bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in glycated hemoglobin levels and cholesterol levels in individuals with diabetes according to Helicobacter pylori infection
Authors: Haj Saeda , Chodick Gabriel , Goren Sophy , Na’amnih Wasef , Shalev Varda , Muhsen Khitam 
Published: April 2021

AbstractThis study examined differences in glycated hemoglobin (HbA1c), fasting plasma glucose and cholesterol levels between H. pylori infected and uninfected persons with diabetes. Anonymized data of Maccabi Healthcare Services in Israel were analyzed, of 12,207 individuals (50.0% H. pylori positive) aged 25–95 years who underwent the urea breath test. The data included HbA1c, fasting plasma glucose and cholesterol levels. The inverse probability of treatment weighting approach was used to account for confounders. Differences between individuals who were H. pylori positive and negative, in HbA1c (> or ≤ 7.0%) and in cholesterol levels were assessed using weighted generalized estimating equations. For men, but not women, the likelihood of having HbA1c > 7.0% was increased in those infected than uninfected with H. pylori: prevalence ratio 1.11 (95% CI 1.00, 1.24), P = 0.04. For both sexes, total cholesterol (P = 0.004) and low-density lipoprotein (LDL) levels (P = 0.006) were higher among those infected than uninfected with H. pylori. No significant differences were found in glucose and HDL levels according to H. pylori infection. The results were consistent in unweighted multivariable analyses. In conclusion, H. pylori infection might be related to worse glycemic control in men, and higher total cholesterol and LDL cholesterol levels in both sexes.
Fast and effective pseudo transfer entropy for bivariate data-driven causal inference
Authors: Silini Riccardo , Masoller Cristina 
Published: April 2021

AbstractIdentifying, from time series analysis, reliable indicators of causal relationships is essential for many disciplines. Main challenges are distinguishing correlation from causality and discriminating between direct and indirect interactions. Over the years many methods for data-driven causal inference have been proposed; however, their success largely depends on the characteristics of the system under investigation. Often, their data requirements, computational cost or number of parameters limit their applicability. Here we propose a computationally efficient measure for causality testing, which we refer to as pseudo transfer entropy (pTE), that we derive from the standard definition of transfer entropy (TE) by using a Gaussian approximation. We demonstrate the power of the pTE measure on simulated and on real-world data. In all cases we find that pTE returns results that are very similar to those returned by Granger causality (GC). Importantly, for short time series, pTE combined with time-shifted (T-S) surrogates for significance testing strongly reduces the computational cost with respect to the widely used iterative amplitude adjusted Fourier transform (IAAFT) surrogate testing. For example, for time series of 100 data points, pTE and T-S reduce the computational time by $$82\%$$

82
%

with respect to GC and IAAFT. We also show that pTE is robust against observational noise. Therefore, we argue that the causal inference approach proposed here will be extremely valuable when causality networks need to be inferred from the analysis of a large number of short time series.
Microscopic imbibition characterization of sandstone reservoirs and theoretical model optimization
Authors: Xu Xuan , Wan Yujin , Li Xizhe , Hu Yong , Tian Shanshan , Mei Qingyan , Jiao Chunyan , Guo Changmin 
Published: April 2021

AbstractTraditional porous media imbibition models deviate from the actual imbibition process in oil and gas reservoirs. Experimental studies on gas–water imbibition in reservoirs were carried out to describe the dynamic profile variation process of wet phase saturation in reservoirs and to further reveal the variation of the imbibition front and the imbibition amount. Optimization and correction methods were established, and experimental verifications were performed. Studies have shown the following: (1) Unlike homogeneous porous media, the water phase imbibition process in oil and gas reservoirs is more complicated, and it is impossible for the maximum saturation of imbibition to reach 100%. (2) Contrary to the theoretical hypothesis, the imbibition of water is not piston-like, and there is a clear transition zone at the imbibition front. This transition zone is the main cause of water saturation variations in the imbibition zone; with the expansion of the imbibition zone, the influence of the transition zone on water saturation weakens. (3) Traditional theoretical models predict a positive correlation between the imbibition amount and the measurements; however, there is a large deviation in the numerical values, which must be corrected. (4) The L-W model was optimized and the parameter group fluid factor F and the reservoir factor R were proposed to characterize the properties of the fluid and the reservoir, respectively. These two parameters have a clear physical significance and are easy to accurately test. After experimental correction, the optimized model is favourably suitable for oil and gas reservoirs.
A paradoxical knowledge gap in science for critically endangered fishes and game fishes during the sixth mass extinction
Authors: Guy Christopher S. , Cox Tanner L. , Williams Jacob R. , Brown Colter D. , Eckelbecker Robert W. , Glassic Hayley C. , Lewis Madeline C. , Maskill Paige A. C. , McGarvey Lauren M. , Siemiantkowski Michael J. 
Published: April 2021

AbstractDespite unprecedented scientific productivity, Earth is undergoing a sixth mass extinction. The disconnect between scientific output and species conservation may be related to scientists studying the wrong species. Given fishes have a high extinction rate, we assessed the paradox between scientific productivity and science needed for conservation by comparing scientific output created for critically endangered fishes and game fishes. We searched 197,866 articles (1964–2018) in 112 journals for articles on 460 critically endangered fishes, 297 game fishes, and 35 fishes classified as critically endangered and game fish—our analysis included freshwater and marine species. Only 3% of the articles in the final database were on critically endangered fishes; 82% of critically endangered fishes had zero articles. The difference between the number of articles on game fishes and critically endangered fishes increased temporally with more articles on game fishes during the extinction crisis. Countries with 10 or more critically endangered fishes averaged only 17 articles from 1964 to 2018. Countries with the most critically endangered fishes are most in need of science. More scientific knowledge is needed on critically endangered fishes to meet the challenges of conserving fishes during the sixth mass extinction.
A 3 pJ/bit free space optical interlink platform for self-powered tetherless sensing and opto-spintronic RF-to-optical transduction
Authors: Wheaton Skyler , Lopez-Dominguez Victor , Almasi Hamid , Cai Jialin , Zeng Zhongming , Khalili Amiri Pedram , Mohseni Hooman 
Published: April 2021

AbstractTetherless sensors have long been positioned to enable next generation applications in biomedical, environmental, and industrial sectors. The main challenge in enabling these advancements is the realization of a device that is compact, robust over time, and highly efficient. This paper presents a tetherless optical tag which utilizes optical energy harvesting to realize scalable self-powered devices. Unlike previous demonstrations of optically coupled sensor nodes, the device presented here amplifies signals and encodes data on the same optical beam that provides its power. This optical interrogation modality results in a highly efficient data link. These optical tags support data rates up to 10 Mb/s with an energy consumption of ~ 3 pJ/bit. As a proof-of-concept application, the optical tag is combined with a spintronic microwave detector based on a magnetic tunnel junction (MTJ). We used this hybrid opto-spintronic system to perform self-powered transduction of RF waves at 1 GHz to optical frequencies at ~ 200 THz, while carrying an audio signal across (see Supplementary Data for audio files).
Image-based personalization of computational models for predicting response of high-grade glioma to chemoradiation
Authors: Hormuth David A. , Al Feghali Karine A. , Elliott Andrew M. , Yankeelov Thomas E. , Chung Caroline 
Published: April 2021

AbstractHigh-grade gliomas are an aggressive and invasive malignancy which are susceptible to treatment resistance due to heterogeneity in intratumoral properties such as cell proliferation and density and perfusion. Non-invasive imaging approaches can measure these properties, which can then be used to calibrate patient-specific mathematical models of tumor growth and response. We employed multiparametric magnetic resonance imaging (MRI) to identify tumor extent (via contrast-enhanced T1-weighted, and T2-FLAIR) and capture intratumoral heterogeneity in cell density (via diffusion-weighted imaging) to calibrate a family of mathematical models of chemoradiation response in nine patients with unresected or partially resected disease. The calibrated model parameters were used to forecast spatially-mapped individual tumor response at future imaging visits. We then employed the Akaike information criteria to select the most parsimonious member from the family, a novel two-species model describing the enhancing and non-enhancing components of the tumor. Using this model, we achieved low error in predictions of the enhancing volume (median: − 2.5%, interquartile range: 10.0%) and a strong correlation in total cell count (Kendall correlation coefficient 0.79) at 3-months post-treatment. These preliminary results demonstrate the plausibility of using multiparametric MRI data to inform spatially-informative, biologically-based predictive models of tumor response in the setting of clinical high-grade gliomas.
Olfactory signals and fertility in olive baboons
Authors: Vaglio Stefano , Minicozzi Pamela , Kessler Sharon E. , Walker David , Setchell Joanna M. 
Published: April 2021

AbstractFemale primates signal impending ovulation with a suite of sexual signals. Studies of these signals have focussed on visual, and to a lesser extent, acoustic signals, neglecting olfactory signals. We aimed to investigate the information content of female olfactory signals in captive olive baboons (Papio anubis) and relate these to the female fertile period. We studied eight adult females living in four groups at the CNRS Station de Primatologie, Rousset-sur-Arc, France. We used vaginal cytology to detect ovulation. We investigated the volatile component of odour signals using solid-phase microextraction and gas chromatography-mass spectrometry. We found a total of 74 volatile compounds, of which we tentatively identified 25, including several ketones, alcohols, aldehydes, terpenes, volatile fatty acids and hydrocarbons that have been identified in odour profiles of other primates. Our results show that vaginal odour intensity differs with sexual cycle stage suggesting that odour might play a role in signalling female baboon fertility. We found differences in vaginal odour between females living in all-female and in mixed sex groups but we could not distinguish the effects of group composition, female age and identity. This study of olfactory signalling improves our understanding of how female primates advertise their sexual receptivity.
Zika-exposed microcephalic neonates exhibit higher degree of inflammatory imbalance in cerebrospinal fluid
Authors: Nascimento-Carvalho Gustavo C. , Nascimento-Carvalho Eduardo C. , Ramos Clara L. , Vilas-Boas Ana-Luisa , Moreno-Carvalho Otávio A. , Vinhaes Caian L. , Barreto-Duarte Beatriz , Queiroz Artur T. L. , Andrade Bruno B. , Nascimento-Carvalho Cristiana M. 
Published: April 2021

AbstractNot every neonate with congenital Zika virus (ZIKV) infection (CZI) is born with microcephaly. We compared inflammation mediators in CSF (cerebrospinal fluid obtained from lumbar puncture) between ZIKV-exposed neonates with/without microcephaly (cases) and controls. In Brazil, in the same laboratory, we identified 14 ZIKV-exposed neonates during the ZIKV epidemic (2015–2016), 7(50%) with and 7(50%) without microcephaly, without any other congenital infection, and 14 neonates (2017–2018) eligible to be controls and to match cases. 29 inflammation mediators were measured using Luminex immunoassay and multidimensional analyses were employed. Neonates with ZIKV-associated microcephaly presented substantially higher degree of inflammatory perturbation, associated with uncoupled inflammatory response and decreased correlations between concentrations of inflammatory biomarkers. The groups of microcephalic and non-microcephalic ZIKV-exposed neonates were distinguished from the control group (area under curve [AUC] = 1; P < 0.0001). Between controls and those non-microcephalic exposed to ZIKV, IL-1β, IL-3, IL-4, IL-7 and EOTAXIN were the top CSF markers. By comparing the microcephalic cases with controls, the top discriminant scores were for IL-1β, IL-3, EOTAXIN and IL-12p70. The degree of inflammatory imbalance may be associated with microcephaly in CZI and it may aid additional investigations in experimental pre-clinical models testing immune modulators in preventing extensive damage of the Central Nervous System.
Multiscale investigation on the chemical and anatomical changes of lignocellulosic biomass for different severities of hydrothermal treatment
Authors: Lancha Julia P. , Perré Patrick , Colin Julien , Lv Pin , Ruscassier Nathalie , Almeida Giana 
Published: April 2021

AbstractThe chemical changes sustained by lignocellulosic biomass during hydrothermal treatment are reflected at multiple scales. This study proposes to benefit from this multiscale nature in order to provide a global understanding of biomass alterations during hydrothermal treatment. For this purpose, complementary imaging techniques—confocal Raman microscopy and X-ray nano-tomography—analysed by image processing and coupled to chemical measurements were used. This unique combination of analyses provided valuable information on topochemical and morphological changes of poplar samples, without the artefacts of sample preparation. At the cell wall level, holocellulose hydrolysis and lignin modifications were observed, which corresponded to anatomical modifications observed at higher scales. Overall, after treatment, samples shrank and had thinner cell walls. When subjected to more severe pre-treatments, cells were disrupted and detached from adjacent cells. Anatomical changes were then used to obtain quantitative indicators of the treatment severity. The effects of treatment at different scales can thus be quantitatively connected in both directions, from micro to macro and from macro to micro.
Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Authors: Sutcliffe Diane J. , Dinasarapu Ashok R. , Visser Jasper E. , Hoed Joery den , Seifar Fatemeh , Joshi Piyush , Ceballos-Picot Irene , Sardar Tejas , Hess Ellen J. , Sun Yan V. , Wen Zhexing , Zwick Michael E. , Jinnah H. A. 
Published: April 2021

AbstractLesch-Nyhan disease (LND) is an inherited disorder caused by pathogenic variants in the HPRT1 gene, which encodes the purine recycling enzyme hypoxanthine–guanine phosphoribosyltransferase (HGprt). We generated 6 induced pluripotent stem cell (iPSC) lines from 3 individuals with LND, along with 6 control lines from 3 normal individuals. All 12 lines had the characteristics of pluripotent stem cells, as assessed by immunostaining for pluripotency markers, expression of pluripotency genes, and differentiation into the 3 primary germ cell layers. Gene expression profiling with RNAseq demonstrated significant heterogeneity among the lines. Despite this heterogeneity, several anticipated abnormalities were readily detectable across all LND lines, including reduced HPRT1 mRNA. Several unexpected abnormalities were also consistently detectable across the LND lines, including decreases in FAR2P1 and increases in RNF39. Shotgun proteomics also demonstrated several expected abnormalities in the LND lines, such as absence of HGprt protein. The proteomics study also revealed several unexpected abnormalities across the LND lines, including increases in GNAO1 decreases in NSE4A. There was a good but partial correlation between abnormalities revealed by the RNAseq and proteomics methods. Finally, functional studies demonstrated LND lines had no HGprt enzyme activity and resistance to the toxic pro-drug 6-thioguanine. Intracellular purines in the LND lines were normal, but they did not recycle hypoxanthine. These cells provide a novel resource to reveal insights into the relevance of heterogeneity among iPSC lines and applications for modeling LND.
Toxicity of biogenic zinc oxide nanoparticles to soil organic matter cycling and their interaction with rice-straw derived biochar
Authors: Shemawar  , Mahmood Abid , Hussain Sabir , Mahmood Faisal , Iqbal Muhammad , Shahid Muhammad , Ibrahim Muhammad , Ali Muhammad Arif , Shahzad Tanvir 
Published: April 2021

AbstractGiven the rapidly increasing use of metal oxide nanoparticles in agriculture as well as their inadvertent addition through sewage sludge application to soils, it is imperative to assess their possible toxic effects on soil functions that are vital for healthy crop production. In this regard, we designed a lab study to investigate the potential toxicity of one of the most produced nanoparticles, i.e. zinc oxide nanoparticles (nZnO), in a calcareous soil. Microcosms of 80 g of dry-equivalent fresh soils were incubated in mason jars for 64 days, after adding 100 or 1000 mg of biogenically produced nZnO kg−1 soil. Moreover, we also added rice-straw derived biochar at 1 or 5% (w: w basis) hypothesizing that the biochar would alleviate nZnO-induced toxicity given that it has been shown to adsorb and detoxify heavy metals in soils. We found that the nZnO decreased microbial biomass carbon by 27.0 to 33.5% in 100 mg nZnO kg−1 soil and by 39.0 to 43.3% in 1000 mg nZnO kg−1 soil treatments across biochar treatments in the short term i.e. 24 days after incubation. However, this decrease disappeared after 64 days of incubation and the microbial biomass in nZnO amended soils were similar to that in control soils. This shows that the toxicity of nZnO in the studied soil was ephemeral and transient which was overcome by the soil itself in a couple of months. This is also supported by the fact that the nZnO induced higher cumulative C mineralization (i.e. soil respiration) at both rates of addition. The treatment 100 mg nZnO kg−1 soil induced 166 to 207%, while 1000 mg nZnO kg−1 soil induced 136 to 171% higher cumulative C mineralization across biochar treatments by the end of the experiment. However, contrary to our hypothesis increasing the nZnO addition from 100 to 1000 mg nZnO kg−1 soil did not cause additional decrease in microbial biomass nor induced higher C mineralization. Moreover, the biochar did not alleviate even the ephemeral toxicity that was observed after 24d of incubation. Based on overall results, we conclude that the studied soil can function without impairment even at 1000 mg kg−1 concentration of nZnO in it.
Antifreeze protein from Ammopiptanthus nanus functions in temperature-stress through domain A
Authors: Yu HaoQiang , Zheng HongYing , Liu Yuan , Yang QingQing , Li WanChen , Zhang YuanYuan , Fu FengLing 
Published: April 2021

AbstractTemperature stress restricts plant growth and development. Antifreeze protein (AFP) can improve plants antifreeze ability. In our previous study, the AnAFP gene cloned from Ammopiptanthus nanus was confirmed to be an excellent candidate enhancing plant cold resistance. But, AnAFP protein shared similar structures with KnS type dehydrins including K, N and S domains except ice crystal binding domain A. Here, we generated AnAFPΔA, AnAFPΔK, AnAFPΔN and AnAFPΔS, and transformed them into ordinary and cold sensitive strains of E. coli, and Arabidopsis KS type dehydrin mutant to evaluate their function. Expression of AnAFPΔA decreases cold and heat tolerance in E. coli, meanwhile, AnAFP enhances heat tolerance in Arabidopsis, suggesting that domain A is a thermal stable functional domain. AnAFP, AnAFPΔA and AnAFPΔS localize in whole cell, but AnAFPΔK and AnAFPΔN only localizes in nucleus and cytoplasm, respectively, exhibiting that K and N domains control localization of AnAFP. Likewise, K domain blocks interaction between AnAFP and AnICE1. The result of RT-qPCR showed that expression of AnAFP, AnICE1 and AnCBF genes was significantly induced by high-temperature, indicating that the AnAFP is likely regulated by ICE1-CBF-COR signal pathway. Taken together, the study provides insights into understanding the mechanism of AnAFP in response to temperature stress and gene resource to improve heat or cold tolerance of plants in transgenic engineering.
High throughput viscoelastic particle focusing and separation in spiral microchannels
Authors: Kumar Tharagan , Ramachandraiah Harisha , Iyengar Sharath Narayana , Banerjee Indradumna , Mårtensson Gustaf , Russom Aman 
Published: April 2021

AbstractPassive particle manipulation using inertial and elasto-inertial microfluidics have received substantial interest in recent years and have found various applications in high throughput particle sorting and separation. For separation applications, elasto-inertial microfluidics has thus far been applied at substantial lower flow rates as compared to inertial microfluidics. In this work, we explore viscoelastic particle focusing and separation in spiral channels at two orders of magnitude higher Reynolds numbers than previously reported. We show that the balance between dominant inertial lift force, dean drag force and elastic force enables stable 3D particle focusing at dynamically high Reynolds numbers. Using a two-turn spiral, we show that particles, initially pinched towards the inner wall using an elasticity enhancer, PEO (polyethylene oxide), as sheath migrate towards the outer wall strictly based on size and can be effectively separated with high precision. As a proof of principle for high resolution particle separation, 15 µm particles were effectively separated from 10 µm particles. A separation efficiency of 98% for the 10 µm and 97% for the 15 µm particles was achieved. Furthermore, we demonstrate sheath-less, high throughput, separation using a novel integrated two-spiral device and achieved a separation efficiency of 89% for the 10 µm and 99% for the 15 µm particles at a sample flow rate of 1 mL/min—a throughput previously only reported for inertial microfluidics. We anticipate the ability to precisely control particles in 3D at extremely high flow rates will open up several applications, including the development of ultra-high throughput microflow cytometers and high-resolution separation of rare cells for point of care diagnostics.