bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dose–effects in behavioural responses of moths to light in a controlled lab experiment
Authors: Jägerbrand Annika , Andersson Petter , Nilsson Tengelin Maria 
Published: June 2023

AbstractInsects play a critical role in providing numerous ecosystem services. However, insect diversity and biomass have been declining dramatically, with artificial light being suggested as a contributing factor. Despite the importance of understanding the dose–effect responses of insects to light emissions, these responses have been rarely studied. We examined the dose–effect responses of the greater wax moth (Galleria mellonella L.) to different light intensities (14 treatments and a dark control) by observing their behavioural responses in a light-tight box equipped with a LED light source (4070 K) and infrared cameras. Our findings reveal dose–effect responses to light, as the frequency of walking on the light source increased with higher light intensity. Additionally, moths exhibited jumps in front of the light source and jump frequency increased with light intensity. No direct flight-to-light behaviour or activity suppression in response to light was observed. Based on our analysis of the dose–effect responses, we identified a threshold value of 60 cd/m2 for attraction (walking on the light source) and the frequency of jumps. The experimental design in this study offers a valuable tool for investigating dose–effect relationships and behavioural responses of various species to different light levels or specific light sources.
A novel computational method enables RNA editome profiling during human hematopoiesis from scRNA-seq data
Authors: Wu Yan , Hao Shijie , Xu Xiaojing , Dong Guoyi , Ouyang Wenjie , Liu Chao , Sun Hai-Xi 
Published: June 2023

AbstractRNA editing is a post-transcriptional modification with a cell-specific manner and important biological implications. Although single-cell RNA-seq (scRNA-seq) is an effective method for studying cellular heterogeneity, it is difficult to detect and study RNA editing events from scRNA-seq data because of the low sequencing coverage. To overcome this, we develop a computational method to systematically identify RNA editing sites of cell types from scRNA-seq data. To demonstrate its effectiveness, we apply it to scRNA-seq data of human hematopoietic stem/progenitor cells (HSPCs) with an annotated lineage differentiation relationship according to previous research and study the impacts of RNA editing on hematopoiesis. The dynamic editing patterns reveal the relevance of RNA editing on different HSPCs. For example, four microRNA (miRNA) target sites on 3ʹ UTR of EIF2AK2 are edited across all HSPC populations, which may abolish the miRNA-mediated inhibition of EIF2AK2. Elevated EIF2AK2 may thus activate the integrated stress response (ISR) pathway to initiate global translational attenuation as a protective mechanism to maintain cellular homeostasis during HSPCs’ differentiation. Besides, our findings also indicate that RNA editing plays an essential role in the coordination of lineage commitment and self-renewal of hematopoietic stem cells (HSCs). Taken together, we demonstrate the capacity of scRNA-seq data to exploit RNA editing events of cell types, and find that RNA editing may exert multiple modules of regulation in hematopoietic processes.
Honey bees (Apis mellifera) preselected for Varroa sensitive hygiene discriminate between live and dead Varroa destructor and inanimate objects
Authors: Sprau Lina , Traynor Kirsten , Rosenkranz Peter 
Published: June 2023

AbstractVarroa destructor is one of the main causes of colony losses of the western honey bee (Apis mellifera). Many efforts exist to breed honey bees resistant to V. destructor. Varroa sensitive hygiene (VSH) is a commonly selected behavioural trait; VSH workers remove the pupae of mite infested brood cells with high efficiency, interrupting the reproduction of the mite. The cues and triggers for this behaviour are not yet fully understood. To determine what elicits this removal behaviour, we examined preselected VSH workers´ responses to four different groups of objects inserted into freshly capped cells: live mites, dead mites, odour reduced mites, and glass beads. These were also compared to control cells that were opened and closed without inserting any object. The pupae in cells containing inorganic objects (glass beads) were removed at similar rates to the control, demonstrating that an object alone does not trigger a removal response. Dead and odour reduced mites were removed at a higher frequency than control cells, but less frequently than live mites. Workers sometimes removed items resting near the top of the cell without removing the pupa. Our results demonstrate that although mite odour from dead mites triggers removal behaviour, the pupa of cells containing live mites were removed more frequently, suggesting that other cues (i.e. odour from feeding wound) or signals (i.e. pupal movement to signal distress) are important. Future research should focus on elucidating these other cues or signals from the brood and mites, as mite presence alone seems to be insufficient.
Neuropsychological deficits in patients with persistent COVID-19 symptoms: a systematic review and meta-analysis
Authors: Sobrino-Relaño Saioa , Balboa-Bandeira Yolanda , Peña Javier , Ibarretxe-Bilbao Naroa , Zubiaurre-Elorza Leire , Ojeda Natalia 
Published: June 2023

AbstractLong-term persistent symptoms of COVID-19 affect 30–80% of patients who have recovered from the disease and may continue for a long time after the disease has been overcome. The duration of these symptoms over time might have consequences that affect different aspects of health, such as cognitive abilities. The main objective of this systematic review and meta-analysis was to objectify the persistent COVID-19 cognitive deficits after acute phase of infection and to summarize the existing evidence. Additionally, we aimed to provide a comprehensive overview to further understand and address the consequences of this disease. Our protocol was registered in PROSPERO (CRD42021260286). Systematic research was conducted in the Web of Science, MEDLINE, PubMed, PsycINFO, Scopus, and Google Scholar databases from January 2020 to September 2021. Twenty-five studies were included, six of which were analyzed for the meta-analysis, and consisted of 175 patients who had recovered from COVID-19 and 275 healthy individuals. Analyses of cognitive performance of post-COVID-19 patients and healthy volunteers were compared using a random-effects model. The results showed an overall medium–high effect size (g = −.68, p = .02) with a 95% CI (−1.05 to −.31), with a significantly moderate level of heterogeneity among studies (Z = 3.58, p < .001; I2 = 63%). The results showed that individuals who had recovered from COVID-19 showed significant cognitive deficits compared to controls. Future studies should carefully assess the long-term progression of cognitive impairments in patients with persistent COVID-19 symptoms, as well as the effectiveness of rehabilitation interventions. Nevertheless, there is an urgent need to know the profile to speed up development of prevention plans as well as specific interventions. Since more information is being obtained and more studies are being conducted on the subject, the need to examine this symptomatology multidisciplinary to achieve greater scientific evidence of its incidence and prevalence has become increasingly clear.
Evaluation of the orally bioavailable 4-phenylbutyrate-tethered trichostatin A analogue AR42 in models of spinal muscular atrophy
Authors: Lumpkin Casey J. , Harris Ashlee W. , Connell Andrew J. , Kirk Ryan W. , Whiting Joshua A. , Saieva Luciano , Pellizzoni Livio , Burghes Arthur H. M. , Butchbach Matthew E. R. 
Published: June 2023

AbstractProximal spinal muscular atrophy (SMA) is a leading genetic cause for infant death in the world and results from the selective loss of motor neurons in the spinal cord. SMA is a consequence of low levels of SMN protein and small molecules that can increase SMN expression are of considerable interest as potential therapeutics. Previous studies have shown that both 4-phenylbutyrate (4PBA) and trichostatin A (TSA) increase SMN expression in dermal fibroblasts derived from SMA patients. AR42 is a 4PBA-tethered TSA derivative that is a very potent histone deacetylase inhibitor. SMA patient fibroblasts were treated with either AR42, AR19 (a related analogue), 4PBA, TSA or vehicle for 5 days and then immunostained for SMN localization. AR42 as well as 4PBA and TSA increased the number of SMN-positive nuclear gems in a dose-dependent manner while AR19 did not show marked changes in gem numbers. While gem number was increased in AR42-treated SMA fibroblasts, there were no significant changes in FL-SMN mRNA or SMN protein. The neuroprotective effect of this compound was then assessed in SMNΔ7 SMA (SMN2+/+;SMNΔ7+/+;mSmn−/−) mice. Oral administration of AR42 prior to disease onset increased the average lifespan of SMNΔ7 SMA mice by ~ 27% (20.1 ± 1.6 days for AR42-treated mice vs. 15.8 ± 0.4 days for vehicle-treated mice). AR42 treatment also improved motor function in these mice. AR42 treatment inhibited histone deacetylase (HDAC) activity in treated spinal cord although it did not affect SMN protein expression in these mice. AKT and GSK3β phosphorylation were both significantly increased in SMNΔ7 SMA mouse spinal cords. In conclusion, presymptomatic administration of the HDAC inhibitor AR42 ameliorates the disease phenotype in SMNΔ7 SMA mice in a SMN-independent manner possibly by increasing AKT neuroprotective signaling.
Integrated bioinformatics and wet-lab analysis revealed cell adhesion prominent genes CDC42, TAGLN and GSN as prognostic biomarkers in colonic-polyp lesions
Authors: Tabatabaei Elmira Sadat , Mazloomnejad Radman , Rejali Leili , Forouzesh Flora , Naderi-Noukabadi Fatemeh , Khanabadi Binazir , Salehi Zahra , Nazemalhosseini-Mojarad Ehsan 
Published: June 2023

AbstractColorectal cancers are derived from intestinal polyps. Normally, alterations in cell adhesion genes expression cause deviation from the normal cell cycle, leading to cancer development, progression, and invasion. The present study aimed to investigate the elusive expression pattern of CDC42, TAGLN, and GSN genes in patients with high and low-risk polyp samples, and also colorectal cancer patients and their adjacent normal tissues. In upcoming study, 40 biopsy samples from Taleghani Hospital (Tehran, Iran) were collected, consisting of 20 colon polyps and 20 paired adjacent normal tissues. The expression of the nominated genesCDC42,TAGLN, andGSNwas analyzed using quantitative polymerase chain reaction (Q-PCR) and relative quantification was determined using the 2−ΔΔCtmethod. ROC curve analysis was performed to compare high-risk and low-risk polyps for the investigated genes. The expression of adhesion molecule genes was also evaluated using TCGA data and the correlation between adhesion molecule gene expression and immunophenotype was analyzed. The role of mi-RNAs and lncRNAs in overexpression of adhesion molecule genes was studied. Lastly, GO and KEGG were performed to identify pathways related to adhesion molecule genes expression in healthy, normal adjacent, and COAD tissues. The results showed that the expression patterns of these genes were significantly elevated in high-risk adenomas compared to low-risk polyps and normal tissues and were associated with various clinicopathological characteristics. The estimated AUC for CDC42, TAGLN, and GSN were 0.87, 0.77, and 0.80, respectively. The study also analyzed COAD cancer patient data and found that the selected gene expression in cancer patients was significantly reduced compared to high-risk polyps and healthy tissues. Survival analysis showed that while the expression level of the GSN gene had no significant relationship with survival rate, the expression of CDC42 and TAGLN genes did have a meaningful relationship, but with opposite effects, suggesting the potential use of these genes as diagnostic or prognostic markers for colorectal cancer. The present study's findings suggest that the expression pattern of CDC42, TAGLN, and GSN genes was significantly increased during the transformation of normal tissue to polyp lesions, indicating their potential as prognostic biomarkers for colorectal polyp development. Further results provide valuable insights into the potential use of these genes as diagnostic or prognostic markers for colorectal cancer. However, further studies are necessary to validate these findings in larger cohorts and to explore the underlying mechanisms of these genes in the development and progression of colorectal cancer.
Mother optimization algorithm: a new human-based metaheuristic approach for solving engineering optimization
Authors: Matoušová Ivana , Trojovský Pavel , Dehghani Mohammad , Trojovská Eva , Kostra Juraj 
Published: June 2023

AbstractThis article’s innovation and novelty are introducing a new metaheuristic method called mother optimization algorithm (MOA) that mimics the human interaction between a mother and her children. The real inspiration of MOA is to simulate the mother’s care of children in three phases education, advice, and upbringing. The mathematical model of MOA used in the search process and exploration is presented. The performance of MOA is assessed on a set of 52 benchmark functions, including unimodal and high-dimensional multimodal functions, fixed-dimensional multimodal functions, and the CEC 2017 test suite. The findings of optimizing unimodal functions indicate MOA’s high ability in local search and exploitation. The findings of optimization of high-dimensional multimodal functions indicate the high ability of MOA in global search and exploration. The findings of optimization of fixed-dimension multi-model functions and the CEC 2017 test suite show that MOA with a high ability to balance exploration and exploitation effectively supports the search process and can generate appropriate solutions for optimization problems. The outcomes quality obtained from MOA has been compared with the performance of 12 often-used metaheuristic algorithms. Upon analysis and comparison of the simulation results, it was found that the proposed MOA outperforms competing algorithms with superior and significantly more competitive performance. Precisely, the proposed MOA delivers better results in most objective functions. Furthermore, the application of MOA on four engineering design problems demonstrates the efficacy of the proposed approach in solving real-world optimization problems. The findings of the statistical analysis from the Wilcoxon signed-rank test show that MOA has a significant statistical superiority compared to the twelve well-known metaheuristic algorithms in managing the optimization problems studied in this paper.
Remodeled eX vivo muscle engineered tissue improves heart function after chronic myocardial ischemia
Authors: Cosentino Marianna , Nicoletti Carmine , Valenti Valentina , Schirone Leonardo , Di Nonno Flavio , Apa Ludovica , Zouhair Mariam , Genovese Desiree , Madaro Luca , Dinarelli Simone , Rossi Marco , Del Prete Zaccaria , Sciarretta Sebastiano , Frati Giacomo , Rizzuto Emanuele , Musarò Antonio 
Published: June 2023

AbstractThe adult heart displays poor reparative capacities after injury. Cell transplantation and tissue engineering approaches have emerged as possible therapeutic options. Several stem cell populations have been largely used to treat the infarcted myocardium. Nevertheless, transplanted cells displayed limited ability to establish functional connections with the host cardiomyocytes. In this study, we provide a new experimental tool, named 3D eX vivo muscle engineered tissue (X-MET), to define the contribution of mechanical stimuli in triggering functional remodeling and to rescue cardiac ischemia. We revealed that mechanical stimuli trigger a functional remodeling of the 3D skeletal muscle system toward a cardiac muscle-like structure. This was supported by molecular and functional analyses, demonstrating that remodeled X-MET expresses relevant markers of functional cardiomyocytes, compared to unstimulated and to 2D- skeletal muscle culture system. Interestingly, transplanted remodeled X-MET preserved heart function in a murine model of chronic myocardial ischemia and increased survival of transplanted injured mice. X-MET implantation resulted in repression of pro-inflammatory cytokines, induction of anti-inflammatory cytokines, and reduction in collagen deposition. Altogether, our findings indicate that biomechanical stimulation induced a cardiac functional remodeling of X-MET, which showed promising seminal results as a therapeutic product for the development of novel strategies for regenerative medicine.
Longitudinal whole blood transcriptomic analysis characterizes neutrophil activation and interferon signaling in moderate and severe COVID-19
Authors: Prebensen Christian , Lefol Yohan , Myhre Peder L. , Lüders Torben , Jonassen Christine , Blomfeldt Anita , Omland Torbjørn , Nilsen Hilde , Berdal Jan-Erik 
Published: June 2023

AbstractA maladaptive inflammatory response has been implicated in the pathogenesis of severe COVID-19. This study aimed to characterize the temporal dynamics of this response and investigate whether severe disease is associated with distinct gene expression patterns. We performed microarray analysis of serial whole blood RNA samples from 17 patients with severe COVID-19, 15 patients with moderate disease and 11 healthy controls. All study subjects were unvaccinated. We assessed whole blood gene expression patterns by differential gene expression analysis, gene set enrichment, two clustering methods and estimated relative leukocyte abundance using CIBERSORT. Neutrophils, platelets, cytokine signaling, and the coagulation system were activated in COVID-19, and this broad immune activation was more pronounced in severe vs. moderate disease. We observed two different trajectories of neutrophil-associated genes, indicating the emergence of a more immature neutrophil phenotype over time. Interferon-associated genes were strongly enriched in early COVID-19 before falling markedly, with modest severity-associated differences in trajectory. In conclusion, COVID-19 necessitating hospitalization is associated with a broad inflammatory response, which is more pronounced in severe disease. Our data suggest a progressively more immature circulating neutrophil phenotype over time. Interferon signaling is enriched in COVID-19 but does not seem to drive severe disease.
Phenotypic and molecular characterization of beta-lactam resistant Multidrug-resistant Enterobacterales isolated from patients attending six hospitals in Northern Nigeria
Authors: Medugu Nubwa , Tickler Isabella A. , Duru Carissa , Egah Ruth , James Abu Ocheiku , Odili Vivian , Hanga Fatima , Olateju Eyinade Kudirat , Jibir Binta , Ebruke Bernard E. , Olanipekun Grace , Tenover Fred C. , Obaro Stephen K. 
Published: June 2023

AbstractInfections caused by multi-drug resistant Enterobacterales (MDR-E) are difficult to treat and cause significant mortality, especially in developing countries. This study characterized the phenotypic and genotypic profiles of 49 randomly selected beta-lactam resistant MDR-E previously isolated from patients being managed in hospitals in Nigeria using whole genome sequencing. The study isolates exhibited 85.5% resistance to 3rd generation cephalosporins and 65.3% resistance to carbapenems. The blaTEM-1B (29, 59.2%),blaCTX-M-15 (38, 77.6%), and blaNDM-1 (17, 51.5%) were the most common penicillinase, ESBL, and carbapenem resistant genes across isolates, respectively. Seventeen (45%) of blaCTX-M-15 was carried on the insertion sequence ISEc9 while blaNDM-1 (11, 64.7%) were associated with ISEc33. None of the 21 plasmids detected were associated with β-lactamase genes. Higher resistance rates were found in E. coli ST-88 (n = 2) and the high-risk ST-692 (n = 2). For Klebsiella species, the high-risk clones ST-476 (n = 8) and ST-147 (n = 3) predominated and had higher phenotypic resistance rates and higher number of AMR genes. The mechanisms and pattern of antibiotic resistance differ from patterns previously described with isolates harbouring a wide range of AMRGs. The detection of several chromosomally mediated carbapenemases in our study also represents a significant finding that warrants further investigation to better understand its’ implications for clinical practice and public health. The selected MDR-Es were found to be pan-susceptible to tigecycline and had very low resistance to fosfomycin, suggesting a potential for these as empiric treatments. A surveillance approach incorporating both conventional laboratory techniques and modern molecular techniques is essential for the comprehensive characterization of the emergence and dissemination of antimicrobial resistance in Enterobacterales infections within Nigeria.
Morphogenesis in space offers challenges and opportunities for soft matter and biophysics
Authors: Ben Amar Martine , Ciarletta Pasquale , Haas Pierre A. 
Published: June 2023

AbstractThe effects of microgravity on soft matter morphogenesis have been documented in countless experiments, but physical understanding is still lacking in many cases. Here we review how gravity affects shape emergence and pattern formation for both inert matter and living systems of different biological complexities. We highlight the importance of building physical models for understanding the experimental results available. Answering these fundamental questions will not only solve basic scientific problems, but will also enable several industrial applications relevant to space exploration.
Exploring residential built-up form typologies in Delhi: a grid-based clustering approach towards sustainable urbanisation
Authors: Marwal Aviral , Silva Elisabete A. 
Published: June 2023

AbstractPrevious studies have established a significant link between urban form and sustainability. However, the diversity of micro-scale urban forms in cities in the global south has received limited attention, hindered by the lack of neighbourhood-level spatial data and maps, which poses challenges in exploring micro-urban form features. The study addresses this gap using a grid-based k-means clustering algorithm to identify residential built-up form typologies in Delhi and assess their impact on sustainable urbanisation. The algorithm clusters 100×100 metre grid cells based on their attributes of accessibility, built-up density, and street design. The results show six distinct built-up form typologies in Delhi. However, only 19% of residential areas meet the criteria for sustainable urbanisation, highlighting the need for planning interventions in most areas. The study methodology can be applied to analyse micro-scale urban form features in other cities in the global south, providing a fresh perspective on urbanisation research.