy , Tarnowski Karol Lech , Kibler Bertrand 
Published: July 2024

AbstractWe present theoretical and experimental evidence of high-gain far-detuned nonlinear frequency conversion, extending towards both the visible and the mid-infrared, in a few-mode graded-index silica fiber pumped at 1.064 $$\upmu \hbox {m}$$

μ
m

, and more specifically achieving gains of hundreds of dB per meter below 0.65 $$\upmu \hbox {m}$$

μ
m

and beyond 3.5 $$\upmu \hbox {m}$$

μ
m

. Interestingly, our findings highlight the potential of graded-index fibers for enabling high-gain wavelength conversion into the strong-loss spectral region of silica. Such advancements require an accurate interpretation of intramodal and intermodal four-wave mixing processes.
The mediation role of hope in the relationship of resilience with depression, anxiety, and stress in caregivers of children and adolescents with cancer
Authors: Rambod Masoume , Nassabeh Fatemeh , Salmanpour Mahdi , Pasyar Nilofar 
Published: July 2024

AbstractThis study aimed to determine the mediation role of hope in the relationship of resilience with depression, anxiety, and stress in caregivers of children and adolescents with cancer. This cross-sectional study was conducted on 200 caregivers of children and adolescents with cancer. Adult Hope Scale, Connor-Davidson Resilience Scale, and Depression, Anxiety and Stress (DAS) scales were used for data collection. The mediator and moderator model was tested using the SPSS macro PROCESS (Model 4, and 5). The mediator model (model 4) indicated that DAS significantly correlated with resilience (β = − 0.54, t-value = − 5.01, p < 0.001), and hope (β = − 0.84, t-value = − 3.45, p = 0.0007). Hope mediated the relationship between resilience and DAS among caregivers of children and adolescents with cancer (Effect = − 0.18, SE = 0.06, 95% CI − 0.33 to − 0.06). The mediator and moderator model (model 5) showed that female caregivers had a stronger correlation between resilience and DAS when compared to their male counterparts (β = − 0.56, t-value = − 3.90, p-value = 0.0001); also, hope mediated the relationship between resilience and DAS among caregivers of children and adolescents with cancer (Effect = − 0.20, SE = 0.08, 95% CI − 0.37 to − 0.04). In conclusion, hope was a mediator, and female caregivers were a moderator in the relationship of resilience with depression, anxiety, and stress, and its promotion might be effective among caregivers of children and adolescents with cancer. It seems that resilience, female caregivers, and hope may provide good protection against depression, anxiety, and stress in caregivers of cancer patients.
Antidepressant drug use after intensive care: a nationwide cohort study
Authors: von Oelreich Erik , Eriksson Jesper , Eriksson Mikael , Larsson Emma , Oldner Anders 
Published: July 2024

AbstractModern intensive care has improved survival rates, but emerging evidence suggests a high prevalence of post-intensive care unit (ICU) health problems, including post-traumatic stress disorder, depression and anxiety. These symptoms may have a detrimental effect on quality of life and increase mortality. The primary objective of this study is to examine the extent of initiation of antidepressant medication among ICU survivors and identify the factors associated with its usage. The secondary objective is to investigate whether the use of these medications is linked to an increased mortality. The nationwide study cohort included 125,130 ICU survivors admitted between 2010 and 2017. Within the first 3 months after ICU discharge, 7% of patients initiated antidepressant medication, by 1 year 15.5% had started medication. We found no tendency to a decrease during the 2-year follow-up period. Factors associated with antidepressant use included middle age, female sex, psychiatric and somatic comorbid conditions, substance dependence, higher illness severity, and longer ICU stay. Antidepressant users had a higher mortality rate, and deaths due to external causes and suicide were more frequent in this group. This study emphasizes the importance of detecting and addressing depression in ICU survivors to improve their quality of life and reduce mortality rates.
The association between acute myocardial infarction and subsequent diagnosis of breast cancer: a nationwide, population-based cohort study
Authors: Lin Chia-Pin , Chou Shing-Hsien , Lin Yu-Sheng , Chiang Hou-Yu , Yang Chan-Keng , Lin Yu-Sheng , Chu Pao-Hsien 
Published: July 2024

AbstractCoronary artery disease (CAD) such as acute myocardial infarction (MI) share several common risk factors with cancers, and each disease may influence the prognosis of the other. Recently, acute MI was demonstrated to accelerate the outgrowth of preexisting breast cancer cells but the risk of breast cancer after MI remains unclear. This study aimed to investigate the association between acute MI and a subsequent diagnosis of breast cancer. Female patients with and without a history of acute MI were identified from nationwide databases in Taiwan. Patients with a diagnosis of cancer, MI or CAD prior to the study period were excluded. After reducing confounding through inverse probability of treatment weighting, we compared the incidence of newly diagnosed breast cancer between patients with a history of acute MI and those without. As a result, a total of 66,445 female patients were obtained, including 15,263 patients with a history of acute MI and 51,182 patients without. The incidences of breast cancer during follow-up were 1.93 (95% confidence interval [CI] 1.78–2.09) and 1.80 (95% CI 1.67–1.93) per 1,000 person-years for patients with and without a history of acute MI, respectively. The hazard ratio (HR) was 1.05 (95% CI 0.78–1.41, P = 0.756). In subgroup analysis, breast cancer risk was significantly associated with acute MI in patients using antidiabetic drugs (HR 1.27; 95% CI 1.02–1.58) and in low to moderate urbanization levels (HR 1.28; 95% CI 1.06–1.53). In conclusion, the risk of newly diagnosed breast cancer was not increased in patients with acute MI when compared to general population without MI or CAD.
Shared neural codes of recognition memory
Authors: Ambrus Géza Gergely 
Published: July 2024

AbstractRecognition memory research has identified several electrophysiological indicators of successful memory retrieval, known as old-new effects. These effects have been observed in different sensory domains using various stimulus types, but little attention has been given to their similarity or distinctiveness and the underlying processes they may share. Here, a data-driven approach was taken to investigate the temporal evolution of shared information content between different memory conditions using openly available EEG data from healthy human participants of both sexes, taken from six experiments. A test dataset involving personally highly familiar and unfamiliar faces was used. The results show that neural signals of recognition memory for face stimuli were highly generalized starting from around 200 ms following stimulus onset. When training was performed on non-face datasets, an early (around 200–300 ms) to late (post-400 ms) differentiation was observed over most regions of interest. Successful cross-classification for non-face stimuli (music and object/scene associations) was most pronounced in late period. Additionally, a striking dissociation was observed between familiar and remembered objects, with shared signals present only in the late window for correctly remembered objects, while cross-classification for familiar objects was successful in the early period as well. These findings suggest that late neural signals of memory retrieval generalize across sensory modalities and stimulus types, and the dissociation between familiar and remembered objects may provide insight into the underlying processes.
Prediction of influential nodes in social networks based on local communities and users’ reaction information
Authors: Rashidi Rohollah , Boroujeni Farsad Zamani , Soltanaghaei MohammadReza , Farhadi Hadi 
Published: July 2024

AbstractIdentifying influential nodes is one of the basic issues in managing large social networks. Identifying influence nodes in social networks and other networks, including transportation, can be effective in applications such as identifying the sources of spreading rumors, making advertisements more effective, predicting traffic, predicting diseases, etc. Therefore, it will be important to identify these people and nodes in social networks from different aspects. In this article, a new method is presented to identify influential nodes in the social network. The proposed method utilizes the combination of users’ social characteristics and their reaction information to identify influential users. Since the identification of these users in the large social network is a complex process and requires high processing power and time, clustering and identifying communities have been used in the proposed method to reduce the complexity of the problem. In the proposed method, the structure of the social network is divided into its constituent communities and thus the problem of identifying influential nodes (in the entire network) turns into several problems of identifying an influential node (in each community). The suggested method for predicting the nodes first predicts the links that may be created in the future and then identifies the influential nodes based on an iterative strategy. The proposed algorithm uses the criteria of centrality and influence domain to identify this category of users and performs the identification process both at the community and network levels. The efficiency of the method has been evaluated using real databases and the results have been compared with previous works. The results demonstrate that the proposed method provides a more suitable performance in detecting the influential nodes and is superior in terms of accuracy, recall and processing time.
Nonlinear similarity characterisation and validation of dynamic response of ship stiffened plate structure under explosion load impacts
Authors: Shi Dongyan , Wang Jiuqiang , Wang Zhikai , Wasim M. K. Helal 
Published: July 2024

AbstractThe similarity test of ship stiffened plate structures under underwater explosions is a cost-effective and efficient method to evaluate the vitality of ships and guide the design of their shock resistance. This study focuses on the nonlinear impact response model tests of ship stiffened plate structures and their similarity laws with actual ships. The vertical motion of the ship stiffened plate structure is characterized by the Hurst index, and an equivalent relationship between the Hurst index of the model and the prototype is derived from classical similarity law. Based on the Hurst index, a similarity transformation relationship between the strain signals of the model and prototype is established. To verify the conclusions, similarity experiments of underwater explosions were conducted on both the model and the prototype. The original signals were grouped by the natural vibration period to determine the variation of the Hurst index over time. The model experiment strain signals for each natural vibration period were converted and compared with the prototype experiment results to verify the method's effectiveness. Simultaneously, the Hurst index of the stiffened plate structure under explosive shock load and its similarity transformation relationship with the prototype were simulated and analyzed. This provides theoretical and technical support for conducting analogous nonlinear response experiments for ship underwater explosions.