bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early to sustained impacts of lethal radiation on circulating miRNAs in a minipig model
Authors: Chakraborty Nabarun , Holmes-Hampton Gregory P. , Gautam Aarti , Kumar Raina , Hritzo Bernadette , Legesse Betre , Dimitrov George , Ghosh Sanchita P. , Hammamieh Rasha 
Published: October 2023

AbstractEarly diagnosis of lethal radiation is imperative since its intervention time windows are considerably short. Hence, ideal diagnostic candidates of radiation should be easily accessible, enable to inform about the stress history and objectively triage subjects in a time-efficient manner. Therefore, the small molecules such as metabolites and microRNAs (miRNAs) from plasma are legitimate biomarker candidate for lethal radiation. Our objectives were to comprehend the radiation-driven molecular pathogenesis and thereby determine biomarkers of translational potential. We investigated an established minipig model of LD70/45 total body irradiation (TBI). In this pilot study, plasma was collected pre-TBI and at multiple time points post-TBI. The majority of differentially expressed miRNAs and metabolites were perturbed immediately after TBI that potentially underlined the severity of its acute impact. The integrative network analysis of miRNA and metabolites showed a cohesive response; the early and consistent perturbations of networks were linked to cancer and the shift in musculoskeletal atrophy synchronized with the comorbidity-networks associated with inflammation and bioenergy synthesis. Subsequent comparative pipeline delivered 92 miRNAs, which demonstrated sequential homology between human and minipig, and potentially similar responses to lethal radiation across these two species. This panel promised to retrospectively inform the time since the radiation occurred; thereby could facilitate knowledge-driven interventions.
Effect of restrictive cumulative fluid balance on 28-day survival in invasively ventilated patients with moderate to severe ARDS due to COVID-19
Authors: Esper Treml Ricardo , Caldonazo Tulio , Filho Pedro Hilton A. , Mori Andréia L. , Carvalho André S. , Serrano Juliana S. F. , Dall-Aglio Pedro A. T. , Radermacher Peter , Manoel João Silva 
Published: October 2023

AbstractThis study aimed to evaluate the effect of two restrictive cumulative fluid balance (CFB) trends on survival and on major clinical outcomes in invasively ventilated patients with moderate to severe respiratory distress syndrome (ARDS) due to SARS-CoV-2. Prospective data collection was conducted on patients in the intensive care unit (ICU) originating from a tertiary university hospital. The primary outcomes were the risk association between the CFB trend during D0to D7and 28-day survival. The secondary outcomes were ICU mortality, in-hospital mortality, the need for invasive ventilation at D28, administration of vasoactive drugs at D7, time on invasive ventilation after D7, and length of ICU and hospital stay. 171 patients were enrolled in the study and divided according to their CFB trends during seven days of follow-up using model-based clustering [median CFB negative trend (n = 89) – 279 ml (− 664 to 203) and (n = 82) median CFB positive trend 1362 ml (619–2026)]. The group with CFB negative trend showed a higher chance of surviving 28-day in the ICU (HR: 0.62, 95% CI 0.41–0.94, p = 0.038). Moreover, this group had a reduced length of stay in the ICU, 11 (8–19) days versus 16.5 (9–29) daysp = 0.004 and presented lower rates (OR = 0.22; 95% CI 0.09–0.52) of invasive ventilation after 28-days in the ICU. In patients invasively ventilated with moderate to severe ARDS due to COVID-19, the collective who showed a negative trend in the CFB after seven days of invasive ventilation had a higher chance of surviving 28 days in the ICU and lower length of stay in the ICU.
Spatial correlation of 2D hard-tissue histology with 3D microCT scans through 3D printed phantoms
Authors: Nolte Philipp , Brettmacher Marcel , Gröger Chris Johann , Gellhaus Tim , Svetlove Angelika , Schilling Arndt F. , Alves Frauke , Rußmann Christoph , Dullin Christian 
Published: October 2023

AbstractHard-tissue histology—the analysis of thin two-dimensional (2D) sections—is hampered by the opaque nature of most biological specimens, especially bone. Therefore, the cutting process cannot be assigned to regions of interest. In addition, the applied cutting-grinding method is characterized by significant material loss. As a result, relevant structures might be missed or destroyed, and 3D features can hardly be evaluated. Here, we present a novel workflow, based on conventual microCT scans of the specimen prior to the cutting process, to be used for the analysis of 3D structural features and for directing the sectioning process to the regions of interest. 3D printed fiducial markers, embedded together with the specimen in resin, are utilized to retrospectively register the obtained 2D histological images into the 3D anatomical context. This not only allows to identify the cutting position, but also enables the co-registration of the cell and extracellular matrix morphological analysis to local 3D information obtained from the microCT data. We have successfully applied our new approach to assess hard-tissue specimens of different species. After matching the predicted microCT cut plane with the histology image, we validated a high accuracy of the registration process by computing quality measures namely Jaccard and Dice similarity coefficients achieving an average score of 0.90 ± 0.04 and 0.95 ± 0.02, respectively. Thus, we believe that the novel, easy to implement correlative imaging approach holds great potential for improving the reliability and diagnostic power of classical hard-tissue histology.
A solvent-free HPLC method for the simultaneous determination of Favipiravir and its hydrolytic degradation product
Authors: Sharaf Yasmine Ahmed , Abd El-Fattah Mai H. , El-Sayed Heba M. , Hassan Said A. 
Published: October 2023

AbstractDuring COVID-19 pandemic, Favipiravir (FPV) showed a great efficacy against COVID-19 virus, it produced noticeable improvements in recovery of the patients. The aim of this study was to develop a new, green and simple method for the simultaneous determination of FPV and its acid-induced degradation product (ADP) in its pure and pharmaceutical dosage forms. This method will be key for the inevitable development of FPV solution and inhaler formulations. A green micellar RP-HPLC method was developed using an RP-VDSPHERE PUR 100 column (5 µm, 250 × 4.6 mm) and an isocratic mixed micellar mobile phase composed of 0.02 M Brij-35, 0.1 M SDS and 0.01 M potassium dihydrogen orthophosphate anhydrous and adjusted to pH 3.0 with 1.0 mL min−1flow rate. The detection was performed at 280 nm with a run time of less than six min. Under the optimized chromatographic conditions, linear relationship has been established between peak area and concentration of FPV and its ADP in the range of 5–100 and 10–100 µg mL−1with elution time of 3.8 and 5.7 min, respectively. The developed method was validated according to the ICH guidelines and applied successfully for determination of FPV in its pharmaceutical dosage form.
Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection
Authors: Ferar Kathleen , Hall Taryn O. , Crawford Dana C. , Rowley Robb , Satterfield Benjamin A. , Li Rongling , Gragert Loren , Karlson Elizabeth W. , de Andrade Mariza , Kullo Iftikhar J. , McCarty Catherine A. , Kho Abel , Hayes M. Geoffrey , Ritchie Marylyn D. , Crane Paul K. , Mirel Daniel B. , Carlson Christopher , Connolly John J. , Hakonarson Hakon , Crenshaw Andrew T. , Carrell David , Luo Yuan , Dikilitas Ozan , Denny Joshua C. , Jarvik Gail P. , Crosslin David R. 
Published: October 2023

AbstractClostridioides difficile (C. diff.) infection (CDI) is a leading cause of hospital acquired diarrhea in North America and Europe and a major cause of morbidity and mortality. Known risk factors do not fully explain CDI susceptibility, and genetic susceptibility is suggested by the fact that some patients with colons that are colonized with C. diff. do not develop any infection while others develop severe or recurrent infections. To identify common genetic variants associated with CDI, we performed a genome-wide association analysis in 19,861 participants (1349 cases; 18,512 controls) from the Electronic Medical Records and Genomics (eMERGE) Network. Using logistic regression, we found strong evidence for genetic variation in the DRB locus of the MHC (HLA) II region that predisposes individuals to CDI (P > 1.0 × 10–14; OR 1.56). Altered transcriptional regulation in the HLA region may play a role in conferring susceptibility to this opportunistic enteric pathogen.
Annealing-free fabrication of high-quality indium tin oxide films for free-carrier-based hybrid metal–semiconductor nanophotonics
Authors: Korneluk Alexander , Szymczak Julia , Stefaniuk Tomasz 
Published: October 2023

AbstractRecent discoveries have revealed that indium tin oxide (ITO), due to the presence of an epsilon-near-zero (ENZ) point and suitable carrier concentration and mobility, can be used to modulate the refractive index, confine fields in the nanoscale, enhance nonlinear effects, achieve ultrafast light switching or to construct so-called time-varying media. While this potential positions ITO as a key material for future nanophotonic devices, producing ITO films with precisely engineered properties remains a significant challenge. Especially when the device’s complex geometry or incorporated materials require the fabrication process to be conducted at substrate temperatures below 100 °C and without any post-annealing treatment. Here we present a comprehensive study on the low-temperature deposition of 70 nm thick ITO films using an e-beam PVD system. The nanolayers evaporated under different conditions were characterized by SEM and AFM microscopy, Hall effect measurement system as well as spectroscopic ellipsometry. We discuss the factors influencing the optical, electrical, and morphological properties of ITO films. We show that smooth nanolayers of similar quality to annealed samples can be obtained at 80 °C by controlling the oxygen plasma parameters, and the ENZ wavelength can be tuned throughout the NIR spectral range. Finally, we show that using the proposed methodology, we fabricated ITO films with resistivity as low as 5.2 × 10–4 Ω cm, smooth surface with RMS < 1 nm, high carrier concentration reaching 1.2 × 1021 cm−3 and high transmittance (85%) in the Vis/NIR spectrum.
Plants forage for soil patches free of plastic pollution but cannot bag the profits
Authors: Speißer Benedikt , van Kleunen Mark 
Published: October 2023

AbstractMicroplastics can affect their surroundings physically and chemically, resulting in diverse effects on plant-soil systems. Similar to other substances (e.g. nutrients and water), microplastics in the environment occur in patches. Such heterogeneous distributions could affect plant responses to plastic pollution. Yet, this has remained untested. We conducted a multispecies experiment including 29 herbaceous plant species and three different microplastic treatments (a control without microplastics, a homogeneous and a heterogeneous microplastic distribution). Based on biomass and root-morphological traits, we assessed how different plastic distributions affect the performance and root-foraging behavior of plants, and whether stronger root foraging is beneficial when microplastics are distributed patchily. Next to general effects on plant productivity and root morphology, we found very strong evidence for root-foraging responses to patchy plastic distributions, with a clear preference for plastic-free patches, resulting in 25% longer roots and 20% more root biomass in the plastic-free patches. Interestingly, however, these foraging responses were correlated with a reduced plant performance, indicating that the benefits of plastic avoidance did not compensate for the associated investments. Our results provide new insights in plant-microplastic interactions and suggest that plants might not just be passively affected by but could also actively respond to environmental plastic pollution.
Alleviation of cadmium and drought stress in wheat by improving growth and chlorophyll contents amended with GA3 enriched deashed biochar
Authors: Anwar Tauseef , Shehzadi Asma , Qureshi Huma , Shah Muhammad Nadeem , Danish Subhan , Salmen Saleh H. , Ansari Mohammad Javed 
Published: October 2023

AbstractDrought and cadmium (Cd) stress are both major issues that significantly affect the growth and development of wheat plants. Both drought stress and Cd toxicity disrupt physiological processes i.e., nutrient uptake, cell expansion, and enzymatic reactions resulting in poor crop growth. To overcome these issues, the use of activated carbon and gibberellic acid (GA3) are considered valuable amendments. However, the current study aimed to add value using GA3-enriched biochar (GA3-BC). That’s why, a lab experiment was conducted on wheat to assess the effectiveness of GA3-BC against Cd and drought stress. For GA3 enrichment in biochar, 10 µg GA3/g biochar was mixed. There were 3 levels of GA3-BC i.e., 0, 0.6 (GA3-BC1), and 0.9% (GA3-BC). All levels were applied in 3 replicates under no stress (0Cd + no drought), drought stress (DS), and 6 mg Cd/ kg soil (6Cd). Results showed that GA3-BC2 caused a significant improvement in shoot length (44.99%), root length (99.73%), seedling length (60.13%) and shoot fresh weight (63.59%) over control at 6Cd + drought stress. A significant improvement in chlorophyll a, chlorophyll b, and total chlorophyll while a decrease in electrolyte leakage and regulation of antioxidants i.e., lipid peroxidation, SOD, CAT, APx, GR, GPx, GST, and DPHH also signified the effectiveness of GA3-BC2 compared to control at 6Cd + drought stress. In conclusion, GA3-BC2 is an efficacious amendment for simultaneously alleviating drought and Cd stress in wheat. More investigations are recommended at the field level on different cereal crops cultivated in different soil textures to declare GA3-BC2 as the best treatment for mitigation of drought stress and Cd toxicity.
Compressed models for co-reference resolution: enhancing efficiency with debiased word embeddings
Authors: Ioannides Georgios , Jadhav Aishwarya , Sharma Aditi , Navali Samarth , Black Alan W. 
Published: October 2023

AbstractThis work presents a comprehensive approach to reduce bias in word embedding vectors and evaluate the impact on various Natural Language Processing (NLP) tasks. Two GloVe variations (840B and 50) are debiased by identifying the gender direction in the word embedding space and then removing or reducing the gender component from the embeddings of target words, while preserving useful semantic information. Their gender bias is assessed through the Word Embedding Association Test. The performance of co-reference resolution and text classification models trained on both original and debiased embeddings is evaluated in terms of accuracy. A compressed co-reference resolution model is examined to gauge the effectiveness of debiasing techniques on resource-efficient models. To the best of the authors’ knowledge, this is the first attempt to apply compression techniques to debiased models. By analyzing the context preservation of debiased embeddings using a Twitter misinformation dataset, this study contributes valuable insights into the practical implications of debiasing methods for real-world applications such as person profiling.
A conceptual framework for assessing behavioral flexibility of species in response to extreme climatic events
Authors: Ameca Eric I. , Chamart Lucy , Garber Paul A. 
Published: October 2023

AbstractInherent differences in the adaptive capacity of species to flexibly respond to extreme climatic events (ECEs) represent a key factor in their survivorship. We introduce and apply a conceptual framework linking knowledge about species’ current ecology and biology with variation in behavioral flexibility to ECEs. We applied it to 199 non-human primate species currently exposed to cyclones across the global tropics. Our findings suggest that species characterized by an increased ability to exploit a broad range of food types, social systems that permit subgrouping, and habitat types that span a range of environmental conditions may have greater success in coping with cyclones than more narrowly constrained or less adaptable primates. Overall, 15% of species, predominantly of the families Atelidae and Cercopithecidae, were assessed as having high or very high flexibility. In contrast, ~ 60% of primates were assessed with low or very low flexibility. These were species mainly belonging to the Cheirogaleidae, Lemuridae, Lepilemuridae, and Indriidae. While much work remains to better understand mechanisms driving differences in behavioral flexibility of species exposed to extreme climate across vertebrate lineages, our framework provides a workable approach that can improve estimates of current vulnerability to these phenomena and better inform conservation and management strategies.
Fuel mixing enhancement of transverse coaxial air and fuel jet by upstream shock wave on in scramjet engines: numerical study
Authors: Abdollahi Seyyed Amirreza , Jafari Moharram , Aminian Saman , Fattahi M. , Uyen P. D. 
Published: October 2023

AbstractIn this study, computational fluid dynamics (CFD) is used to disclose the impacts of upstream shock waves on fuel mixing of cross coaxial air and fuel jet at a scramjet engine. This study has tried to investigate the impact of three different lobe injectors (2-lobe, 3-lobe, and 4-lobe nozzle) on the fuel penetrations along the scramjet combustor. The supersonic air stream is M = 4 while cross hydrogen and air jet are released in sonic velocity. This study uses CFD simulations to analyze the effects of upstream shock waves on fuel mixing in the transverse coaxial jet and assess their potential for improving combustion efficiency. The results demonstrate that the usage of upstream shock waves significantly increases shock interactions and augments the vortex region downstream of the jet. Our results show that the impacts of shock waves on the penetration of fuel jet released from the coaxial lobe nozzle are substantial.
Hemoglobin as a prognostic marker for neurological outcomes in post-cardiac arrest patients: a meta-analysis
Authors: Hou Hongxiang , Pang Li , Zhao Liang , Liu Zuolong , Xing Ji-Hong 
Published: October 2023

AbstractThe aim of this study was to investigate the relationship between serum level of hemoglobin and neurological outcomes following cardiac arrest. Relevant studies were identified by searching electronic databases including PubMed, Web of Science, Cochrane Library, and Embase from June 2012 through April 2023. Articles were rigorously reviewed for their study inclusion and exclusion criteria. Pooled effect date was determined using the standardized mean difference (SMD) and 95% confidence intervals (CI). The Newcastle–Ottawa Scale was used to evaluate study quality. Subgroup analyses were conducted to determine confounding factors affecting patient outcomes. Study heterogeneity, sensitivity, and publication bias were also determined.This meta-analysis included 11 studies involving 2519 patients. Our results suggest that high serum level of hemoglobin may improve neurological prognosis(SMD = 0.60, 95%CI = 0.49–0.71, I2 = 10.85). The findings of this study indicate that serum level of hemoglobin may be associated with better neurological prognosis, perhaps an appropriate increase in serum haemoglobin levels can improve the neurological prognosis of patients in cardiac arrest.
Predicting survival of advanced laryngeal squamous cell carcinoma: comparison of machine learning models and Cox regression models
Authors: Zhang Yi-Fan , Shen Yu-Jie , Huang Qiang , Wu Chun-Ping , Zhou Liang , Ren Heng-Lei 
Published: October 2023

AbstractLaryngeal squamous cell carcinoma (LSCC) is a common tumor type. High recurrence rates remain an important factor affecting the survival and quality of life of advanced LSCC patients. We aimed to build a new nomogram and a random survival forest model using machine learning to predict the risk of LSCC progress. The study included 671 patients with AJCC stages III–IV LSCC. To develop a prognostic model, Cox regression analyses were used to assess the relationship between clinic-pathologic factors and disease-free survival (DFS). RSF analysis was also used to predict the DFS of LSCC patients. The ROC curve revealed that the Cox model exhibited good sensitivity and specificity in predicting DFS in the training and validation cohorts (1 year, validation AUC = 0.679, training AUC = 0.693; 3 years, validation AUC = 0.716, training AUC = 0.655; 5 years, validation AUC = 0.717, training AUC = 0.659). Random survival forest analysis showed that N stage, clinical stage, and postoperative chemoradiotherapy were prognostically significant variables associated with survival. The random forest model exhibited better prediction ability than the Cox regression model in the training cohort; however, the two models showed similar prediction ability in the validation cohort.
Combinatorial multimer staining and spectral flow cytometry facilitate quantification and characterization of polysaccharide-specific B cell immunity
Authors: Hoving Dennis , Marques Alexandre H. C. , Huisman Wesley , Nosoh Beckley A. , de Kroon Alicia C. , van Hengel Oscar R. J. , Wu Bing-Ru , Steenbergen Rosanne A. M. , van Helden Pauline M. , Urban Britta C. , Dhar Nisha , Ferreira Daniela M. , Kwatra Gaurav , Hokke Cornelis H. , Jochems Simon P. 
Published: October 2023

AbstractBacterial capsular polysaccharides are important vaccine immunogens. However, the study of polysaccharide-specific immune responses has been hindered by technical restrictions. Here, we developed and validated a high-throughput method to analyse antigen-specific B cells using combinatorial staining with fluorescently-labelled capsular polysaccharide multimers. Concurrent staining of 25 cellular markers further enables the in-depth characterization of polysaccharide-specific cells. We used this assay to simultaneously analyse 14 Streptococcus pneumoniae or 5 Streptococcus agalactiae serotype-specific B cell populations. The phenotype of polysaccharide-specific B cells was associated with serotype specificity, vaccination history and donor population. For example, we observed a link between non-class switched (IgM+) memory B cells and vaccine-inefficient S. pneumoniae serotypes 1 and 3. Moreover, B cells had increased activation in donors from South Africa, which has high-incidence of S. agalactiae invasive disease, compared to Dutch donors. This assay allows for the characterization of heterogeneity in B cell immunity that may underlie immunization efficacy.