bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanotoxicity of multifunctional stoichiometric cobalt oxide nanoparticles (SCoONPs) with repercussions toward apoptosis, necrosis, and cancer necrosis factor (TNF-α) at nano-biointerfaces
Authors: Kumar Rajiv , Chhikara Bhupender S , Er Zeybekler Simge , Gupta Dhruv Sanjay , Kaur Ginpreet , Chhillar Mitrabasu , Aggarwal Anil K , Rahdar Abbas 
Published: September 2023

AbstractIntroductionApoptosis, necrosis, and cancer necrosis factor (TNF-a) are all impacted by the nanotoxicity of multifunctional stoichiometric cobalt oxide nanoparticles (SCoONPs) at nano-biointerfaces. The creation of multi-functional nanoparticles has had a considerable impact on the transport of drugs and genes, nanotheranostics (in-vivo imaging, concurrent diagnostics), interventions for external healing, the creation of nano-bio interfaces, and the instigation of desired changes in nanotherapeutics.ObjectivesThe quantitative structure-activity relationships, chemical transformations, biological interactions as well as toxicological analyses are considered as main objectives. Discrete dimensions of SCoNPs-cell interaction interfaces, their characteristic physical features (size, shape, shell structure, and surface chemistry), impact on cell proliferation and differentiation are the key factors responsible for nanotoxicity.MethodsThe development of multi-functional nanoparticles has been significant in drug/gene delivery, nanotheranostics (in-vivo imaging, coinciding diagnostics), and external healing interventions, designing a nano-bio interface, as well as inciting desired alterations in nanotherapeutics. Every so often, the cellular uptake of multi-functional cobalt [Co, CoO, Co2(CO)8 and Co3O4] nanoparticles (SCoONPs) influences cellular mechanics and initiates numerous repercussions (oxidative stress, DNA damage, cytogenotoxicity, and chromosomal damage) in pathways, including the generation of dysregulating factors involved in biochemical transformations.ResultsThe concerns and influences of multifunctional SCoNPs on different cell mechanisms (mitochondria impermeability, hydrolysis of ATP, the concentration of Ca2+, impaired calcium clearance, defective autophagy, apoptosis, and necrosis), and interlinked properties (adhesion, motility, and internalization dynamics, role in toxicity, surface hydrophilic and hydrophobicity, biokinetics and biomimetic behaviors of biochemical reactions) have also been summarized. SCoONPs have received a lot of interest among the nanocarriers family because of its advantageous qualities such as biodegradability, biocompatibility, nontoxicity, and nonimmunogenicity.ConclusionVarious applications, such as bio-imaging, cell labeling, gene delivery, enhanced chemical stability, and increased biocompatibility, concerning apoptosis, necrosis, and nano-bio interfaces, along with suitable examples. In this analysis, the multi-functional cobalt [Co, CoO, Co2(CO)8 and Co3O4] nanoparticles (SCoNPs) intricacies (cytogenotoxicity, clastogenicity, and immunomodulatory), nanotoxicity, and associated repercussions have been highlighted and explained.
Voluntary thermal maximum of grassland vipers (Vipera spp.): environmental drivers and local adaptation
Authors: Radovics Dávid , Sos Tibor , Mebert Konrad , Üveges Bálint , Budai Mátyás , Rák Gergő , Szabolcs Márton , Lengyel Szabolcs , Mizsei Edvárd 
Published: September 2023

Abstract
The thermal tolerance of ectotherms is a critical factor that influences their distribution, physiology, behaviour, and, ultimately, survival. Understanding the factors that shape thermal tolerance in these organisms is, therefore, of great importance for predicting their responses to forecasted climate warming. Here, we investigated the voluntary thermal maximum (VTmax) of nine grassland viper taxa and explored the factors that influence this trait. The small size of these vipers and the open landscape they inhabit render them particularly vulnerable to overheating and dehydration. We found that the VTmax of grassland vipers is influenced by environmental temperature, precipitation, short-wave flux, and individual body size, rather than by phylogenetic relatedness. Vipers living in colder environments exhibited a higher VTmax, contradicting the hypothesis that environmental temperature is positively related to VTmax. Our findings emphasize the importance of considering local to regional adaptations and environmental conditions when studying thermal physiology and the evolution of thermal tolerance in ectotherms.
Food fraud: insights from investigating a near-fatal poisoning with global implications
Authors: Cao Zhao , Yemets Masha , Muneem Sadia , Shannon Kyle , Gowher Fatima , Malloy Jennifer , Kafka Erin , Mitchell Clifford , King Joshua , Urban Sinisa 
Published: September 2023

SUMMARYRisks of food fraud have been exacerbated by ongoing supply-chain shortages and reduced regulatory oversight caused by the COVID19 pandemic. Since food fraud cases involve adulterants that are deliberately disguised, resulting poisonings are especially difficult to investigate and treat. We encountered a near-fatal poisoning with “weight-loss candlenuts” that are readily available online. We leveraged state-of-the-art high-resolution mass spectrometry (HRMS) and discovered that commonly used spectral libraries and toxin/poison standards panels do not contain the materials needed to identify the causative agents of this nearly lethal poisoning. By building new methods, we ultimately found ‘Nuez de la India’ contain high levels of uncommon cardiac glycosides, while deploying HRMS as a novel ‘chemical fingerprinting’ tool revealed them to be mislabeled yellow oleander seeds. Our work presents a rapid investigative strategy to empower future investigations, and provides guiding principles to food safety programs for treating, and indeed preventing, these potentially fatal poisonings that are increasing worldwide.
The Patient Safety Curriculum: An Interventional Study on the Effectiveness of Patient Safety Education for Jordanian Nursing Students
Authors: Al-Nawafleh Ahmad H. , Musleh Sultan , Nawafleh Nofal 
Published: September 2023

AbstractThe purpose of the study was to assess the effectiveness of the World Health Organization’s (WHO) patient safety curriculum (PSC) in improving the patient safety education for nursing students in Jordanian higher education programmes.MethodsAn interventional design adopting a pre-test and post-test was used. A questionnaire survey was administered to 373 nursing students before and after the curriculum. Students were asked to complete pre-test and post-test questionnaires on self-awareness of patient safety.Resultsstudents had moderate knowledge of factors that influence patient safety and scored as the highest, (mean 3.45, SD 0.94). The greatest improvement was in the role of the health organisation in error reporting (the mean difference was 0.97, P=0.001). Taking into consideration the essential measurements, the results obtained after the post-test regarding the two patient safety topics showed a significant increase after completing the training, demonstrating that the patient safety course was effective.Conclusionthe study highlights the importance of developing a curriculum in nursing schools that incorporates patient safety education. The WHO PSC guide can be a great start in this domain.
Estimating the distribution of reedPhragmites australisin Britain demonstrates challenges of remotely sensing rare land cover types at large spatial scales
Authors: Davies Jacob G. , Dytham Calvin , Robinson Robert A , Beale Colin M. 
Published: September 2023

AbstractReedPhragmites australisis important for biodiversity, for ecosystem services, and as a resource for humans. Already one of the mostly widely distributed wetland plants globally, reed has recently expanded outside of its native range, modifying ecosystems. However, like most wetland plant communities, reedbed has rarely been mapped at large geographical scales, restricting the information available to ecologists and resource managers. Using Sentinel-2 data and machine learning in open-source software, we produce the first remotely-sensed reedbed map of Britain. A random forest was trained on 79.2 ha of reedbed and 2,719.2 ha of non-reedbed land cover, using free online imagery. Accuracy was high within the training area (AUC > 0.998); however, field validation accuracy was much lower (AUC = 0.671), with many false positives (commission error of 93.4%). A similar workflow carried out in Google Earth Engine, using nearly an order of magnitude more images, gave a lower commission error but a disproportionately higher omission error. Due to the classification error, our map is more useful for a non-spatial estimate of the overall reedbed extent in Britain, rather than for the spatial location of reedbeds in Britain. Using the known commission and omission error, we estimate that in 2015 - 2017 c. 7800 ha of Britain was reedbed. Our study highlights the issues that present enduring barriers to accurate land cover classification at large spatial scales, perhaps suggesting fruitful areas for technological innovation. Even with a ‘big data’ approach and even if technological issues are resolved, ecological factors such as confusion land cover types and geographical variation in temporal reflectance function will probably continue to impose upper limits on the size of area for which land cover can be classified accurately, and therefore on the utility of remote sensing to resource managers.
Pre-zygotic mate selection affects progeny fitness and is only partially correlated with the expression ofNaS-like RNases
Authors: Baraniecka Patrycja , Seibt Wibke , Groten Karin , Kessler Danny , McGale Erica , Gase Klaus , Baldwin Ian T. , Pannell John R. 
Published: September 2023

SummaryNicotiana attenuatastyles preferentially select pollen from accessions with corresponding expression patterns ofNaS-like-RNases (SLRs), and the post-pollination ethylene burst (PPEB) is an accurate predictor of seed siring success. However, the ecological consequences of mate selection, its effect on the progeny, and the role of SLRs in the control of ethylene signaling are still not well understood.We explored the link between the magnitude of the ethylene burst and transcript and protein abundance of the SLRs in a set of recombinant inbred lines (RILs) and investigated the fitness consequences of mate selection for the next generation. Genome Wide Association Study (GWAS) identified novel candidate genes potentially involved in the control of mate selection.We found that high levels of PPEB are associated with the absence of SLR2 but not with the expression of SLR1 in most of the tested RILs. Maternal genotypes that favor certain pollen produce offspring with longer roots when pollinated with these donors, but the selection for beneficial traits is abolished when the maternal genotype selects only against certain pollen donors.We conclude that mate selection mechanisms affect the offspring number and performance in ways that might be adaptive.
NanoLAS: a Comprehensive Nanobody Database with Data Integration, Consolidation, and Application
Authors: Xiong Shuchang , Liu Zhengwen , Yi Xin , Liu Kai , Huang Bingding , Wang Xin 
Published: September 2023

AbstractNanobodies, a unique subclass of antibodies first discovered in camelid animals, are composed solely of a single heavy chain’s variable region (VHH). Their significantly reduced molecular weight, in comparison to conventional antibodies, confers numerous advantages in the treatment of various diseases. As research and applications involving nanobodies expand, the quantity of identified nanobodies is also rapidly growing. However, the existing antibody databases are deficient in type and coverage, failing to satisfy the comprehensive needs of researchers and thus, impeding progress in nanobody research.In response to this, we have amalgamated data from multiple sources to successfully assemble a new and comprehensive nanobody database. This database has currently included the latest nanobody data, provides researchers with an excellent search and data display interface, thus facilitating the progression of nanobody research and their application in disease treatment.In summary, the newly constructed Nanobody Library and Archive System (NanoLAS) may significantly enhance the retrieval efficiency and application potential of nanobodies. We envision that NanoLAS will serve as an accessible, robust, and efficient tool for nanobody research and development, propelling advancements in the field of biomedicine.Database URLhttps://www.nanolas.cloud
Gel-Shrink Softlithography: Enabling 3D Tissue Culture Microstructure Miniaturization and Tacky Super-Soft Material Molding
Authors: Huang Cheng-Kuang , Lim Chwee Teck 
Published: September 2023

AbstractIn this study, we introduce an innovative hydrogel soft lithography technique that leverages the significant volume change of hydrogels during hydration. Through a systematic desiccation process applied to hydrogels containing microfeatures, we achieved a remarkable 2-fold reduction in feature dimensions. These shrunken hydrogel structures were then readily molded using standard soft lithography methods. Furthermore, we demonstrated the technique’s utility in rectifying surface imperfections commonly found in 3D printed structures, offering promising prospects in fields like tissue engineering. Additionally, our study discovered a unique capability of hydrated hydrogel molds in molding super-soft, tacky elastomeric materials, exemplified by CY25-276 and low cross-linker ratio PDMS. This development opens doors to studying cellular forces through traction force microscopy to a broader spectrum of 3D structural contexts. In support of our efforts in microfabrication advancement, we explored multicellular responses to surface curvatures of diminishing dimensions. Our findings reveal a curvature-dependent alignment pattern: cells residing on convex surfaces align with the direction of least curvature, while those in concave regions align with the direction of the strongest curvature. These results underscore the critical influence of geometric complexity in biological systems and highlight the need for continuously improving methods to replicate geometric qualities relevant to these environments.
Cognitive tasks, anatomical MRI, and functional MRI data evaluating the construct of self-regulation
Authors: Bissett Patrick G. , Eisenberg Ian W. , Shim Sunjae , Rios Jaime Ali H. , Jones Henry M. , Hagen Mckenzie P. , Enkavi A. Zeynep , Li Jamie K. , Mumford Jeanette A. , MacKinnon David P. , Marsch Lisa A. , Poldrack Russell A. 
Published: September 2023

AbstractWe describe the following shared data from N=103 healthy adults who completed a broad set cognitive tasks, surveys, and neuroimaging measurements to examine the construct of self-regulation. The neuroimaging acquisition involved task-based fMRI, resting fMRI, and structural MRI. Each subject completed the following ten tasks in the scanner across two 90- minute scanning sessions: attention network test (ANT), cued task switching, Columbia card task, dot pattern expectancy (DPX), delay discounting, simple and motor selective stop signal, Stroop, a towers task, and a set of survey questions. Subjects also completed resting state scans. The dataset is shared openly through the OpenNeuro project, and the dataset is formatted according to the Brain Imaging Data Structure (BIDS) standard.
Mechanisms analysis for Formononetin counteracted-Osimertinib resistance in Non-small-cell lung cancer cells: from the insight into the gene transcriptional level
Authors: Yin Runyang , Gao Jing , Liu Yang 
Published: September 2023

AbstractBackgroundsOsimertinib resistance in Non-Small-Cell Lung Cancers (NSCLC) is a difficult problem to be solved in clinic. Formononetin is one of the main isoflavone components, which has strong anti-cancer effects in NSCLC. However, the potential effects and the mechanisms of Formononetin to counteract the Osimertinib resistant in NSCLC is remain to be uncovered.MethodsOsimertinib-resistant NSCLC cell line (H1975_OR) was generated by increasingly adding of Osimertinib in H1975 cell culture medium. The Formononetin was used to induce H1975_OR cell apoptosis an to inhibit cell proliferation and clonal formation. The RNA-sequencing was used to study the potential mechanisms for Formononetin to counteract the Osimertinib resistant in NSCLC.ResultsFormononetin could significantly induced cell apoptosis, whereas, dramatically inhibited cell proliferation and clinal formation in H1975_OR cells. Formononetin induced tremendous alterations of gene expression in H1975_OR cells and these genes can be clustered into unique GO, KEGG and GSEA pathways.ConclusionOur results preliminarily uncovered the underlying mechanisms for Formononetin counteracted Osimertinib-resistance in NSCLC cells and provided a potential treatment method for Osimertinib resistant NSCLC patients.
Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet
Authors: Saliba Nahima , Gagliano Gabriella , Gustavsson Anna-Karin 
Published: September 2023

AbstractMulti-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample. This easily adaptable novel microfluidic fabrication pipeline allows for the incorporation of reflective optics into microfluidic channels without disrupting efficient and automated solution exchange. By combining these innovations with point spread function engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets, we demonstrate whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
Quantification of Human Papillomavirus cell - free DNA from low volume blood plasma samples by digital PCR
Authors: Rosing Fabian , Meier Matthias , Schroeder Lea , Laban Simon , Hoffmann Thomas , Kaufmann Andreas , Siefer Oliver , Würdemann Nora , Klußmann Jens Peter , Rieckmann Thorsten , Alt Yvonne , Faden Daniel , Waterboer Tim , Höfler Daniela 
Published: September 2023

AbstractThe incidence rate of human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is increasing in many countries with high human development index. HPV cell-free DNA (cfDNA) isolated from relatively large amounts of blood plasma (typically 3-4 ml) has been successfully used for therapy surveillance of HPV-OPC patients. A currently highly discussed application of HPV-cfDNA is early detection of HPV-OPC in symptom-free individuals. This requires particularly sensitive and specific cfDNA detection methods as viral copy numbers can be very low. To study the predictive power of pre-diagnostic HPV-cfDNA, archived samples from epidemiological cohorts with limited plasma volume are an important source.To establish a cfDNA detection workflow optimized for low plasma volumes we compared two cfDNA purification methods (MagNA Pure 96 and QIAamp ccfDNA/RNA) and two digital PCR systems (Biorad QX200 and QIAGEN QIAcuity One). Final assay validation included 65 low volume plasma samples from OPC patients with defined HPV status (34 HPV16+, 1 HPV33+, 2 HPV58+, 28 HPV-negative) stored for 2-9 years.MagNA Pure 96 yielded a 28% higher cfDNA isolation efficiency in comparison to the QIAamp ccfDNA/RNA kit. Both digital PCR systems showed comparable analytic sensitivity (limit of detection 6-17 copies for both HPV16 and HPV33), but the higher multiplexing capacity allowed the QIAcuity to detect both HPV types in the same assay. In the validation set, the assay had a sensitivity of 80% (n=28/35) for detecting HPV16 and HPV33, and a specificity of 97% (n=29/30). In samples with ≥750 µl plasma available, the sensitivity was 85% (n=17/20), while in samples with <750 µl plasma the sensitivity was 73% (n=11/15).Despite the expected drop in sensitivity with decreased plasma volume, the assay is sensitive and highly specific even in low volume samples, and thus suited for studies exploring HPV-cfDNA as an early HPV-OPC detection marker in low volume archival material.
Seizure Event Detection Using Intravital Two-Photon Calcium Imaging Data
Authors: Stern Matthew A. , Cole Eric R. , Gross Robert E. , Berglund Ken 
Published: September 2023

AbstractSignificanceGenetic cellular calcium imaging has emerged as a powerful tool to investigate how different types of neurons interact at the microcircuit level to produce seizure activity, with newfound potential to understand epilepsy. Although many methods exist to measure seizure-related activity in traditional electrophysiology, few yet exist for calcium imaging.AimTo demonstrate an automated algorithmic framework to detect seizure-related events using calcium imaging – including the detection of pre-ictal spike events, propagation of the seizure wavefront, and terminal spreading waves for both population-level activity and that of individual cells.ApproachWe developed an algorithm for precise recruitment detection of population and individual cells during seizure-associated events, which broadly leverages averaged population activity and high-magnitude slope features to detect single-cell pre-ictal spike and seizure recruitment. We applied this method to data recorded using awakein vivotwo-photon calcium imaging during pentylenetetrazol induced seizures in mice.ResultsWe demonstrate that our detected recruitment times are concordant with visually identified labels provided by an expert reviewer and are sufficiently accurate to model the spatiotemporal progression of seizure-associated traveling waves.ConclusionsOur algorithm enables accurate cell recruitment detection and will serve as a useful tool for researchers investigating seizure dynamics using calcium imaging.
The unreasonable effectiveness of the total quasi-steady state approximation, and its limitations
Authors: Eilertsen Justin , Schnell Santiago , Walcher Sebastian 
Published: September 2023

AbstractIn this note, we discuss the range of parameters for which the total quasi-steady-state approximation of the Michaelis–Menten reaction mechanism holds validity. We challenge the prevalent notion that total quasi-steady-state approximation is “roughly valid” across all parameters, showing that its validity cannot be assumed, even roughly, across the entire parameter space — when the initial substrate concentration is high. On the positive side, we show that the linearized one-dimensional equation for total substrate is a valid approximation when the initial reduced substrate concentrations0/KMis small. Moreover, we obtain a precise picture of the long-term time course of both substrate and complex.