bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient low cost means of biophysical gene transfection in primary cells
Authors: Huang Shudi , Henderson Tyler R. , Dojo Soeandy Chesarahmia , Lezhanska Anastasiya , Henderson Jeffrey T. 
Published: June 2024

AbstractEfficient, facile gene modification of cells has become an indispensable part of modern molecular biology. For the majority of cell lines and several primary populations, such modifications can be readily performed through a variety of methods. However, many primary cell lines such as stem cells frequently suffer from poor transfection efficiency. Though several physical approaches have been introduced to circumvent these issues, they often require expensive/specialized equipment and/or consumables, utilize substantial cell numbers and often still suffer from poor efficiency. Viral methods are capable of transducing difficult cellular populations, however such methods can be time consuming for large arrays of gene targets, present biohazard concerns, and result in expression of viral proteins; issues of concern for certain experimental approaches. We report here a widely applicable, low-cost (< $100 CAD) method of electroporation, applicable to small (1–10 μl) cell volumes and composed of equipment readily available to the average investigator. Using this system we observe a sixfold increase in transfection efficiency in embryonic stem cell lines compared to commercial devices. Due to efficiency gains and reductions in volume and applied voltage, this process improves the survival of sensitive stem cell populations while reducing reagent requirements for protocols such as Cas9/gRNAs transfections.
Optogenetic inhibition of the limbic corticothalamic circuit does not alter spontaneous oscillatory activity, auditory-evoked oscillations, and deviant detection
Authors: Gonzalez-Burgos Irene , Valencia Miguel , Redondo Roger , Janz Philipp 
Published: June 2024

AbstractAberrant neuronal circuit dynamics are at the core of complex neuropsychiatric disorders, such as schizophrenia (SZ). Clinical assessment of the integrity of neuronal circuits in SZ has consistently described aberrant resting-state gamma oscillatory activity, decreased auditory-evoked gamma responses, and abnormal mismatch responses. We hypothesized that corticothalamic circuit manipulation could recapitulate SZ circuit phenotypes in rodent models. In this study, we optogenetically inhibited the mediodorsal thalamus-to-prefrontal cortex (MDT-to-PFC) or the PFC-to-MDT projection in rats and assessed circuit function through electrophysiological readouts. We found that MDT–PFC perturbation could not recapitulate SZ-linked phenotypes such as broadband gamma disruption, altered evoked oscillatory activity, and diminished mismatch negativity responses. Therefore, the induced functional impairment of the MDT–PFC pathways cannot account for the oscillatory abnormalities described in SZ.
Basketball technique action recognition using 3D convolutional neural networks
Authors: Wang Jingfei , Zuo Liang , Cordente Martínez Carlos 
Published: June 2024

AbstractThis research investigates the recognition of basketball techniques actions through the implementation of three-dimensional (3D) Convolutional Neural Networks (CNNs), aiming to enhance the accurate and automated identification of various actions in basketball games. Initially, basketball action sequences are extracted from publicly available basketball action datasets, followed by data preprocessing, including image sampling, data augmentation, and label processing. Subsequently, a novel action recognition model is proposed, combining 3D convolutions and Long Short-Term Memory (LSTM) networks to model temporal features and capture the spatiotemporal relationships and temporal information of actions. This facilitates the facilitating automatic learning of the spatiotemporal features associated with basketball actions. The model’s performance and robustness are further improved through the adoption of optimization algorithms, such as adaptive learning rate adjustment and regularization. The efficacy of the proposed method is verified through experiments conducted on three publicly available basketball action datasets: NTURGB + D, Basketball-Action-Dataset, and B3D Dataset. The results indicate that this approach achieves outstanding performance in basketball technique action recognition tasks across different datasets compared to two common traditional methods. Specifically, when compared to the frame difference-based method, this model exhibits a significant accuracy improvement of 15.1%. When compared to the optical flow-based method, this model demonstrates a substantial accuracy improvement of 12.4%. Moreover, this method showcases strong robustness, accurately recognizing actions under diverse lighting conditions and scenes, achieving an average accuracy of 93.1%. The research demonstrates that the method reported here effectively captures the spatiotemporal relationships of basketball actions, thereby providing reliable technical assessment tools for basketball coaches and players.
Dynamic analysis and optimal control of knowledge diffusion model in regional innovation ecosystem under digitalization
Authors: He Zitong , Wang Haijun , Hu Yuhan , Ma Xiaolin , Zhao Huiyan 
Published: June 2024

AbstractKnowledge diffusion in regional innovation ecosystems is an important factor that influences the regional innovation efficiency. In regional innovation ecosystems under digital empowerment, the knowledge diffusion enables the optimal allocation of innovation resources and promotes the sustainable development and ecological evolution of regional innovation ecosystems. In this paper, a SEIR (Susceptible–Exposed–Infected–Recovered) model is proposed for knowledge diffusion in regional innovation ecosystems under digitization. The basic reproduction number of the proposed model is calculated and its stability is validated. Finally, the expressions for the optimal control system and the optimal control parameters are presented. According to the research conclusions of this paper, the knowledge-diffusion ability of innovation agents in an innovation ecosystem affects the knowledge diffusion in a system; the contact rate between innovation agents affects the efficiency of knowledge diffusion in the system and the structure of the system; the digital transmission ability of innovation agents affects the breadth of knowledge diffusion in the system; and the self-learning ability of innovation agents affects the efficiency of knowledge diffusion in the system.The digital technologies help heterogeneous innovation agents in regional innovation ecosystems to break down the knowledge silos. At the same time, the digital technologies enhance the ability of innovation agents to absorb and learn knowledge in regional innovation ecosystems under digitization, thereby increasing the infection rate of knowledge diffusion in such systems.These conclusions extend the theoretical boundaries of innovation ecosystems and knowledge diffusion and offer management implications for enterprises and governments in decision-making.
Heteroatom-doped carbon dots from medicinal plants as novel biomaterials for as-use biomedical applications in comparison with synthetic drug, zaltoprofen
Authors: Kota Sobha , Dumpala Pradeep , Sajja Radhika , Anantha Ratnakumari 
Published: June 2024

AbstractFN-doped carbon dots were synthesized using powdered leaves of Moringa oleifera L./Chromolaena odorata L./Tridax procumbens L./Tinospora cordifolia L./ and Lantana camara L., along with a precursor called 4,5-difluoro-1,2-benzenediamine (DFBD) and compared against the drug zaltoprofen derived carbon dots. They were assessed for their optical and structural characteristics using photoluminescence (optimal emission λ of 600 nm), vibrational (FTIR) spectroscopy (characteristic wave numbers of 1156 and 1269 cm−1 for C–F), as well as X-ray diffraction (XRD) (highest intensity at 27.56°) and high-resolution transmission electron microscopy (HR-TEM) (particles in the size range of 15–20 nm). Further, field emission scanning electron microscopy (FESEM) / energy dispersive spectroscopy (EDX) indicated FN doping of oval/oblong carbon dots. Membrane protection in percent is found to be 55.3 and 80.4 for FN-CDs and Z-FN-CDs respectively. The DPPH-free radical scavenging activity by FN-CDs was 69.4%, while with Z-FN-CDs, it was 54.2%. When tested on six bacterial strains (three each for gram-positive and gram-negative), the FN-CDs displayed a halo (ZOI) between 9 and 19 mm, whereas the Z-FN-CDs displayed a clearance zone between 9 and 17 mm. The FN-CDs showed significant emission-red-shift effects and demonstrated concentration-dependent biocompatibility and viability in neuroblastoma and beta-TC6-cell lines.
Gastroenterologist and surgeon perceptions of recommendations for optimal endoscopic localization of colorectal neoplasms
Authors: Johnson Garrett , Singh Harminder , Helewa Ramzi M. , Sibley Kathryn M. , Reynolds Kristin A. , El-Kefraoui Charbel , Doupe Malcolm B. 
Published: June 2024

AbstractNational consensus recommendations have recently been developed to standardize colorectal tumour localization and documentation during colonoscopy. In this qualitative semi-structured interview study, we identified and contrast the perceived barriers and facilitators to using these new recommendations according to gastroenterologists and surgeons in a large central Canadian city. Interviews were analyzed according to the Consolidated Framework for Implementation Research (CFIR) through directed content analysis. Solutions were categorized using the Expert Recommendations for Implementing Change (ERIC) framework. Eleven gastroenterologists and ten surgeons participated. Both specialty groups felt that the new recommendations were clearly written, adequately addressed current care practice tensions, and offered a relative advantage versus existing practices. The new recommendations appeared appropriately complex, applicable to most participants, and could be trialed and adapted prior to full implementation. Major barriers included a lack of relevant external or internal organizational incentives, non-existing formal feedback processes, and a lack of individual familiarity with the evidence behind some recommendations. With application of the ERIC framework, common barriers could be addressed through accessing new funding, altering incentive structures, changing record systems, educational interventions, identifying champions, promoting adaptability, and employing audit/feedback processes. Future research is needed to test strategies for feasibility and effectiveness.
An immunogenic cell death-related lncRNA signature correlates with prognosis and tumor immune microenvironment in bladder cancer
Authors: Luo Jinhong , Luo Feiye , Li Qin , Liu Qinghong , Wang Jinshan 
Published: June 2024

AbstractImmunogenic cell death (ICD) is a newly discovered form of cellular demise that triggers adaptive immune responses mediated by T cells. However, the immunogenic cell death-related lncRNAs (ICDRLs) involved in bladder cancer (BC) development and progression remain to be further elucidated. Molecular profiling data and clinicopathological information for BC patients were obtained from TCGA, and the ICDRGs list was obtained from published literature. For the identification of ICDRLs, Pearson co-expression analysis was performed, and a prognostic signature based on 13 ICDRLs was constructed by univariate assays and LASSO assays. Herein, an ICDRLSig consisting of 13 ICDRLs was constructed. KM curves and ROC curves demonstrated that the constructed signature in the TCGA training, testing, entire and external sets have good predictive performance. Multivariate assays illuminated that the signature is an independent predictor for BC patients’ OS, exhibiting greater predictive power for the survival than traditional clinicopathological features. Additionally, patients in the high-ICDRLSig risk subgroup had more abundant immune infiltration, higher immune checkpoint gene expression, lower TMB and poorer response to immunotherapy. We have developed a novel ICDRLSig that can be exploited for survival prediction and provide a reference for further individualized treatment.
Single-cell RNA-seq reveals the effects of the FecB mutation on the transcriptome profile in ovine cumulus cells
Authors: Guo Xiaofei , Fang Yi , Liang Rong , Wang Xiangyu , Zhang Jinlong , Dong Chunxiao , Wang Biao , Liu Yu , Chu Mingxing , Zhang Xiaoshen , Zhong Rongzhen 
Published: June 2024

AbstractGenetic variations in the ovine ovulation rate, which are associated with the FecB mutation, provide useful models by which to explore the mechanisms regulating the development of mammalian antral follicles. In order to study the effects of the FecB mutation on cumulus cell differentiation, preovulatory follicles were aspirated and cumulus cells were isolated from three FecB genotypes (homozygous, heterozygous and wild type) of Small Tail Han (STH) sheep superstimulated with FSH. Transcriptome information from tens of thousands of cumulus cells was determined with the 10 × Genomics single-cell RNA-seq technology. Under the superovulation treatment, the observed number of preovulatory follicles in the ovaries of FecB carriers was still significantly higher than that in the wild-type (P < 0.05). The expression patterns of cumulus cells differed between FecB carriers and wild-type ewes. The screened cumulus cells could also be further divided into different cell clusters, and the differentiation states and fates of each group of cumulus cells also remained different, which supports the notion that heterogeneity in gene expression is prevalent in single cells. The oxidative phosphorylation pathway was significantly enriched in differentially expressed genes among the cell differentiation branch nodes of cumulus cells and among the differentially expressed genes of cumulus cells from the three genotypes. Combined with the important role of oxidative phosphorylation in the maturation of COCs, we suggest that the oxidative phosphorylation pathway of cumulus cells plays a crucial role in the differentiation process of cumulus cells and the mutation effect of the FecB gene.
Prediction of land use for the next 30 years using the PLUS model's multi-scenario simulation in Guizhou Province, China
Authors: Liu Juncong , Liu Bangyu , Wu Linjing , Miao Haiying , Liu Jiegang , Jiang Ke , Ding Hu , Gao Weichang , Liu Taoze 
Published: June 2024

AbstractLand use changes significantly impact the structure and functioning of ecosystems. The current research focus lies in how to utilize economic and policy instruments to regulate conflicts among stakeholders effectively. The objective is to facilitate rational planning and sustainable development of land utilization resources. The PLUS model integrates a rule-based mining method for land expansion analysis and a CA model based on multi-type stochastic seeding mechanism, which can be used to mine the driving factors of land expansion and predict the patch-level evolution of land use landscapes. Using the PLUS model, a simulation was conducted to study the future land use distribution in the research area over the next 30 years. Based on land use data from Guizhou Province in 2000, 2010, and 2020, a total of 16 driving factors were selected from three aspects: geographical environment, transportation network, and socio-economic conditions. Four scenarios, namely natural development, urban development, ecological conservation, and farmland rotection, were established. Comparative analysis of the simulated differences among the various scenarios was performed. (1) The overall accuracy of the land use simulation using the PLUS model in the study area was 0.983, with a Kappa coefficient of 0.972 and a FoM coefficient of 0.509. The research accuracy meets the simulation requirements. (2) Through the simulation of four different scenarios, the study investigated the land use changes in Guizhou Province over the next 30 years. Each scenario exhibited distinct impacts on land utilization. Comprehensive comparison of the different simulation results revealed that the farmland protection scenario aligns with the sustainable development goals of the research area. Currently, there is a relative scarcity of research on land use simulation, particularly in model application, for Guizhou Province. This study aims to provide a reference for the rational planning of land resources and high-quality urban construction in Guizhou, promoting the high-quality economic development in tandem with advanced ecological and environmental protection.
SNX16 is required for hepatocellular carcinoma survival via modulating the EGFR-AKT signaling pathway
Authors: Yuan Lebin , Meng Yanqiu , Xiang Jiajia 
Published: June 2024

AbstractSorting nexin 16 (SNX16), a pivotal sorting nexin, emerges in tumor progression complexity, fueling research interest. However, SNX16’s biological impact and molecular underpinnings in hepatocellular carcinoma (HCC) remain elusive. This study probes SNX16’s function, clinical relevance via mRNA, and protein expression in HCC. Overexpression/knockdown assays of SNX16 were employed to elucidate impacts on HCC cell invasion, proliferation, and EMT. Additionally, the study delved into SNX16’s regulation of the EGFR-AKT signaling cascade mechanism. SNX16 overexpression in HCC correlates with poor patient survival; enhancing proliferation, migration, invasion, and tumorigenicity, while SNX16 knockdown suppresses these processes. SNX16 downregulation curbs phospho-EGFR, dampening AKT signaling. EGFR suppression counters SNX16-overexpression-induced HCC proliferation, motility, and invasiveness. Our findings delineate SNX16’s regulatory role in HCC, implicating it as a prospective therapeutic target.
Molecular profiling of pediatric and young adult colorectal cancer reveals a distinct genomic landscapes and potential therapeutic avenues
Authors: Busico A. , Gasparini P. , Rausa E. , Cattaneo L. , Bozzi F. , Silvestri M. , Capone I. , Conca E. , Tamborini E. , Perrone F. , Vitellaro M. , Ricci M.T. , Casanova M. , Chiaravalli S. , Bergamaschi L. , Massimino M. , Milione M. , Sozzi G. , Pruneri G. , Ferrari A. , Signoroni S. 
Published: June 2024

AbstractColorectal cancer (CRC) is a global health concern, and the incidence of early onset (EO) CRC, has an upward trend. This study delves into the genomic landscape of EO-CRC, specifically focusing on pediatric (PED) and young adult (YA) patients, comparing them with adult (AD) CRC. In this retrospective monocentric investigation, we performed targeted next-generation sequencing to compare the mutational profile of 38 EO-CRCs patients (eight PED and 30 YA) to those of a ‘control group’ consisting of 56 AD-CRCs. Our findings reveal distinct molecular profiles in EO-CRC, notably in the WNT and PI3K-AKT pathways. In pediatrics, we observed a significantly higher frequency of RNF43 mutations, whereas APC mutations were more prevalent in adult cases. These observations suggest age-related differences in the activation of the WNT pathway. Pathway and copy number variation analysis reveal that AD-CRC and YA-CRC have more similarities than the pediatric patients. PED shows a peculiar profile with CDK6 amplification and the enrichment of lysine degradation pathway. These findings may open doors for personalized therapies, such as PI3K-AKT pathway inhibitors or CDK6 inhibitors for pediatric patients. Additionally, the distinct molecular signatures of EO-CRC underscore the need for age-specific treatment strategies and precision medicine. This study emphasizes the importance of comprehensive molecular investigations in EO-CRCs, which can potentially improve diagnostic accuracy, prognosis, and therapeutic decisions for these patients. Collaboration between the pediatric and adult oncology community is fundamental to improve oncological outcomes for this rare and challenging pediatric tumor.
Sex-specific relationship patterns between body morphology and maturity status with change of direction and agility in elite adolescent volleyball players
Authors: Koźlenia Dawid , Popowczak Marek , Horička Pavol , Šimonek Jaromir , Domaradzki Jarosław 
Published: June 2024

AbstractThis study explored sex-specific patterns in the relationship between maturity, body morphology, and change of direction (COD) and agility (AG) in adolescent volleyball players. The sample comprised 22 males and 24 females aged 15–17 with at least 4 years of sports experience. Measurements included body height, weight, muscle and fat mass, leg length, and center of mass. The study determined the Age of Peak Height Velocity (APHV) and evaluated sensorimotor ability through pre-planned COD and not-planned AG five-time shuttle runs, measuring the time difference as the index of reactivity. Positive correlations were found between COD and AG with fat mass index (FMI) in boys, while negative relative lower limb length (rLL) correlated with COD. In females, age of peak height velocity (APHV) showed a significant negative relationship with sensorimotor ability. Linear and polynomial regressions confirmed predictive and curvilinear relationships, respectively. Cluster analysis identified different associations in boys and girls, emphasizing sex-specific patterns. Body fat percentage had a negative impact on COD-AG in boys, while the optimal lower limb length proportion positively influenced COD due to enhanced maneuverability. Maturation affected sensorimotor abilities in girls. The findings suggest a need for a tailored approach to COD-AG development based on sex-specific considerations in adolescent volleyball players.
Age-related differences in network controllability are mitigated by redundancy in large-scale brain networks
Authors: Stanford William , Mucha Peter J. , Dayan Eran 
Published: June 2024

AbstractThe aging brain undergoes major changes in its topology. The mechanisms by which the brain mitigates age-associated changes in topology to maintain robust control of brain networks are unknown. Here we use diffusion MRI data from cognitively intact participants (n = 480, ages 40–90) to study age-associated differences in the average controllability of structural brain networks, topological features that could mitigate these differences, and the overall effect on cognitive function. We find age-associated declines in average controllability in control hubs and large-scale networks, particularly within the frontoparietal control and default mode networks. Further, we find that redundancy, a hypothesized mechanism of reserve, quantified via the assessment of multi-step paths within networks, mitigates the effects of topological differences on average network controllability. Lastly, we discover that average network controllability, redundancy, and grey matter volume, each uniquely contribute to predictive models of cognitive function. In sum, our results highlight the importance of redundancy for robust control of brain networks and in cognitive function in healthy-aging.