bluuebunny/crossref_metadata_2025_split huggingface dataset:
The presence of Superfund sites as a determinant of life expectancy in the United States
Authors: Kiaghadi Amin , Rifai Hanadi S. , Dawson Clint N. 
Published: April 2021

AbstractSuperfund sites could affect life expectancy (LE) via increasing the likelihood of exposure to toxic chemicals. Here, we assess to what extent such presence could alter the LE independently and in the context of sociodemographic determinants. A nationwide geocoded statistical modeling at the census tract level was undertaken to estimate the magnitude of impact. Results showed a significant difference in LE among census tracts with at least one Superfund site and their neighboring tracts with no sites. The presence of a Superfund site could cause a decrease of −0.186 ± 0.027 years in LE. This adverse effect could be as high as −1.22 years in tracts with Superfund sites and high sociodemographic disadvantage. Specific characteristics of Superfund sites such as being prone to flooding and the absence of a cleanup strategy could amplify the adverse effect. Furthermore, the presence of Superfund sites amplifies the negative influence of sociodemographic factors at lower LEs.
Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis
Authors: Garnish Sarah E. , Meng Yanxiang , Koide Akiko , Sandow Jarrod J. , Denbaum Eric , Jacobsen Annette V. , Yeung Wayland , Samson Andre L. , Horne Christopher R. , Fitzgibbon Cheree , Young Samuel N. , Smith Phoebe P. C. , Webb Andrew I. , Petrie Emma J. , Hildebrand Joanne M. , Kannan Natarajan , Czabotar Peter E. , Koide Shohei , Murphy James M. 
Published: April 2021

AbstractPhosphorylation of the MLKL pseudokinase by the RIPK3 kinase leads to MLKL oligomerization, translocation to, and permeabilization of, the plasma membrane to induce necroptotic cell death. The precise choreography of MLKL activation remains incompletely understood. Here, we report Monobodies, synthetic binding proteins, that bind the pseudokinase domain of MLKL within human cells and their crystal structures in complex with the human MLKL pseudokinase domain. While Monobody-32 constitutively binds the MLKL hinge region, Monobody-27 binds MLKL via an epitope that overlaps the RIPK3 binding site and is only exposed after phosphorylated MLKL disengages from RIPK3 following necroptotic stimulation. The crystal structures identified two distinct conformations of the MLKL pseudokinase domain, supporting the idea that a conformational transition accompanies MLKL disengagement from RIPK3. These studies provide further evidence that MLKL undergoes a large conformational change upon activation, and identify MLKL disengagement from RIPK3 as a key regulatory step in the necroptosis pathway.
A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction
Authors: Ho Trevor Y. H. , Shao Alexander , Lu Zeyu , Savilahti Harri , Menolascina Filippo , Wang Lei , Dalchau Neil , Wang Baojun 
Published: April 2021

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.
Efficient calculation of carrier scattering rates from first principles
Authors: Ganose Alex M. , Park Junsoo , Faghaninia Alireza , Woods-Robinson Rachel , Persson Kristin A. , Jain Anubhav 
Published: April 2021

AbstractThe electronic transport behaviour of materials determines their suitability for technological applications. We develop a computationally efficient method for calculating carrier scattering rates of solid-state semiconductors and insulators from first principles inputs. The present method extends existing polar and non-polar electron-phonon coupling, ionized impurity, and piezoelectric scattering mechanisms formulated for isotropic band structures to support highly anisotropic materials. We test the formalism by calculating the electronic transport properties of 23 semiconductors, including the large 48 atom CH3NH3PbI3 hybrid perovskite, and comparing the results against experimental measurements and more detailed scattering simulations. The Spearman rank coefficient of mobility against experiment (rs = 0.93) improves significantly on results obtained using a constant relaxation time approximation (rs = 0.52). We find our approach offers similar accuracy to state-of-the art methods at approximately 1/500th the computational cost, thus enabling its use in high-throughput computational workflows for the accurate screening of carrier mobilities, lifetimes, and thermoelectric power.
Discovery of temperature-induced stability reversal in perovskites using high-throughput robotic learning
Authors: Zhao Yicheng , Zhang Jiyun , Xu Zhengwei , Sun Shijing , Langner Stefan , Hartono Noor Titan Putri , Heumueller Thomas , Hou Yi , Elia Jack , Li Ning , Matt Gebhard J. , Du Xiaoyan , Meng Wei , Osvet Andres , Zhang Kaicheng , Stubhan Tobias , Feng Yexin , Hauch Jens , Sargent Edward H. , Buonassisi Tonio , Brabec Christoph J. 
Published: April 2021

AbstractStability of perovskite-based photovoltaics remains a topic requiring further attention. Cation engineering influences perovskite stability, with the present-day understanding of the impact of cations based on accelerated ageing tests at higher-than-operating temperatures (e.g. 140°C). By coupling high-throughput experimentation with machine learning, we discover a weak correlation between high/low-temperature stability with a stability-reversal behavior. At high ageing temperatures, increasing organic cation (e.g. methylammonium) or decreasing inorganic cation (e.g. cesium) in multi-cation perovskites has detrimental impact on photo/thermal-stability; but below 100°C, the impact is reversed. The underlying mechanism is revealed by calculating the kinetic activation energy in perovskite decomposition. We further identify that incorporating at least 10 mol.% MA and up to 5 mol.% Cs/Rb to maximize the device stability at device-operating temperature (<100°C). We close by demonstrating the methylammonium-containing perovskite solar cells showing negligible efficiency loss compared to its initial efficiency after 1800 hours of working under illumination at 30°C.
Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant
Authors: Mori Yutaro , Noda Shuhei , Shirai Tomokazu , Kondo Akihiko 
Published: April 2021

AbstractThe C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO–stat fed-batch fermentation, we produce 2.13 ± 0.17 g L−1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.
Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress
Authors: Barraud Nicolas , Létoffé Sylvie , Beloin Christophe , Vinh Joelle , Chiappetta Giovanni , Ghigo Jean-Marc 
Published: April 2021

AbstractCommunities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen, and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG, and GltD altered important biofilm properties, including motility, biofilm maturation, or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.
Genetic variation and population structure in China summer maize germplasm
Authors: Shu Guoping , Cao Gangqiang , Li Niannian , Wang Aifang , Wei Fang , Li Ting , Yi Li , Xu Yunbi , Wang Yibo 
Published: April 2021

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.
Sex and Tamoxifen confound murine experimental studies in cardiovascular tissue engineering
Authors: Blum Kevin M. , Roby Lauren C. , Zbinden Jacob C. , Chang Yu-Chun , Mirhaidari Gabriel J. M. , Reinhardt James W. , Yi Tai , Barker Jenny C. , Breuer Christopher K. 
Published: April 2021

AbstractTissue engineered vascular grafts hold promise for the creation of functional blood vessels from biodegradable scaffolds. Because the precise mechanisms regulating this process are still under investigation, inducible genetic mouse models are an important and widely used research tool. However, here we describe the importance of challenging the baseline assumption that tamoxifen is inert when used as a small molecule inducer in the context of cardiovascular tissue engineering. Employing a standard inferior vena cava vascular interposition graft model in C57BL/6 mice, we discovered differences in the immunologic response between control and tamoxifen-treated animals, including occlusion rate, macrophage infiltration and phenotype, the extent of foreign body giant cell development, and collagen deposition. Further, differences were noted between untreated males and females. Our findings demonstrate that the host-response to materials commonly used in cardiovascular tissue engineering is sex-specific and critically impacted by exposure to tamoxifen, necessitating careful model selection and interpretation of results.
Quantitative structure–activity relationship models for genotoxicity prediction based on combination evaluation strategies for toxicological alternative experiments
Authors: Yang Xiaotong , Zhang Zhengbao , Li Qing , Cai Yongming 
Published: April 2021

AbstractMutagenicity exerts adverse effects on humans. Conventional methods cannot simultaneously predict the toxicity of a large number of compounds. Most mutagenicity prediction models are based on a single experimental type and lack other experimental combination data as support, resulting in limited application scope and predictive ability. In this study, we partitioned data from GENE-TOX, CPDB, and Chemical Carcinogenesis Research Information System according to the weight-of-evidence method for modelling. In our data set, in vivo and in vitro experiments in groups as well as prokaryotic and eukaryotic cell experiments were included in accordance with the ICH guideline. We compared the two experimental combinations mentioned in the weight-of-evidence method and reintegrated the experimental data into three groups. Nine sub-models and three fusion models were established using random forest (RF), support vector machine (SVM), and back propagation (BP) neural network algorithms. When fusing base models under the same algorithm according to the ensemble rules, all models showed excellent predictive performance. The RF, SVM, and BP fusion models reached a prediction accuracy rate of 83.4%, 80.5%, 79.0% respectively. The area under the curve (AUC) reached 0.853, 0.897, 0.865 respectively. Therefore, the established fusion QSAR models can serve as an early warning system for mutagenicity of compounds.
Inverse association between serum bilirubin level and testosterone deficiency in middle-aged and older men
Authors: Park Hye-Min , Kim Haeyoung , Lee Hye Sun , Lee Yong-Jae 
Published: April 2021

AbstractLow serum bilirubin levels have been associated with increased risk of cardiovascular disease (CVD) and metabolic syndrome. Testosterone deficiency could also contribute to increased risk of CVD and metabolic syndrome. Therefore, this study aimed to examine the relationship between serum bilirubin level and testosterone deficiency in 1284 Korean men aged 45 to 70 years. Serum bilirubin level was categorized into quartiles: Q1 ≤ 0.7, Q2 0.8–0.9, Q3 1.0–1.1, and Q4 ≥ 1.2 mg/dL. Testosterone deficiency was defined as level less than 8.0 nmol/L, as suggested by the position statement of International Society of Andrology. The overall prevalence of testosterone deficiency was 5.8% and significantly decreased with the quartiles from Q1 to Q4. Compared with the referent fourth quartile (serum bilirubin ≥ 1.2 mg/dL), the ORs (95% CIs) for testosterone deficiency was 2.29 (1.04–4.94) for the first quartile after adjusting for age, fasting glucose, triglyceride, HDL-cholesterol, leukocyte count, hemoglobin, smoking status, and alcohol intake. We found inversely graded associations of serum bilirubin level with testosterone deficiency. These findings suggest that low bilirubin level may be interpreted as a state of testosterone deficiency in middle-aged and older men.
Towards spatially resolved magnetic small-angle scattering studies by polarized and polarization-analyzed neutron dark-field contrast imaging
Authors: Valsecchi Jacopo , Kim Youngju , Lee Seung Wook , Saito Kotaro , Grünzweig Christian , Strobl Markus 
Published: April 2021

AbstractIn the past decade neutron dark-field contrast imaging has developed from a qualitative tool depicting microstructural inhomogeneities in bulk samples on a macroscopic scale of tens to hundreds of micrometers to a quantitative spatial resolved small-angle scattering instrument. While the direct macroscopic image resolution around tens of micrometers remains untouched microscopic structures have become assessable quantitatively from the nanometer to the micrometer range. Although it was found that magnetic structures provide remarkable contrast we could only recently introduce polarized neutron grating interferometric imaging. Here we present a polarized and polarization analyzed dark-field contrast method for spatially resolved small-angle scattering studies of magnetic microstructures. It is demonstrated how a polarization analyzer added to a polarized neutron grating interferometer does not disturb the interferometric measurements but allows to separate and measure spin-flip and non-spin-flip small-angle scattering and thus also the potential for a distinction of nuclear and different magnetic contributions in the analyzed small-angle scattering.
Interaction of surface pattern and contour shape in the tilt after effects evoked by symmetry
Authors: Sakai Ko , Sakata Yui , Kurematsu Ken 
Published: April 2021

AbstractIntegration of multiple properties of an object is a fundamental function of the visual cortex in object recognition. For instance, surface patterns and contour shapes are thought to be crucial characteristics that jointly contribute to recognition. However, the mechanisms of integration and corresponding cortical representations have not been fully clarified. We investigated the integration of surfaces and shapes by examining the tilt after effects (TAEs) evoked by the symmetry of patterns and contours. As symmetry in both pattern and contour evokes TAEs, we can directly measure the interaction between the two. The measured TAEs exhibited mutual transfer between the symmetry of the pattern (SP) and that of the contour shape (SS), i.e., adaptation by SP (SS) evoked TAEs when tested by SS (SP), suggesting the existence of an integrated representation. Next, we examined the interaction between SP and SS when both were simultaneously presented in adaptation. Congruent adaptors wherein their symmetry axes aligned evoked compressive interaction, whereas incongruent adaptors wherein the axes of SP and SS tilted to the opposite directions evoked subtractive interaction. These results suggest the existence of a cortical representation that integrates the properties of the surface and shape with suppressive interactions, which can provide crucial insights into the formation of object representation as well as the integration of visual information in the cortex.
In vitro evaluation of simulated stereotactic radiotherapy for wet age-related macular degeneration on three different cell lines
Authors: Vounotrypidis Efstathios , Hillenmayer Anna , Wertheimer Christian M. , Athanasiou Alexis , Siedlecki Jakob , Orth Michael , Ohlmann Andreas , Priglinger Siegfried G. , Wolf Armin 
Published: April 2021

AbstractLow energy stereotactic radiotherapy has been proposed for the treatment of neovascular age related macular degeneration. We investigated the in vitro effect of the radiotherapy on pericytes, retinal pigment epithelium and endothelial cells. Primary human retinal pigment epithelium cells, human umbilical vein endothelial cells and human pericytes from Placenta were cultivated. In a pairwise protocol, one plate was irradiated at a dose of 16 Gy, while the second plate served as a non-irradiated control. Thereafter, cells were cultivated either in serum-free (non-permissive) or serum-stimulated (permissive) conditions. A life/dead assay, an XTT and a BrdU assay were performed up to 7 days after irradiation. No cell death occurred at any timepoint in any cell line after treatment nor in the control. Compared to the unirradiated controls, cell viability and metabolic activity were significantly reduced in irradiated cells in the XTT assay, except for non-permissive RPE cells. In the BrdU assay, proliferation was inhibited. While no cell death was detected in vitro, viability and proliferative capacity of all cell lines were significantly reduced. Therefore, it seems that low energy stereotactic radiotherapy inhibits angiogenesis without a direct induction of apoptosis but influencing microvascular function and stability.
High-fidelity and high-resolution phase mapping of granites via confocal Raman imaging
Authors: Polavaram Krishna C. , Garg Nishant 
Published: April 2021

AbstractIn physical sciences such as chemistry and earth sciences, specifically for characterization of minerals in a rock, automated, objective mapping methods based on elemental analysis have replaced traditional optical petrography. However, mineral phase maps obtained from these newer approaches rely on conversion of elemental compositions to mineralogical compositions and thus cannot distinguish mineral polymorphs. Secondly, these techniques often require laborious sample preparations such as sectioning, polishing, and coating which are time-consuming. Here, we develop a new Raman imaging protocol that is capable of mapping unpolished samples with an auto-focusing Z-mapping feature that allows direct fingerprinting of different polymorphs. Specifically, we report a new methodology for generating high fidelity phase maps by exploiting characteristic peak intensity ratios which can be extended to any multi-phase, heterogenous system. Collectively, these enhancements allow us to rapidly map an unpolished granite specimen (~ 2 × 2 mm) with an exceptionally high accuracy (> 97%) and an extremely fine spatial resolution (< 0.3–2 µm).
Development of a chiral HPLC method for the separation and quantification of hydroxychloroquine enantiomers
Authors: Xiong Xisheng , Wang Kun , Tang Tao , Fang Jinzhi , Chen Yijun 
Published: April 2021

AbstractHydroxychloroquine (2-[[4-[(7-Chloroquinolin-4-yl) amino]pentyl](ethyl) amino]-ethanol, HCQ), an effective anti-malarial drug, has been tested in the clinics for potential treatment of severe coronavirus disease 2019 (COVID-19). Despite the controversy around the clinical benefits of HCQ, the existence of a chiral center in the molecule to possess two optical isomers suggests that there might be an enantiomeric difference on the treatment of COVID-19. Due to their poor resolution and the inability of quantification by previously reported methods for the analysis of HCQ enantiomers, it is necessary to develop an analytical method to achieve baseline separation for quantitative and accurate determination of the enantiomeric purity in order to compare the efficacy and toxicity profiles of different enantiomers. In this study, we developed and validated an accurate and reproducible normal phase chiral high-performance liquid chromatography (HPLC) method for the analysis of two enantiomers of HCQ, and the method was further evaluated with biological samples. With this newly developed method, the relative standard deviations of all analytes were lower than 5%, and the limits of quantification were 0.27 μg/ml, 0.34 μg/ml and 0.20 μg/ml for racemate, R- and S-enantiomer, respectively. The present method provides an essential analytical tool for preclinical and clinical evaluation of HCQ enantiomers for potential treatment of COVID-19.