bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full-length transcriptome analysis of multiple organs and identification of adaptive genes and pathways in Mikania micrantha
Authors: Ruan Xiaoxian , Wang Zhen , Su Yingjuan , Wang Ting 
Published: February 2022

AbstractMikania micranthais a notorious invasive weed that has caused huge economic loss and negative ecological consequences in invaded areas. This species can adapt well to invasive environments with various stress factors. The identification of gene families and functional pathways related to environmental adaptability is lack inM. micranthaat the multi-organ full-length transcriptome level. In this study, we sequenced the transcriptomes of fiveM. micranthaorgans using PacBio single-molecule real-time sequencing and Illumina RNA sequencing technologies. Based on the transcriptome data, full-length transcripts were captured and gene expression patterns among the five organs were analyzed. KEGG enrichment analysis of genes with higher expression indicated their special roles in environmental stress response and adversity adaptation in the various five organs. The gene families and pathways related to biotic and abiotic factors, including terpene synthases, glutathione S-transferases, antioxidant defense system, and terpenoid biosynthesis pathway, were characterized. The expression levels of most differentially expressed genes in the antioxidant defense system and terpenoid biosynthesis pathway were higher in root, stem, and leaf than in the other two organs, suggesting that root, stem, and leaf have strong ability to respond to adverse stresses and form the important organs of terpenoid synthesis and accumulation. Additionally, a large number of transcription factors and alternative splicing events were predicted. This study provides a comprehensive transcriptome resource forM. micrantha, and our findings facilitate further research on the adaptive evolution and functional genomics of this species.
PD-1 blockade enhances chemotherapy toxicity in oesophageal adenocarcinoma
Authors: Davern Maria , O’ Brien Rebecca M. , McGrath Jason , Donlon Noel E. , Melo Ashanty M. , Buckley Croí E. , Sheppard Andrew D. , Reynolds John V. , Lynam-Lennon Niamh , Maher Stephen G. , Lysaght Joanne 
Published: February 2022

AbstractChemotherapy upregulates immune checkpoint (IC) expression on the surface of tumour cells and IC-intrinsic signalling confers a survival advantage against chemotherapy in several cancer-types including oesophageal adenocarcinoma (OAC). However, the signalling pathways mediating chemotherapy-induced IC upregulation and the mechanisms employed by ICs to protect OAC cells against chemotherapy remain unknown. Longitudinal profiling revealed that FLOT-induced IC upregulation on OE33 OAC cells was sustained for up to 3 weeks post-treatment, returning to baseline upon complete tumour cell recovery. Pro-survival MEK signalling mediated FLOT-induced upregulation of PD-L1, TIM-3, LAG-3 and A2aR on OAC cells promoting a more immune-resistant phenotype. Single agent PD-1, PD-L1 and A2aR blockade decreased OAC cell viability, proliferation and mediated apoptosis. Mechanistic insights demonstrated that blockade of the PD-1 axis decreased stem-like marker ALDH and expression of DNA repair genes. Importantly, combining single agent PD-1, PD-L1 and A2aR blockade with FLOT enhanced cytotoxicity in OAC cells. These findings reveal novel mechanistic insights into the immune-independent functions of IC-intrinsic signalling in OAC cells with important clinical implications for boosting the efficacy of the first-line FLOT chemotherapy regimen in OAC in combination with ICB, to not only boost anti-tumour immunity but also to suppress IC-mediated promotion of key hallmarks of cancer that drive tumour progression.
GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson’s disease
Authors: McIntyre Lauren M. , Huertas Francisco , Morse Alison M. , Kaletsky Rachel , Murphy Coleen T. , Kalia Vrinda , Miller Gary W. , Moskalenko Olexander , Conesa Ana , Mor Danielle E. 
Published: February 2022

AbstractParkinson’s disease (PD) is a disabling neurodegenerative disorder in which multiple cell types, including dopaminergic and cholinergic neurons, are affected. The mechanisms of neurodegeneration in PD are not fully understood, limiting the development of therapies directed at disease-relevant molecular targets. C. elegans is a genetically tractable model system that can be used to disentangle disease mechanisms in complex diseases such as PD. Such mechanisms can be studied combining high-throughput molecular profiling technologies such as transcriptomics and metabolomics. However, the integrative analysis of multi-omics data in order to unravel disease mechanisms is a challenging task without advanced bioinformatics training. Galaxy, a widely-used resource for enabling bioinformatics analysis by the broad scientific community, has poor representation of multi-omics integration pipelines. We present the integrative analysis of gene expression and metabolite levels of a C. elegans PD model using GAIT-GM, a new Galaxy tool for multi-omics data analysis. Using GAIT-GM, we discovered an association between branched-chain amino acid metabolism and cholinergic neurons in the C. elegans PD model. An independent follow-up experiment uncovered cholinergic neurodegeneration in the C. elegans model that is consistent with cholinergic cell loss observed in PD. GAIT-GM is an easy to use Galaxy-based tool for generating novel testable hypotheses of disease mechanisms involving gene-metabolite relationships.
Significance of induced hybridized metallic and non-metallic nanoparticles in single-phase nano liquid flow between permeable disks by analyzing shape factor
Authors: Bilal S. , Shah Imtiaz Ali , Ramzan Muhammad , Nisar Kottakkaran Sooppy , Elfasakhany Ashraf , Eed Emad M. , Ghazwani Hassan Ali S. 
Published: February 2022

AbstractThe current communication is designed by keeping in the mind high heat transfer capabilities of nanoliquids with the dispersion of diversified-natured nanoparticles in poorly conducting base liquids. Here, an amalgamation of metallic (Cu) and hybridization of metallic and non-metallic oxide (Cu-TiO2) nanoparticles to uplift thermophysical attributes of water is deliberated. The magnetically affected flow between rotating disks under the impact and permeability aspect is assumed. Empirical relations for effective dynamic viscosity, density, and heat capacitance to show mesmerizing features of obliged nanoparticles are also expressed. In addition, mathematical relations also depend on morphological factors like shape, size, and diameter of inducted nanoparticles. The mathematical formulation of the problem is conceded in the form of a system of ODEs after using similarity transformation on dimensional PDEs. Simulations of the complex coupled differential structure are solved by using a numerical approach by employing shooting and Runge–Kutta procedures jointly. The impact of flow concerning variables on associated distributions is revealed through tabular and graphical manner. Quantities of engineering interest associated with work like wall friction and thermal flux coefficients at walls of the disk are also calculated. It is deduced from an examination that the addition of metallic particles raises heat transfer more than non-metallic particles. A significant impression of magnetic field on shear stress is executed by hybrid nanoparticles along the surface of disks. In addition, elevation in Nusselt number and depreciation in skin friction coefficient is revealed against increasing magnitude of nanoparticle volume fraction. A positive trend in skin friction coefficient is manifested against the increasing magnitude of Reynold number. It is also observed that by increasing the size and shape of hybrid nanoparticles thermal conductivity and viscosity of the base fluid increases.
Novel roles of phentolamine in protecting axon myelination, muscle atrophy, and functional recovery following nerve injury
Authors: Zainul Zarin , Ma Bo , Koka Mert , Wilkerson Jenny L. , Ortiz Yuma T. , Kerosuo Laura , Chandran Vijayendran 
Published: February 2022

AbstractIncomplete functional recovery after peripheral nerve injury (PNI) often results in devastating physical disabilities in human patients. Despite improved progress in surgical and non-surgical approaches, achieving complete functional recovery following PNI remains a challenge. This study demonstrates that phentolamine may hold a significant promise in treating nerve injuries and denervation induced muscle atrophy following PNI. In a sciatic nerve crush injury mouse model, we found that phentolamine treatment enhanced motor and functional recovery, protected axon myelination, and attenuated injury-induced muscle atrophy in mice at 14 days post-injury (dpi) compared to saline treatment. In the soleus of phentolamine treated animals, we observed the downregulation of phosphorylated signal transducer and activator of transcription factor 3 (p-STAT3) as well as muscle atrophy-related genes Myogenin, muscle ring finger 1 (MuRF-1), and Forkhead box O proteins (FoxO1, FoxO3). Our results show that both nerve and muscle recovery are integral components of phentolamine treatment-induced global functional recovery in mice at 14 dpi. Moreover, phentolamine treatment improved locomotor functional recovery in the mice after spinal cord crush (SCC) injury. The fact that phentolamine is an FDA approved non-selective alpha-adrenergic blocker, clinically prescribed for oral anesthesia reversal, hypertension, and erectile dysfunction makes this drug a promising candidate for repurposing in restoring behavioral recovery following PNI and SCC injuries, axonal neuropathy, and muscle wasting disorders.
Laser-based ultrasound interrogation of surface and sub-surface features in advanced manufacturing materials
Authors: Harke Kathryn Jinae , Calta Nicholas , Tringe Joseph , Stobbe David 
Published: February 2022

AbstractStructures formed by advanced manufacturing methods increasingly require nondestructive characterization to enable efficient fabrication and to ensure performance targets are met. This is especially important for aerospace, military, and high precision applications. Surface acoustic waves (SAW) generated by laser-based ultrasound can detect surface and sub-surface defects relevant for a broad range of advanced manufacturing processes, including laser powder bed fusion (LPBF). In particular, an all-optical SAW generation and detection configuration can effectively interrogate laser melt lines. Here we report on scattered acoustic energy from melt lines, voids, and surface features. Sub-surface voids are also characterized using X-ray Computed Tomography (CT). High resolution CT results are presented and compared with SAW measurements. Finite difference simulations inform experimental measurements and analysis.
Morphological variation in paediatric lower limb bones
Authors: Carman Laura , Besier Thor F. , Choisne Julie 
Published: February 2022

AbstractAvailable methods for generating paediatric musculoskeletal geometry are to scale generic adult geometry, which is widely accessible but can be inaccurate, or to obtain geometry from medical imaging, which is accurate but time-consuming and costly. A population-based shape model is required to generate accurate and accessible musculoskeletal geometry in a paediatric population. The pelvis, femur, and tibia/fibula were segmented from 333 CT scans of children aged 4–18 years. Bone morphology variation was captured using principal component analysis (PCA). Subsequently, a shape model was developed to predict bone geometry from demographic and linear bone measurements and validated using a leave one out analysis. The shape model was compared to linear scaling of adult and paediatric bone geometry. The PCA captured growth-related changes in bone geometry. The shape model predicted bone geometry with root mean squared error (RMSE) of 2.91 ± 0.99 mm in the pelvis, 2.01 ± 0.62 mm in the femur, and 1.85 ± 0.54 mm in the tibia/fibula. Linear scaling of an adult mesh produced RMSE of 4.79 ± 1.39 mm in the pelvis, 4.38 ± 0.72 mm in the femur, and 4.39 ± 0.86 mm in the tibia/fibula. We have developed a method for capturing and predicting lower limb bone shape variation in a paediatric population more accurately than linear scaling without using medical imaging.
Encoding in a social feedback context enhances and biases behavioral and electrophysiological correlates of long-term recognition memory
Authors: Schindler Sebastian , Vormbrock Ria , Kissler Johanna 
Published: February 2022

AbstractEncoding often occurs in social contexts, yet research has hardly addressed their role in verbal memory. In three experiments, we investigated the behavioral and neural effects of encoding context on memory for positive, negative, and neutral adjectives, contrasting a social-feedback group (N = 24) with an explicit verbal-learning (N = 24) and a levels-of-processing group (N = 24). Participants in the social-feedback group were not aware of a recognition session one week later, but their memory was better than the explicit learning or the levels-of-processing groups'. However, they also exhibited the strongest response bias, particularly for positive words. Brain event-related potentials (ERPs) revealed largest early negativities (EPN) and late positivities (LPP) in the social-feedback group. Only in the subsequent slow-wave did the explicit learning group show higher amplitudes than the other two groups, suggesting reliance on strategic rather than automatic processes. Still, context-driven incidental encoding outweighed explicit instructions, specifying a decisive role of social factors in memory.
The shell shape optimization and fluid–structure interaction simulation of hose pump in water-fertilizer integrated fertilizer application
Authors: Ma Xiao , Zhang Lixin , Wang Wendong , Yan Yongchun , Du Chanchan 
Published: February 2022

AbstractAs a new type of under-film drip irrigation, water-fertilizer integrated fertilizer application device in Northwest China, the hose pump has achieved excellent results in practical applications, but its pulsation has exhibited some adverse effects on the fertilization process. By analyzing the cause of pulsation and flow characteristics, we proposed a shell optimization method to reduce pulsation. We used a release time deformation curve as the shape curve of the outlet shell of the hose pump. Based on the fluid–structure interaction analysis, we developed a numerical model of an optimized three roller hose pump and a conventional three roller hose pump for dynamic simulations. The simulation results showed the optimized hose pump flow pressure variation range was reduced by 26.92%, the average fluid flow velocity increased by about 10%, and mass flow rate improved by 8.84% over the conventional hose pump. We tested the optimized hose pump prototype and the conventional hose pump on the test bench. The test results showed that the pulsating pressure variation range of the optimized pump decreased by about 20%, and flow output increased by about 8.63%. These results suggest that shell shape optimization assist in the decrease of flow pulsation and contribute to further hose pump popularization.
Optimization of supercritical-CO2 extraction and pharmacokinetics in SD rats of alkaloids form Sophora moorcroftiana seed
Authors: Hu Chunhui , Gan Xuehui , Jia Qiangqiang , Gao Pan , Du Tao , Zhang Fabin 
Published: February 2022

AbstractThe total alkaloids extracted from the seeds of Sophora moorcroftiana (TAs-SM) have the potential to treat alveolar echinococcosis, a disease included by the WHO in a list of 17 key neglected diseases world-wide. The aims of the current study were first to develop a supercritical fluid extraction (SFE) method for optimizing TAs-SM extraction, and second, to develop an optimized method for evaluating TAs-SM pharmacokinetics in vivo. The Box–Behnken response surface method was used to optimize the extraction process, and ultra-high liquid chromatography coupled with high resolution electrospray mass spectrometry (UPLC-HR-ESI-MS) was used to determine the pharmacokinetics of TAs-SM in SD rats. The results indicated the following optimal SFE extraction conditions: pressure = 31 MPa, temperature = 70 °C, time = 162.18 min. With these parameters, total alkaloids could be extracted from each gram of S. moorcroftiana, with the total content being 68.88 μg. The linear range of UPLC-HR-ESI-MS is 0.78–200.00 ng/ml, R2 > 0.99, and the sample recovery is 99–113%. The precision, accuracy, selectivity and stability of the method meet the requirements of US FDA guidelines. To our knowledge this study is the first to establish an SFE method for extracting TAs-SM and the first to employ UPLC-HR-ESI-MS for measuring TAs-SM in rats. These findings provide important contributions for using TAs-SM in further drug development and clinical applications.
Process optimization and modeling of Cd2+ biosorption onto the free and immobilized Turbinaria ornata using Box–Behnken experimental design
Authors: Fawzy Mustafa A. , Darwish Hadeer , Alharthi Sarah , Al-Zaban Mayasar I. , Noureldeen Ahmed , Hassan Sedky H. A. 
Published: February 2022

AbstractThe release of effluents containing cadmium ions into aquatic ecosystems is hazardous to humans and marine organisms. In the current investigation, biosorption of Cd2+ ions from aqueous solutions by freely suspended and immobilized Turbinaria ornata biomasses was studied. Compared to free cells (94.34%), the maximum Cd2+ removal efficiency reached 98.65% for immobilized cells obtained via Box–Behnken design under optimized conditions comprising algal doses of 5.04 g L−1 and 4.96 g L−1, pH values of 5.06 and 6.84, and initial cadmium concentrations of 25.2 mg L−1 and 26.19 mg L−1, respectively. Langmuir, Freundlich, and Temkin isotherm models were suitably applied, providing the best suit of data for free and immobilized cells, but the Dubinin–Radushkevich model only matched the immobilized algal biomass. The maximum biosorption capacity of Cd2+ ions increased with the immobilized cells (29.6 mg g−1) compared to free cells (23.9 mg g−1). The Cd2+ biosorption data obtained for both biomasses followed pseudo-second-order and Elovich kinetic models. In addition, the biosorption process is controlled by film diffusion followed by intra-particle diffusion. Cd2+ biosorption onto the free and immobilized biomasses was spontaneous, feasible, and endothermic in nature, according to the determined thermodynamic parameters. The algal biomass was further examined via SEM/EDX and FTIR before and after Cd2+ biosorption. SEM/EDX analysis revealed Cd2+ ion binding onto the algal surface. Additionally, FTIR analysis confirmed the presence of numerous functional groups (hydroxyl, carboxyl, amine, phosphate, etc.) participating in Cd2+ biosorption. This study verified that immobilized algal biomasses constitute a cost-effective and favorable biosorbent material for heavy metal removal from ecosystems.
Time and spatially resolved tracking of the air quality in local public transport
Authors: Salthammer Tunga , Fauck Christian , Omelan Alexander , Wientzek Sebastian , Uhde Erik 
Published: February 2022

AbstractAs an indoor environment, public transport is subject to special conditions with many passengers in a comparatively small space. Therefore, both an efficient control of the climatic parameters and a good air exchange are necessary to avoid transmission and spread of respiratory diseases. However, in such a dynamic system it is practically impossible to determine pathogenic substances with the necessary temporal and spatial resolution, but easy-to-measure parameters allow the air quality to be assessed in a passenger compartment. Carbon dioxide has already proven to be a useful indicator, especially in environments with a high occupancy of people. Airborne particulate matter can also be an important aspect for assessing the air quality in an indoor space. Consequently, the time courses of temperature, relative humidity, carbon dioxide and particulate matter (PM10) were tracked and evaluated in local public transport buses, trams and trains in the Brunswick/Hanover region. In all measurements, the climatic conditions were comfortable for the passengers. Carbon dioxide was strongly correlated with occupancy and has proven to be the most informative parameter. The PM10 concentration, however, often correlated with the dynamics of people when getting on and off, but not with the occupancy. Sensors, equipped with integrated GPS, were installed in the passenger cabins and were found to be useful for recording location-related effects such as stops. The results of this study show that the online recording of simple parameters is a valuable tool for assessing air quality as a function of time, location and number of people. When the occupancy is high, a low carbon dioxide level indicates good ventilation, which automatically reduces the risk of infection. It is therefore recommended to take more advantage of low-cost sensors as a control for air conditioning systems in passenger cabins and for evaluations of the dynamics in public transport.
Intra-topic latency as an automated behavioral marker of treatment response in autism spectrum disorder
Authors: McKernan Elizabeth P. , Kumar Manoj , Di Martino Adriana , Shulman Lisa , Kolevzon Alexander , Lord Catherine , Narayanan Shrikanth , Kim So Hyun 
Published: February 2022

AbstractData science advances in behavioral signal processing and machine learning hold the promise to automatically quantify clinically meaningful behaviors that can be applied to a large amount of data. The objective of this study was to identify an automated behavioral marker of treatment response in social communication in children with autism spectrum disorder (ASD). First, using an automated computational method, we successfully derived the amount of time it took for a child with ASD and an adult social partner (Npairs = 210) to respond to each other while they were engaged in conversation bits (“latency”) using recordings of brief, natural social interactions. Then, we measured changes in latency at pre- and post-interventions. Children with ASD who were receiving interventions showed significantly larger reduction in latency compared to those who were not receiving interventions. There was also a significant group difference in the changes in latency for adult social partners. Results suggest that the automated measure of latency derived from natural social interactions is a scalable and objective method to quantify treatment response in children with ASD.
Association between serum free hemoglobin level and cerebral white matter hyperintensity volume in older adults
Authors: Oh Dae Jong , Kim Jun Sung , Lee Subin , Yang Hee Won , Bae Jong Bin , Han Ji Won , Kim Ki Woong 
Published: February 2022

AbstractThe association between serum free hemoglobin (sfHb) level and white matter hyperintensity (WMH) volume is controversial. This study is to examine this association considering nonlinearity, sex dimorphism, and WMH type. We enrolled 704 older adults among the participants of the Korean Longitudinal Study on Cognitive Aging and Dementia and visitors to the Dementia Clinic of Seoul National University Bundang Hospital. We measured sfHb level in the venous blood and WMH volume (VWMH) using fluid-attenuated inversion recovery magnetic resonance images. The association between sfHb level and periventricular VWMH was linear in men (linear regression; β =  − 0.18, p = 0.006) and U-shaped in women (restricted cubic spline; F = 6.82, p < 0.001). sfHb level was not associated with deep VWMH in either sex. These findings were also observed in participants without anemia. To conclude, sfHb level is associated with periventricular VWMH in older adults of both sexes. Maintaining an optimal sfHb level may contribute to the prevention of WMH.