bluuebunny/crossref_metadata_2025_split huggingface dataset:
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression
Authors: Rohr Michael , Beardsley Jordan , Nakkina Sai Preethi , Zhu Xiang , Aljabban Jihad , Hadley Dexter , Altomare Deborah 
Published: August 2021

AbstractTranscriptional profiling of pre- and post-malignant colorectal cancer (CRC) lesions enable temporal monitoring of molecular events underlying neoplastic progression. However, the most widely used transcriptomic dataset for CRC, TCGA-COAD, is devoid of adenoma samples, which increases reliance on an assortment of disparate microarray studies and hinders consensus building. To address this, we developed a microarray meta-dataset comprising 231 healthy, 132 adenoma, and 342 CRC tissue samples from twelve independent studies. Utilizing a stringent analytic framework, select datasets were downloaded from the Gene Expression Omnibus, normalized by frozen robust multiarray averaging and subsequently merged. Batch effects were then identified and removed by empirical Bayes estimation (ComBat). Finally, the meta-dataset was filtered for low variant probes, enabling downstream differential expression as well as quantitative and functional validation through cross-platform correlation and enrichment analyses, respectively. Overall, our meta-dataset provides a robust tool for investigating colorectal adenoma formation and malignant transformation at the transcriptional level with a pipeline that is modular and readily adaptable for similar analyses in other cancer types.
A near-global, high resolution land surface parameter dataset for the variable infiltration capacity model
Authors: Schaperow Jacob R. , Li Dongyue , Margulis Steven A. , Lettenmaier Dennis P. 
Published: August 2021

AbstractHydrologic models predict the spatial and temporal distribution of water and energy at the land surface. Currently, parameter availability limits global-scale hydrologic modelling to very coarse resolution, hindering researchers from resolving fine-scale variability. With the aim of addressing this problem, we present a set of globally consistent soil and vegetation parameters for the Variable Infiltration Capacity (VIC) model at 1/16° resolution (approximately 6 km at the equator), with spatial coverage from 60°S to 85°N. Soil parameters derived from interpolated soil profiles and vegetation parameters estimated from space-based MODIS measurements have been compiled into input files for both the Classic and Image drivers of the VIC model, version 5. Geographical subsetting codes are provided, as well. Our dataset provides all necessary land surface parameters to run the VIC model at regional to global scale. We evaluate VICGlobal’s ability to simulate the water balance in the Upper Colorado River basin and 12 smaller basins in the CONUS, and their ability to simulate the radiation budget at six SURFRAD stations in the CONUS.
Effects of interobserver and interdisciplinary segmentation variabilities on CT-based radiomics for pancreatic cancer
Authors: Wong Jeffrey , Baine Michael , Wisnoskie Sarah , Bennion Nathan , Zheng Dechun , Yu Lei , Dalal Vipin , Hollingsworth Michael A. , Lin Chi , Zheng Dandan 
Published: August 2021

AbstractRadiomics is a method to mine large numbers of quantitative imaging features and develop predictive models. It has shown exciting promise for improved cancer decision support from early detection to personalized precision treatment, and therefore offers a desirable new direction for pancreatic cancer where the mortality remains high despite the current care and intense research. For radiomics, interobserver segmentation variability and its effect on radiomic feature stability is a crucial consideration. While investigations have been reported for high-contrast cancer sites such as lung cancer, no studies to date have investigated it on CT-based radiomics for pancreatic cancer. With three radiation oncology observers and three radiology observers independently contouring on the contrast CT of 21 pancreatic cancer patients, we conducted the first interobserver segmentation variability study on CT-based radiomics for pancreatic cancer. Moreover, our novel investigation assessed whether there exists an interdisciplinary difference between the two disciplines. For each patient, a consensus tumor volume was generated using the simultaneous truth and performance level expectation algorithm, using the dice similarity coefficient (DSC) to assess each observer’s delineation against the consensus volume. Radiation oncology observers showed a higher average DSC of 0.81 ± 0.06 than the radiology observers at 0.69 ± 0.16 (p = 0.002). On a panel of 1277 radiomic features, the intraclass correlation coefficients (ICC) was calculated for all observers and those of each discipline. Large variations of ICCs were observed for different radiomic features, but ICCs were generally higher for the radiation oncology group than for the radiology group. Applying a threshold of ICC > 0.75 for considering a feature as stable, 448 features (35%) were found stable for the radiation oncology group and 214 features (16%) were stable from the radiology group. Among them, 205 features were found stable for both groups. Our results provide information for interobserver segmentation variability and its effect on CT-based radiomics for pancreatic cancer. An interesting interdisciplinary variability found in this study also introduces new considerations for the deployment of radiomics models.
Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli
Authors: Bellenberg Sören , Salas Beatriz , Ganji Suresh , Jorquera-Román Cristian , Valenzuela Maria Luisa , Buetti-Dinh Antoine , Unelius C. Rikard , Dopson Mark , Vera Mario 
Published: August 2021

AbstractBioleaching of metal sulfide ores involves acidophilic microbes that catalyze the chemical dissolution of the metal sulfide bond that is enhanced by attached and planktonic cell mediated oxidation of iron(II)-ions and inorganic sulfur compounds. Leptospirillum spp. often predominate in sulfide mineral-containing environments, including bioheaps for copper recovery from chalcopyrite, as they are effective primary mineral colonizers and oxidize iron(II)-ions efficiently. In this study, we demonstrated a functional diffusible signal factor interspecies quorum sensing signaling mechanism in Leptospirillum ferriphilum and Leptospirillum ferrooxidans that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source. In addition, pure diffusible signal factor and extracts from supernatants of pyrite grown Leptospirillum spp. inhibited biological iron oxidation in various species, and that pyrite grown Leptospirillum cells were less affected than iron grown cells to self inhibition. Finally, transcriptional analyses for the inhibition of iron-grown L. ferriphilum cells due to diffusible signal factor was compared with the response to exposure of cells to N- acyl-homoserine-lactone type quorum sensing signal compounds. The data suggested that Leptospirillum spp. diffusible signal factor production is a strategy for niche protection and defense against other microbes and it is proposed that this may be exploited to inhibit unwanted acidophile species.
A differential equations model-fitting analysis of COVID-19 epidemiological data to explain multi-wave dynamics
Authors: Beira Maria Jardim , Sebastião Pedro José 
Published: August 2021

AbstractCompartmental epidemiological models are, by far, the most popular in the study of dynamics related with infectious diseases. It is, therefore, not surprising that they are frequently used to study the current COVID-19 pandemic. Taking advantage of the real-time availability of COVID-19 related data, we perform a compartmental model fitting analysis of the portuguese case, using an online open-access platform with the integrated capability of solving systems of differential equations. This analysis enabled the data-driven validation of the used model and was the basis for robust projections of different future scenarios, namely, increasing the detected infected population, reopening schools at different moments, allowing Easter celebrations to take place and population vaccination. The method presented in this work can easily be used to perform the non-trivial task of simultaneously fitting differential equation solutions to different epidemiological data sets, regardless of the model or country that might be considered in the analysis.
Hyperglycaemia up-regulates placental growth factor (PlGF) expression and secretion in endothelial cells via suppression of PI3 kinase-Akt signalling and activation of FOXO1
Authors: Sissaoui Samir , Egginton Stuart , Ting Ling , Ahmed Asif , Hewett Peter W. 
Published: August 2021

AbstractPlacenta growth factor (PlGF) is a pro-inflammatory angiogenic mediator that promotes many pathologies including diabetic complications and atherosclerosis. Widespread endothelial dysfunction precedes the onset of these conditions. As very little is known of the mechanism(s) controlling PlGF expression in pathology we investigated the role of hyperglycaemia in the regulation of PlGF production in endothelial cells. Hyperglycaemia stimulated PlGF secretion in cultured primary endothelial cells, which was suppressed by IGF-1-mediated PI3K/Akt activation. Inhibition of PI3K activity resulted in significant PlGF mRNA up-regulation and protein secretion. Similarly, loss or inhibition of Akt activity significantly increased basal PlGF expression and prevented any further PlGF secretion in hyperglycaemia. Conversely, constitutive Akt activation blocked PlGF secretion irrespective of upstream PI3K activity demonstrating that Akt is a central regulator of PlGF expression. Knock-down of the Forkhead box O-1 (FOXO1) transcription factor, which is negatively regulated by Akt, suppressed both basal and hyperglycaemia-induced PlGF secretion, whilst FOXO1 gain-of-function up-regulated PlGF in vitro and in vivo. FOXO1 association to a FOXO binding sequence identified in the PlGF promoter also increased in hyperglycaemia. This study identifies the PI3K/Akt/FOXO1 signalling axis as a key regulator of PlGF expression and unifying pathway by which PlGF may contribute to common disorders characterised by endothelial dysfunction, providing a target for therapy.
Allopatric humpback whales of differing generations share call types between foraging and wintering grounds
Authors: Epp Mikala V. , Fournet Michelle E. H. , Silber Gregory K. , Davoren Gail K. 
Published: August 2021

AbstractHumpback whales (Megaptera novaeangliae) are a cosmopolitan baleen whale species with geographically isolated lineages. Despite last sharing an ancestor ~ 2–3 million years ago, Atlantic and Pacific foraging populations share five call types. Whether these call types are also shared between allopatric breeding and foraging populations is unclear, but would provide further evidence that some call types are ubiquitous and fixed. We investigated whether these five call types were present on a contemporary foraging ground (Newfoundland, 2015–2016) and a historic breeding ground (Hawaii, 1981–1982). Calls were classified using aural/visual (AV) characteristics; 16 relevant acoustic variables were measured and a Principal Component Analysis (PCA) was used to examine within-call and between-population variation. To assess whether between-population variation influenced classification, all 16 variables were included in classification and regression tree (CART) and random forest analyses (RF). All five call types were identified in both populations. Between-population variation in combined acoustic variables (PC1, PC2, PC3) was lower within call types than among call types, and high agreement between AV and quantitative classification (CART: 83% agreement; RF: 77% agreement) suggested that acoustic characteristics were more similar within than among call types. Findings indicate that these five call types are shared across allopatric populations, generations, and behavioural contexts.
Zeolite addition to improve biohydrogen production from dark fermentation of C5/C6-sugars and Sargassum sp. biomass
Authors: Silva R. M. , Abreu A. A. , Salvador A. F. , Alves M. M. , Neves I. C. , Pereira M. A. 
Published: August 2021

AbstractThermophilic biohydrogen production by dark fermentation from a mixture (1:1) of C5 (arabinose) and C6 (glucose) sugars, present in lignocellulosic hydrolysates, and from Sargassum sp. biomass, is studied in this work in batch assays and also in a continuous reactor experiment. Pursuing the interest of studying interactions between inorganic materials (adsorbents, conductive and others) and anaerobic bacteria, the biological processes were amended with variable amounts of a zeolite type-13X in the range of zeolite/inoculum (in VS) ratios (Z/I) of 0.065–0.26 g g−1. In the batch assays, the presence of the zeolite was beneficial to increase the hydrogen titer by 15–21% with C5 and C6-sugars as compared to the control, and an increase of 27% was observed in the batch fermentation of Sargassum sp. Hydrogen yields also increased by 10–26% with sugars in the presence of the zeolite. The rate of hydrogen production increased linearly with the Z/I ratios in the experiments with C5 and C6-sugars. In the batch assay with Sargassum sp., there was an optimum value of Z/I of 0.13 g g−1 where the H2 production rate observed was the highest, although all values were in a narrow range between 3.21 and 4.19 mmol L−1 day−1. The positive effect of the zeolite was also observed in a continuous high-rate reactor fed with C5 and C6-sugars. The increase of the organic loading rate (OLR) from 8.8 to 17.6 kg m−3 day−1 of COD led to lower hydrogen production rates but, upon zeolite addition (0.26 g g−1 VS inoculum), the hydrogen production increased significantly from 143 to 413 mL L−1 day−1. Interestingly, the presence of zeolite in the continuous operation had a remarkable impact in the microbial community and in the profile of fermentation products. The effect of zeolite could be related to several properties, including the porous structure and the associated surface area available for bacterial adhesion, potential release of trace elements, ion-exchanger capacity or ability to adsorb different compounds (i.e. protons). The observations opens novel perspectives and will stimulate further research not only in biohydrogen production, but broadly in the field of interactions between bacteria and inorganic materials.
An eye tracking based virtual reality system for use inside magnetic resonance imaging systems
Authors: Qian Kun , Arichi Tomoki , Price Anthony , Dall’Orso Sofia , Eden Jonathan , Noh Yohan , Rhode Kawal , Burdet Etienne , Neil Mark , Edwards A. David , Hajnal Joseph V. 
Published: August 2021

AbstractPatients undergoing Magnetic Resonance Imaging (MRI) often experience anxiety and sometimes distress prior to and during scanning. Here a full MRI compatible virtual reality (VR) system is described and tested with the aim of creating a radically different experience. Potential benefits could accrue from the strong sense of immersion that can be created with VR, which could create sense experiences designed to avoid the perception of being enclosed and could also provide new modes of diversion and interaction that could make even lengthy MRI examinations much less challenging. Most current VR systems rely on head mounted displays combined with head motion tracking to achieve and maintain a visceral sense of a tangible virtual world, but this technology and approach encourages physical motion, which would be unacceptable and could be physically incompatible for MRI. The proposed VR system uses gaze tracking to control and interact with a virtual world. MRI compatible cameras are used to allow real time eye tracking and robust gaze tracking is achieved through an adaptive calibration strategy in which each successive VR interaction initiated by the subject updates the gaze estimation model. A dedicated VR framework has been developed including a rich virtual world and gaze-controlled game content. To aid in achieving immersive experiences physical sensations, including noise, vibration and proprioception associated with patient table movements, have been made congruent with the presented virtual scene. A live video link allows subject-carer interaction, projecting a supportive presence into the virtual world.
Optimization of harvest and extraction factors by full factorial design for the improved yield of C-glucosyl xanthone mangiferin from Swertia chirata
Authors: Kaur Prabhjot , Gupta R. C. , Dey Abhijit , Malik Tabarak , Pandey Devendra Kumar 
Published: August 2021

AbstractSwertia chirataBuch.-Ham. ex C.B. Clarke is an important medicinal plant used in various herbal formulations as it shows significant biological activities such as hepatoprotective, hypoglycemic, anti-inflammatory, antimalarial, antioxidant and anti-parkinson. C-glucosyl xanthone glycoside (mangiferin) is known as bio-marker compound of genusSwertiaL. Development of efficient extraction methods of C-glucosyl xanthone mangiferin fromSwertia chiratawas attempted by optimizing the pre-harvest, post-harvest and extraction techniques by full factorial design. Firstly, a full factorial design was implemented to evaluate the single and interactive effects of pre-harvest (growth stage and plant part), post-harvest (drying condition and storage periods) followed by selection of best extraction technique such as heat reflux extraction (HRE), microwave assisted extraction (MAE) and ultrasound assistant extraction (UAE) at different solvent types on mangiferin yield. HPTLC and HPLC techniques were used for the determination of mangiferin content in extracts generated from different plant samples. In addition, anti-oxidant and anti-diabetic properties were determined by using DPPH assay and percentage inhibition of α‑amylase enzyme. Substantial variation of mangiferin yield, ranged from 1.46 to 4.86% was observed, depending on the growth stage, plant part, drying condition, storage periods and extraction method. Results showed that drying of the leaves ofSwertia chiratain the shade harvested at budding stage and stored for not more than 1 month was recommended for obtaining a higher mangiferin yield. Among different extraction techniques, MAE and UAE in 50% aqueous ethanol solvent were found to be efficient and cost-effective with better yield of mangiferin (4.82% and 4.86%, respectively) as compared to HRE (4.14%). Highest DPPH activity and percentage inhibition of α‑amylase was observed in the aqueous ethanol extract ofS. chirataleaves harvested at bud-stage of plant followed by flowering stage. The study shows that optimization of various factors by full factorial design was found to be an effective procedure to improve mangiferin yield fromSwertia chirataand can be used for extraction of mangiferin.
Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling
Authors: Mishra Swapnil , Scott James A. , Laydon Daniel J. , Flaxman Seth , Gandy Axel , Mellan Thomas A. , Unwin H. Juliette T. , Vollmer Michaela , Coupland Helen , Ratmann Oliver , Monod Melodie , Zhu Harrison H. , Cori Anne , Gaythorpe Katy A. M. , Whittles Lilith K. , Whittaker Charles , Donnelly Christl A. , Ferguson Neil M. , Bhatt Samir 
Published: August 2021

AbstractThe UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in the UK, Sweden and Denmark shaped COVID-19 mortality in each country, using a counterfactual assessment: what would the impact have been, had each country adopted the others’ policies? Using a Bayesian semi-mechanistic model without prior assumptions on the mechanism or effectiveness of interventions, we estimate the time-varying reproduction number for the UK, Sweden and Denmark from daily mortality data. We use two approaches to evaluate counterfactuals which transpose the transmission profile from one country onto another, in each country’s first wave from 13th March (when stringent interventions began) until 1st July 2020. UK mortality would have approximately doubled had Swedish policy been adopted, while Swedish mortality would have more than halved had Sweden adopted UK or Danish strategies. Danish policies were most effective, although differences between the UK and Denmark were significant for one counterfactual approach only. Our analysis shows that small changes in the timing or effectiveness of interventions have disproportionately large effects on total mortality within a rapidly growing epidemic.
Tumorigenic mesenchymal clusters are less sensitive to moderate osmotic stresses due to low amounts of junctional E-cadherin
Authors: Mohammed Danahe , Park Chan Young , Fredberg Jeffrey J. , Weitz David A. 
Published: August 2021

AbstractThe migration of tumorigenic cells is a critical step for metastatic breast cancer progression. Although the role of the extracellular matrix in breast cancer cell migration has been extensively described, the effect of osmotic stress on the migration of tumor breast cohorts remains unclear. Most of our understanding on the effect of osmotic stresses on cell migration comes from studies at the level of the single cell in isolation and does not take cell–cell interactions into account. Here, we study the impact of moderate osmotic stress on the migration of cell clusters composed of either non-tumorigenic or tumorigenic cells. We observe a decrease in migration distance and speed for non-tumorigenic cells but not for tumorigenic ones. To explain these differences, we investigate how osmotic stress impacts the mechanical properties of cell clusters and affects their volumes. Our findings show that tumorigenic mesenchymal cells are less sensitive to osmotic stress than non-tumorigenic cells and suggest that this difference is associated with a lower expression of E-cadherin. Using EGTA treatments, we confirm that the establishment of cell–cell adhesive interactions is a key component of the behavior of cell clusters in response to osmotic stress. This study provides evidence on the low sensitivity of mesenchymal tumorigenic clusters to moderate osmotic stress and highlights the importance of cadherin-based junctions in the response to osmotic stress.
Substitution of I222L-E119V in neuraminidase from highly pathogenic avian influenza H7N9 virus exhibited synergistic resistance effect to oseltamivir in mice
Authors: Tang Jing , Gao Rongbao , Liu Liqi , Zhang Shuxia , Liu Jia , Li Xiyan , Fang Qiongqiong , Feng Zhaomin , Xu Cuiling , Huang Weijuan , Wang Dayan 
Published: August 2021

AbstractThat the high frequency and good replication capacity of strains with reduced susceptibility to neuraminidase inhibitors (NAIs) in highly pathogenic avian influenza H7N9 (HPAI H7N9) virus made it a significance to further study its drug resistance. HPAI H7N9 viruses bearing NA I222L or E119V substitution and two mutations of I222L-E119V as well as their NAIs-sensitive counterpart were generated by reverse genetics for NA inhibition test and replication capability evaluation in vitro. The attenuated H7N9/PR8 recombinant viruses were developed to study the pathogenicity and drug resistance brought by the above substitutions to mice. The IC50 fold change of oseltamivir to HPAI H7N9 with NA222L-119V is 306.34 times than that of its susceptible strain, and 3.5 times than the E119V mutant virus. HPAI H7N9 bearing NA222L-119V had good replication ability with peak value of more than 6log10 TCID50/ml in MDCK cells. H7N9/PR8 virus bearing NA222L-119V substitutions leaded to diffuse pneumonia, significant weight loss and fatality in mice. NA E119V made H7N9/PR8 virus resistant to oseltamivir, and I222L-E119V had synergistic resistance to oseltamivir in mice. Due to the good fitness of drug resistant strains of HPAI H7N9 virus, it is necessary to strengthen drug resistance surveillance and new drug research.