bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocell arrays for simultaneous detection of diverse analytes
Authors: Zhang Yan , Kojima Taisuke , Kim Ge-Ah , McNerney Monica P. , Takayama Shuichi , Styczynski Mark P. 
Published: September 2021

AbstractSimultaneous detection of multiple analytes from a single sample (multiplexing), particularly when done at the point of need, can guide complex decision-making without increasing the required sample volume or cost per test. Despite recent advances, multiplexed analyte sensing still typically faces the critical limitation of measuring only one type of molecule (e.g., small molecules or nucleic acids) per assay platform. Here, we address this bottleneck with a customizable platform that integrates cell-free expression (CFE) with a polymer-based aqueous two-phase system (ATPS), producing membrane-less protocells containing transcription and translation machinery used for detection. We show that multiple protocells, each performing a distinct sensing reaction, can be arrayed in the same microwell to detect chemically diverse targets from the same sample. Furthermore, these protocell arrays are compatible with human biofluids, maintain function after lyophilization and rehydration, and can produce visually interpretable readouts, illustrating this platform’s potential as a minimal-equipment, field-deployable, multi-analyte detection tool.
Structural basis for UFM1 transfer from UBA5 to UFC1
Authors: Kumar Manoj , Padala Prasanth , Fahoum Jamal , Hassouna Fouad , Tsaban Tomer , Zoltsman Guy , Banerjee Sayanika , Cohen-Kfir Einav , Dessau Moshe , Rosenzweig Rina , Isupov Michail N. , Schueler-Furman Ora , Wiener Reuven 
Published: September 2021

AbstractUfmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1’s active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1’s conjugation machinery and may serve as a basis for the development of ufmylation inhibitors.
Structural and functional characterization of the bacterial biofilm activator RemA
Authors: Hoffmann Tamara , Mrusek Devid , Bedrunka Patricia , Burchert Fabiana , Mais Christopher-Nils , Kearns Daniel B. , Altegoer Florian , Bremer Erhard , Bange Gert 
Published: September 2021

AbstractBacillus subtilis can form structurally complex biofilms on solid or liquid surfaces, which requires expression of genes for matrix production. The transcription of these genes is activated by regulatory protein RemA, which binds to poorly conserved, repetitive DNA regions but lacks obvious DNA-binding motifs or domains. Here, we present the structure of the RemA homologue from Geobacillus thermodenitrificans, showing a unique octameric ring with the potential to form a 16-meric superstructure. These results, together with further biochemical and in vivo characterization of B. subtilis RemA, suggests that the protein can wrap DNA around its ring-like structure through a LytTR-related domain.
Reversible electrochemical oxidation of sulfur in ionic liquid for high-voltage Al−S batteries
Authors: Li Huan , Meng Rongwei , Guo Yong , Chen Biao , Jiao Yan , Ye Chao , Long Yu , Tadich Anton , Yang Quan-Hong , Jaroniec Mietek , Qiao Shi-Zhang 
Published: September 2021

AbstractSulfur is an important electrode material in metal−sulfur batteries. It is usually coupled with metal anodes and undergoes electrochemical reduction to form metal sulfides. Herein, we demonstrate, for the first time, the reversible sulfur oxidation process in AlCl3/carbamide ionic liquid, where sulfur is electrochemically oxidized by AlCl4− to form AlSCl7. The sulfur oxidation is: 1) highly reversible with an efficiency of ~94%; and 2) workable within a wide range of high potentials. As a result, the Al−S battery based on sulfur oxidation can be cycled steadily around ~1.8 V, which is the highest operation voltage in Al−S batteries. The study of sulfur oxidation process benefits the understanding of sulfur chemistry and provides a valuable inspiration for the design of other high-voltage metal−sulfur batteries, not limited to Al−S configurations.
Wells–Dawson phosphotungstates as mushroom tyrosinase inhibitors: a speciation study
Authors: Lampl Raphael , Breibeck Joscha , Gumerova Nadiia I. , Galanski Mathea Sophia , Rompel Annette 
Published: September 2021

AbstractIn order to elucidate the active polyoxotungstate (POT) species that inhibit fungal polyphenol oxidase (AbPPO4) in sodium citrate buffer at pH 6.8, four Wells–Dawson phosphotungstates [α/β-PV2WVI18O62]6− (intact form), [α2-PV2WVI17O61]10− (monolacunary), [PV2WVI15O56]12− (trilacunary) and [H2PV2WVI12O48]12− (hexalacunary) were investigated. The speciation of the POT solutions under the dopachrome assay (50 mM Na-citrate buffer, pH 6.8; L-3,4−dihydroxyphenylalanine as a substrate) conditions were determined by 183W-NMR, 31P-NMR spectroscopy and mass spectrometry. The intact Wells–Dawson POT [α/β-PV2WVI18O62]6− shows partial (~ 69%) disintegration into the monolacunary [α2-PV2WVI17O61]10− anion with moderate activity (Ki = 9.7 mM). The monolacunary [α2-PV2WVI17O61]10− retains its structural integrity and exhibits the strongest inhibition of AbPPO4 (Ki = 6.5 mM). The trilacunary POT [PV2WVI15O56]12− rearranges to the more stable monolacunary [α2-PV2WVI17O61]10− (~ 62%) accompanied by release of free phosphates and shows the weakest inhibition (Ki = 13.6 mM). The hexalacunary anion [H2PV2WVI12O48]12− undergoes time-dependent hydrolysis resulting in a mixture of [H2PV2WVI12O48]12−, [PV8WVI48O184]40−, [PV2WVI19O69(H2O)]14− and [α2-PV2WVI17O61]10− which together leads to comparable inhibitory activity (Ki = 7.5 mM) after 48 h. For the solutions of [α/β-PV2WVI18O62]6−, [α2-PV2WVI17O61]10− and [PV2WVI15O56]12− the inhibitory activity is correlated to the degree of their rearrangement to [α2-PV2WVI17O61]10−. The rearrangement of hexalacunary [H2PV2WVI12O48]12− into at least four POTs with a negligible amount of monolacunary anion interferes with the correlation of activity to the degree of their rearrangement to [α2-PV2WVI17O61]10−. The good inhibitory effect of the Wells–Dawson [α2-PV2WVI17O61]10− anion is explained by the low charge density of its protonated forms Hx[α2-PV2WVI17O61](10−x)− (x = 3 or 4) at pH 6.8.
A guide for the use of fNIRS in microcephaly associated to congenital Zika virus infection
Authors: Sato João Ricardo , Junior Claudinei Eduardo Biazoli , de Araújo Elidianne Layanne Medeiros , de Souza Rodrigues Júlia , Andrade Suellen Marinho 
Published: September 2021

AbstractCongenital Zika Syndrome (CZS) is characterized by changes in cranial morphology associated with heterogeneous neurological manifestations and cognitive and behavioral impairments. In this syndrome, longitudinal neuroimaging could help clinicians to predict developmental trajectories of children and tailor treatment plans accordingly. However, regularly acquiring magnetic resonance imaging (MRI) has several shortcomings besides cost, particularly those associated with childrens' clinical presentation as sensitivity to environmental stimuli. The indirect monitoring of local neural activity by non-invasive functional near-infrared spectroscopy (fNIRS) technique can be a useful alternative for longitudinally accessing the brain function in children with CZS. In order to provide a common framework for advancing longitudinal neuroimaging assessment, we propose a principled guideline for fNIRS acquisition and analyses in children with neurodevelopmental disorders. Based on our experience on collecting fNIRS data in children with CZS we emphasize the methodological challenges, such as clinical characteristics of the sample, desensitization, movement artifacts and environment control, as well as suggestions for tackling such challenges. Finally, metrics based on fNIRS can be associated with established clinical metrics, thereby opening possibilities for exploring this tool as a long-term predictor when assessing the effectiveness of treatments aimed at children with severe neurodevelopmental disorders.
Modeling and evaluation of causal factors in emergency responses to fire accidents involving oil storage system
Authors: Yuan Changfeng , Zhang Yulong , Wang Jiahui , Tong Yating 
Published: September 2021

AbstractAccording to the statistics of 160 typical fire and explosion accidents in oil storage areas at home and abroad nearly 50 years, 122 of them occurred the secondary accidents in the emergency responses. Based on 122 accident cases, 21 causal factors leading to secondary accidents are summarized. In order to quantify the influencing degree of these causal factors on the accident consequences, a multiple linear regression model was established between them. In the modeling process, these factors are decomposed into the criterion layer, variable layer, and bottom layer. The improved analytic hierarchy process (IAHP) was used to establish the relationship between the bottom factors and variable factors, and the regression analysis method was used to establish the relational model between variable layer and criterion layer. For 122 cases of the secondary accidents, this study took the year as a statistical dimension, and obtained 40 groups of sample data. The first 34 groups of sample data were used to build the causal factors model, and the last 6 groups of sample data were tested the generalization ability of the model by using the established regression model combined with grey prediction model. The results show that the prediction ability of the established model was better than that of the grey prediction model alone. Moreover, the relative contribution and change trend of the causal factors were evaluated using the mutation progression method, and corresponding preventive countermeasures were proposed. It was found that human professional skills, knowledge and literacy, environmental issues, and firefighting facilities are the main influencing factors that lead to the secondary accidents. These three kinds of factors show a gradual improvement trend, and the existing prevention measures should be maintained and further improved. The problem of inherent objects or equipment factors has not been effectively improved and has a worsening trend, which is the focus of prevention in the future, and the prevention and control efforts need to be moderately increased. The research results have important guiding significance for understanding the quantitative influences of causal factors on the accident consequences, improving emergency response capabilities, reducing accident losses, and avoiding secondary accidents.
Using least angular regression to model the antibacterial potential of metronidazole complexes
Authors: Mehmood Tahir , Iqbal Mudassir , Rafique Bushra 
Published: September 2021

AbstractImidazole has anti-inflammatory, antituberculotic, antimicrobial, antimycotic, antiviral, and antitumor properties in the human body, to name a few. Metronidazole [1-(2-Hydroxyethyl)-2-methyl-5-nitroimidazole] is a widely used antiprotozoan and antibacterial medication. Using fourier transform infrared spectroscopy, the current study models the antibacterial activity of already synthesised Metronidazole (MTZ) complexes ($$MTZ-Benz$$

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) against E. coli, B. bronceptica, S. epidermidis, B. pumilus and S. aureus. To characterise the Metronidazole complexes for antibacterial activity against 05 microbes, the least angular regression and least absolute shrinkage selection operators were used. Asymmetric Least Squares was used to correct the spectrum baseline. Least angular regression outperforms cross-validated root mean square error in the fitted models. Using Least angular regression, influential wavelengths that explain the variation in antibacterial activity of Metronidazole complexes were identified and mapped against functional groups.
Spring arctic oscillation as a trigger of summer drought in Siberian subarctic over the past 1494 years
Authors: Churakova Sidorova Olga V. , Siegwolf Rolf T. W. , Fonti Marina V. , Vaganov Eugene A. , Saurer Matthias 
Published: September 2021

AbstractRapid changes in the hydrological and temperature regimes over the past decades at the northern latitudes enhance significantly permafrost degradation accelerating carbon release, increase the frequency of drought events and extensive wildfires. However, the mechanisms and dynamics driving drought events and their influence on Siberian forests are currently the subject of numerous research activities. Newly developed and annually resolved stable carbon and oxygen isotope chronologies of larch tree-ring cellulose (δ13Ccell and δ18Ocell) for the period 516–2009 CE allowed the reconstruction of July precipitation and Arctic Oscillation (AO) in May, respectively. Unprecedented drought events occurred towards twentieth–twenty-first centuries as indicated by the July precipitation reconstruction. Positive AO phases in May were most pronounced during the second part of the first millennium, but also increased in frequency in the modern period of the twentieth–twenty-first centuries. Negative AO phases are associated with cold anomalies and show a remarkable decrease in the nineteenth century caused by a series of major volcanic eruptions. Our findings help explaining the increased frequency of Siberian forest fires over the past decades in Central Siberia consistent with a reduction of summer precipitation, triggered by a positive phase of the Arctic Oscillation in May.
Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil
Authors: Raczka Nanette C. , Piñeiro Juan , Tfaily Malak M. , Chu Rosalie K. , Lipton Mary S. , Pasa-Tolic Ljiljana , Morrissey Ember , Brzostek Edward 
Published: September 2021

AbstractMicrobial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic capabilities, growth rates). Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater diversity of fungi and bacteria than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in which species were active decomposers and the abundance of metabolic products that were reduced or saturated in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and their ability to decompose and assimilate substrates. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.
Joint contributions of metacognition and self-beliefs to uncertainty-guided checking behavior
Authors: Baptista Axel , Maheu Maxime , Mallet Luc , N’Diaye Karim 
Published: September 2021

AbstractChecking behavior is a natural and adaptive strategy for resolving uncertainty in everyday situations. Here, we aimed at investigating the psychological drivers of checking and its regulation by uncertainty, in non-clinical participants and controlled experimental settings. We found that the sensitivity of participants’ explicit confidence judgments to actual performance (explicit metacognition) predicted the extent to which their checking strategy was regulated by uncertainty. Yet, a more implicit measure of metacognition (derived from asking participants to opt between trials) did not contribute to the regulation of checking behavior. Meanwhile, how participants scaled on questionnaires eliciting self-beliefs such as self-confidence and self-reported obsessive–compulsive symptoms also predicted participants’ uncertainty-guided checking tendencies. Altogether, these findings demonstrate that checking behavior is likely the outcome of a core explicit metacognitive process operating at the scale of single decisions, while remaining influenced by general self-beliefs. Our findings are thus consistent with two mechanisms (micro vs. macro) through which this otherwise adaptive behavior could go awry in certain psychiatric disorders such as obsessive–compulsive disorder.
Fast data-driven learning of parallel MRI sampling patterns for large scale problems
Authors: Zibetti Marcelo V. W. , Herman Gabor T. , Regatte Ravinder R. 
Published: September 2021

AbstractIn this study, a fast data-driven optimization approach, named bias-accelerated subset selection (BASS), is proposed for learning efficacious sampling patterns (SPs) with the purpose of reducing scan time in large-dimensional parallel MRI. BASS is applicable when Cartesian fully-sampled k-space measurements of specific anatomy are available for training and the reconstruction method for undersampled measurements is specified; such information is used to define the efficacy of any SP for recovering the values at the non-sampled k-space points. BASS produces a sequence of SPs with the aim of finding one of a specified size with (near) optimal efficacy. BASS was tested with five reconstruction methods for parallel MRI based on low-rankness and sparsity that allow a free choice of the SP. Three datasets were used for testing, two of high-resolution brain images ($$\text {T}_{2}$$T2-weighted images and, respectively,$$\text {T}_{1\rho }$$T1ρ-weighted images) and another of knee images for quantitative mapping of the cartilage. The proposed approach has low computational cost and fast convergence; in the tested cases it obtained SPs up to 50 times faster than the currently best greedy approach. Reconstruction quality increased by up to 45% over that provided by variable density and Poisson disk SPs, for the same scan time. Optionally, the scan time can be nearly halved without loss of reconstruction quality. Quantitative MRI and prospective accelerated MRI results show improvements. Compared with greedy approaches, BASS rapidly learns effective SPs for various reconstruction methods, using larger SPs and larger datasets; enabling better selection of sampling-reconstruction pairs for specific MRI problems.
Rare and low-frequency exonic variants and gene-by-smoking interactions in pulmonary function
Authors: Yang Tianzhong , Jackson Victoria E. , Smith Albert V. , Chen Han , Bartz Traci M. , Sitlani Colleen M. , Psaty Bruce M. , Gharib Sina A. , O’Connor George T. , Dupuis Josée , Xu Jiayi , Lohman Kurt , Liu Yongmei , Kritchevsky Stephen B. , Cassano Patricia A. , Flexeder Claudia , Gieger Christian , Karrasch Stefan , Peters Annette , Schulz Holger , Harris Sarah E. , Starr John M. , Deary Ian J. , Manichaikul Ani , Oelsner Elizabeth C. , Barr R. G. , Taylor Kent D. , Rich Stephen S. , Bonten Tobias N. , Mook-Kanamori Dennis O. , Noordam Raymond , Li-Gao Ruifang , Jarvelin Marjo-Riitta , Wielscher Matthias , Terzikhan Natalie , Lahousse Lies , Brusselle Guy , Weiss Stefan , Ewert Ralf , Gläser Sven , Homuth Georg , Shrine Nick , Hall Ian P. , Tobin Martin , London Stephanie J. , Wei Peng , Morrison Alanna C. 
Published: September 2021

AbstractGenome-wide association studies have identified numerous common genetic variants associated with spirometric measures of pulmonary function, including forced expiratory volume in one second (FEV1), forced vital capacity, and their ratio. However, variants with lower minor allele frequencies are less explored. We conducted a large-scale gene-smoking interaction meta-analysis on exonic rare and low-frequency variants involving 44,429 individuals of European ancestry in the discovery stage and sought replication in the UK BiLEVE study with 45,133 European ancestry samples and UK Biobank study with 59,478 samples. We leveraged data on cigarette smoking, the major environmental risk factor for reduced lung function, by testing gene-by-smoking interaction effects only and simultaneously testing the genetic main effects and interaction effects. The most statistically significant signal that replicated was a previously reported low-frequency signal in GPR126, distinct from common variant associations in this gene. Although only nominal replication was obtained for a top rare variant signal rs142935352 in one of the two studies, interaction and joint tests for current smoking and PDE3B were significantly associated with FEV1. This study investigates the utility of assessing gene-by-smoking interactions and underscores their effects on potential pulmonary function.
Mechanical analysis of non-Newtonian nanofluid past a thin needle with dipole effect and entropic characteristics
Authors: Ramzan Muhammad , Khan Noor Saeed , Kumam Poom 
Published: September 2021

AbstractThe study concerns with the mechanical characteristics of heat and mass transfer flow of a second grade nanofluid as well as gyrotatic microorganism motion past a thin needle with dipole effect, entropy generation, thermal radiation, Arrhenius activation energy and binar chemical reaction. The governing equations and boundary conditions are simplified by the use of suitable similarity transformations. Homotopy analysis method is implemented to obtain the series solution of non-linear ordinary differential equations. Physical behaviors of heat and mass transfer flow with gyrotatic microorganisms and entropy generation are investigated through the embedded parameters. The nanofluid velocity is enhanced for higher values of the ferromagnetic parameter, local Grashof number, bioconvection Rayleigh number and radiation parameter. The Reynolds number, radiation parameter and Eckert number decrease the nanofluid temperature. The entropy generation is increased with the enhancement of radiation parameter, Eckert number, Lewis number, temperature difference parameter, dimensionless constant parameter, Curie temperature, Prandtl number and concentration difference parameter.