bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomass Pretreatment and Enzymatic Hydrolysis Dynamics Analysis Based on Particle Size Imaging
Authors: Kapsokalyvas Dimitrios , Wilbers Arnold , Boogers Ilco A.L.A. , Appeldoorn Maaike M. , Kabel Mirjam A. , Loos Joachim , Van Zandvoort Marc A.M.J. 
Published: October 2018

AbstractParameters such as pretreatment method, enzyme type and concentration, determine the conversion efficiency of biomass’ cellulose and hemicellulose to glucose and mainly xylose in biomass-based fuel production. Chemical quantification of these processes offers no information on the effect of enzymatic hydrolysis (EH) on particle morphology. We report on the development of a microscopy method for imaging pretreated biomass particles at different EH stages. The method was based on acquiring large field of view images, typically 20×10 mm2 containing thousands of particles. Morphology of particles with lengths between 2 μm and 5 mm could be visualized and analyzed. The particle length distribution of corn stover samples, pretreated with increasing amounts of sulfuric acid at different EH stages, was measured. Particle size was shown to be dependent on pretreatment severity and EH time. The methodology developed could offer an alternative method for characterization of EH of biomass for second generation biofuels and visualization of recalcitrant structures.
The mass impacts on chemosynthetic primary producers: potential implications on anammox communities and their consequences
Authors: Pérez Noel , Velazco-Vargas Jorge Luis , Martin Osmel , Cardenas Rolando , Martínez-Frías Jesús 
Published: October 2018

AbstractThe potential of a mass asteroid impact on Earth to disturb the chemosynthetic communities at global scale is discussed. Special emphasis is made on the potential influence on anammox communities and their implications in the nitrogen biogeochemical cycle. According to our preliminary estimates, anammox communities could be seriously affected as a consequence of global cooling and the large process of acidification usually associated with the occurrence of this kind of event. The scale of affectations could vary in a scenario like the Chicxulub as a function of the amount of soot, depth of the water column and the deposition rate for sulphates assumed in each case. The most severe affectations take place where the amount of soot and sulphates produced during the event is higher and the scale of time of settlements for sulphates is short, of the order of 10 h. In this extreme case, the activity of anammox is considerably reduced, a condition that may persist for several years after the impact. Furthermore, the impact of high levels of other chemical compounds like sulphates and nitrates associated with the occurrence of this kind of event are also discussed.
Gravitational Potential Energy in Iberia: A Driver of Active Deformation in High‐Topography Regions
Authors: Neres M. , Neves M. C. , Custódio S. , Palano M. , Fernandes R. , Matias L. , Carafa M. , Terrinha P. 
Published: October 2018

AbstractIn this study, we present a new estimation of the gravitational potential energy (GPE) in Iberia and use numerical modeling to evaluate its relative contribution to the present‐day stress field and deformation. We also present an improved (larger time span and denser coverage) compilation of Global Navigation Satellite System velocities, which we use to compute the strain rate field of Iberia. We take advantage of recent neotectonic modeling developed for Iberia and northwest Africa to study the isolated dynamic contribution of GPE‐related stresses. We present two models—one including only the stress generated by GPE and another reproducing the net stress field—and compare their predictions with the most up‐to‐date compilations of stress indicators, hypocenter clusters, and geodetic strain rates. The main effect of GPE is to induce second‐order spatial variations in the stress field. GPE appears to play an important role in high‐topography regions, where it explains deviatoric stress patterns mainly associated with extensional regimes. In north Iberia, especially in the Pyrenees and Cantabria, GPE causes an extensional regime over the highest peaks. In the Iberian Chain and eastern Betics, GPE is in agreement with the observed extensional deformation. Normal focal mechanisms of shallow earthquake clusters appear to be related with GPE maxima and GPE‐induced extensional regimes. Wavelength analysis suggests that both GPE and the long‐wavelength topography of intraplate Iberia record the plate boundary forces that acted in Iberia during the Alpine orogeny at Eocene to lower Miocene times.
Electron Reconnection in the Magnetopause Current Layer
Authors: Norgren C. , Graham D. B. , Khotyaintsev Yu. V. , André M. , Vaivads A. , Hesse M. , Eriksson E. , Lindqvist P.‐A. , Lavraud B. , Burch J. , Fuselier S. , Magnes W. , Gershman D. J. , Russell C. T. 
Published: October 2018

AbstractThe electron dynamics within thin current sheets plays a key role both for the process of magnetic reconnection and other energy transfer mechanisms but, from an observational point of view, is not well understood. In this paper we report observations of a reconnecting current sheet with intermediate guide field BG=0.5Bin, where Bin is the magnetic field amplitude in the inflow regions. The current sheet width is comparable to electron spatial scales. It shows a bifurcated structure and is embedded within the magnetopause current layer with thickness of several ion scales. The electron scale current sheet has strong out‐of‐plane and in‐plane currents, Hall electric and magnetic fields, a finite magnetic field component normal to the current sheet, and nongyrotropic electron distributions formed due to finite gyroradius effects at the boundary of the current sheet. Comparison between test particle simulations and electron data shows that electrons approaching from the edge of the largest magnetic curvature are scattered to perpendicular pitch angles in the center of the current sheet while electrons entering from the opposite side remain close to field aligned. The comparison also shows that an observed depletion in phase space at antiparallel pitch angles can be explained if an out‐of‐plane electric field, which due to the guide field is close to antiparallel to the magnetic field, is present in the center of the current sheet. This electric field would be consistent with the reconnection electric field, and we therefore interpret the depletion of electron phase space density as a manifestation of ongoing reconnection.
Coseismic Throw Variation Across Along‐Strike Bends on Active Normal Faults: Implications for Displacement Versus Length Scaling of Earthquake Ruptures
Authors: Iezzi Francesco , Mildon Zoë , Walker Joanna Faure , Roberts Gerald , Goodall Huw , Wilkinson Maxwell , Robertson Jennifer 
Published: October 2018

AbstractFault bends, and associated changes in fault dip, play a key role in explaining the scatter in maximum offset versus surface rupture length fault scaling relationships. Detailed field measurements of the fault geometry and magnitude of slip in the 2016–2017 Central Italy earthquake sequence, alongside three examples from large historical normal‐faulting earthquakes in different tectonic settings, provide multiple examples in which coseismic throw increases across bends in fault strike where dip also increases beyond what is necessary to accommodate a uniform slip vector. Coseismic surface ruptures produced by two mainshocks of the 2016–2017 Central Italy earthquake sequence (24 August 2016 Mw6.0 and 30 October 2016 Mw6.5) cross a ~0.83‐km amplitude along‐strike bend, and the coseismic throws for both earthquakes increase by a factor of 2–3, where the strike of the fault changes by ~28oand the dip increases by 20–25o. We present similar examples from historical normal faulting earthquakes (1887, Sonora earthquake, Mw7.5; 1981, Corinth earthquakes, Mw6.7–6.4; and 1983, Borah Peak earthquake, Mw7.3). We demonstrate that it is possible to estimate the expected change in throw across a bend by applying equations that relate strike, dip, and slip vector to horizontal strain conservation along a nonplanar fault for a single earthquake rupture. The calculated slip enhancement in bends can explain much of the scatter in maximum displacement (Dmax) versus surface rupture length scaling relationships. If fault bends are unrecognized, they can introduce variation inDmaxthat may lead to erroneous inferences of stress drop variability for earthquakes, and exaggerate maximum earthquake magnitudes derived from vertical offsets in paleoseismic data sets.
Xenos peckii vision inspires an ultrathin digital camera
Authors: Keum Dongmin , Jang Kyung-Won , Jeon Daniel S. , Hwang Charles S. H. , Buschbeck Elke K. , Kim Min H. , Jeong Ki-Hun 
Published: October 2018

AbstractIncreased demand for compact devices leads to rapid development of miniaturized digital cameras. However, conventional camera modules contain multiple lenses along the optical axis to compensate for optical aberrations that introduce technical challenges in reducing the total thickness of the camera module. Here, we report an ultrathin digital camera inspired by the vision principle of Xenos peckii, an endoparasite of paper wasps. The male Xenos peckii has an unusual visual system that exhibits distinct benefits for high resolution and high sensitivity, unlike the compound eyes found in most insects and some crustaceans. The biologically inspired camera features a sandwiched configuration of concave microprisms, microlenses, and pinhole arrays on a flat image sensor. The camera shows a field-of-view (FOV) of 68 degrees with a diameter of 3.4 mm and a total track length of 1.4 mm. The biologically inspired camera offers a new opportunity for developing ultrathin cameras in medical, industrial, and military fields.
Global long non-coding RNA expression in the rostral anterior cingulate cortex of depressed suicides
Authors: Zhou Yi , Lutz Pierre-Eric , Wang Yu Chang , Ragoussis Jiannis , Turecki Gustavo 
Published: October 2018

AbstractLong non-coding RNAs (lncRNAs) are an emerging class of regulatory RNA that may be implicated in psychiatric disorders. Here we performed RNA-sequencing in the rostral anterior cingulate cortex of 26 depressed suicides and 24 matched controls. We first performed differential lncRNA expression analysis, and then conducted Weighted Gene Co-expression Network Analysis (WGCNA) to identify co-expression modules associating with depression and suicide. We identified 23 differentially expressed lncRNAs (FDR < 0.1) as well as their differentially expressed overlapping and antisense protein-coding genes. Several of these overlapping or antisense genes were associated with interferon signaling, which is a component of the innate immune response. Using WGCNA, we identified modules of highly co-expressed genes associated with depression and suicide and found protein-coding genes highly connected to differentially expressed lncRNAs within these modules. These protein-coding genes were located distal to their associated lncRNAs and were found to be part of several GO terms enriched in the significant modules, which include: cytoskeleton organization, plasma membrane, cell adhesion, nucleus, DNA-binding, and regulation of dendrite development and morphology. Altogether, we report that lncRNAs are differentially expressed in the brains of depressed individuals who died by suicide and may represent regulators of important molecular functions and biological processes.
SOX17 regulates uterine epithelial–stromal cross-talk acting via a distal enhancer upstream of Ihh
Authors: Wang Xiaoqiu , Li Xilong , Wang Tianyuan , Wu San-Pin , Jeong Jae-Wook , Kim Tae Hoon , Young Steven L. , Lessey Bruce A. , Lanz Rainer B. , Lydon John P. , DeMayo Francesco J. 
Published: October 2018

AbstractMammalian pregnancy depends on the ability of the uterus to support embryo implantation. Previous studies reveal the Sox17 gene as a downstream target of the Pgr-Gata2-dependent transcription network that directs genomic actions in the uterine endometrium receptive for embryo implantation. Here, we report that ablating Sox17 in the uterine epithelium impairs leukemia inhibitory factor (LIF) and Indian hedgehog homolog (IHH) signaling, leading to failure of embryo implantation. In vivo deletion of the SOX17-binding region 19 kb upstream of the Ihh locus by CRISPR-Cas technology reduces Ihh expression specifically in the uterus and alters proper endometrial epithelial–stromal interactions, thereby impairing pregnancy. This SOX17-binding interval is also bound by GATA2, FOXA2, and PGR. This cluster of transcription factor binding is common in 737 uterine genes and may represent a key regulatory element essential for uterine epithelial gene expression.
Late Bayesian inference in mental transformations
Authors: Remington Evan D. , Parks Tiffany V. , Jazayeri Mehrdad 
Published: October 2018

AbstractMany skills rely on performing noisy mental computations on noisy sensory measurements. Bayesian models suggest that humans compensate for measurement noise and reduce behavioral variability by biasing perception toward prior expectations. Whether a similar strategy is employed to compensate for noise in downstream mental and sensorimotor computations is not known. We tested humans in a battery of tasks and found that tasks which involved more complex mental transformations resulted in increased bias, suggesting that humans are able to mitigate the effect of noise in both sensorimotor and mental transformations. These results indicate that humans delay inference in order to account for both measurement noise and noise in downstream computations.
A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection
Authors: Fourati Slim , Talla Aarthi , Mahmoudian Mehrad , Burkhart Joshua G. , Klén Riku , Henao Ricardo , Yu Thomas , Aydın Zafer , Yeung Ka Yee , Ahsen Mehmet Eren , Almugbel Reem , Jahandideh Samad , Liang Xiao , Nordling Torbjörn E. M. , Shiga Motoki , Stanescu Ana , Vogel Robert ,   The Respiratory Viral DREAM Challenge Consortium, Abdallah Emna Ben , Aghababazadeh Farnoosh Abbas , Amadoz Alicia , Bhalla Sherry , Bleakley Kevin , Bongen Erika , Borzacchielo Domenico , Bucher Philipp , Carbonell-Caballero Jose , Chaudhary Kumardeep , Chinesta Francisco , Chodavarapu Prasad , Chow Ryan D , Cokelaer Thomas , Cubuk Cankut , Dhanda Sandeep Kumar , Dopazo Joaquin , Faux Thomas , Feng Yang , Flinta Christofer , Guziolowski Carito , He Di , Hidalgo Marta R. , Hou Jiayi , Inoue Katsumi , Jaakkola Maria K , Ji Jiadong , Kumar Ritesh , Kumar Sunil , Kursa Miron Bartosz , Li Qian , Łopuszyński Michał , Lu Pengcheng , Magnin Morgan , Mao Weiguang , Miannay Bertrand , Nikolayeva Iryna , Obradovic Zoran , Pak Chi , Rahman Mohammad M. , Razzaq Misbah , Ribeiro Tony , Roux Olivier , Saghapour Ehsan , Saini Harsh , Sarhadi Shamim , Sato Hiroki , Schwikowski Benno , Sharma Alok , Sharma Ronesh , Singla Deepak , Stojkovic Ivan , Suomi Tomi , Suprun Maria , Tian Chengzhe , Tomalin Lewis E. , Xie Lei , Yu Xiang , Pandey Gaurav , Chiu Christopher , McClain Micah T. , Woods Christopher W. , Ginsburg Geoffrey S. , Elo Laura L. , Tsalik Ephraim L. , Mangravite Lara M. , Sieberts Solveig K. 
Published: October 2018

AbstractThe response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses.
Gene synthesis allows biologists to source genes from farther away in the tree of life
Authors: Kunjapur Aditya M. , Pfingstag Philipp , Thompson Neil C. 
Published: October 2018

AbstractGene synthesis enables creation and modification of genetic sequences at an unprecedented pace, offering enormous potential for new biological functionality but also increasing the need for biosurveillance. In this paper, we introduce a bioinformatics technique for determining whether a gene is natural or synthetic based solely on nucleotide sequence. This technique, grounded in codon theory and machine learning, can correctly classify genes with 97.7% accuracy on a novel data set. We then classify ∼19,000 unique genes from the Addgene non-profit plasmid repository to investigate whether natural and synthetic genes have differential use in heterologous expression. Phylogenetic analysis of distance between source and expression organisms reveals that researchers are using synthesis to source genes from more genetically-distant organisms, particularly for longer genes. We provide empirical evidence that gene synthesis is leading biologists to sample more broadly across the diversity of life, and we provide a foundational tool for the biosurveillance community.
Nuclear lactate dehydrogenase A senses ROS to produce α-hydroxybutyrate for HPV-induced cervical tumor growth
Authors: Liu Yuan , Guo Ji-Zheng , Liu Ying , Wang Kui , Ding Wencheng , Wang Hui , Liu Xiang , Zhou Shengtao , Lu Xiao-Chen , Yang Hong-Bin , Xu Chenyue , Gao Wei , Zhou Li , Wang Yi-Ping , Hu Weiguo , Wei Yuquan , Huang Canhua , Lei Qun-Ying 
Published: October 2018

AbstractIt is well known that high-risk human papilloma virus (HR-HPV) infection is strongly associated with cervical cancer and E7 was identified as one of the key initiators in HPV-mediated carcinogenesis. Here we show that lactate dehydrogenase A (LDHA) preferably locates in the nucleus in HPV16-positive cervical tumors due to E7-induced intracellular reactive oxygen species (ROS) accumulation. Surprisingly, nuclear LDHA gains a non-canonical enzyme activity to produce α-hydroxybutyrate and triggers DOT1L (disruptor of telomeric silencing 1-like)-mediated histone H3K79 hypermethylation, resulting in the activation of antioxidant responses and Wnt signaling pathway. Furthermore, HPV16 E7 knocking-out reduces LDHA nuclear translocation and H3K79 tri-methylation in K14-HPV16 transgenic mouse model. HPV16 E7 level is significantly positively correlated with nuclear LDHA and H3K79 tri-methylation in cervical cancer. Collectively, our findings uncover a non-canonical enzyme activity of nuclear LDHA to epigenetically control cellular redox balance and cell proliferation facilitating HPV-induced cervical cancer development.
Multi-hierarchical profiling the structure-activity relationships of engineered nanomaterials at nano-bio interfaces
Authors: Cai Xiaoming , Dong Jun , Liu Jing , Zheng Huizhen , Kaweeteerawat Chitrada , Wang Fangjun , Ji Zhaoxia , Li Ruibin 
Published: October 2018

AbstractIncreasing concerns over the possible risks of nanotechnology necessitates breakthroughs in structure–activity relationship (SAR) analyses of engineered nanomaterials (ENMs) at nano-bio interfaces. However, current nano-SARs are often based on univariate assessments and fail to provide tiered views on ENM-induced bio-effects. Here we report a multi-hierarchical nano-SAR assessment for a representative ENM, Fe2O3, by metabolomics and proteomics analyses. The established nano-SAR profile allows the visualizing of the contributions of seven basic properties of Fe2O3 to its diverse bio-effects. For instance, although surface reactivity is responsible for Fe2O3-induced cell migration, the inflammatory effects of Fe2O3 are determined by aspect ratio (nanorods) or surface reactivity (nanoplates). These nano-SARs are examined in THP-1 cells and animal lungs, which allow us to decipher the detailed mechanisms including NLRP3 inflammasome pathway and monocyte chemoattractant protein-1-dependent signaling. This study provides more insights for nano-SARs, and may facilitate the tailored design of ENMs to render them desired bio-effects.
Shear-band affected zone revealed by magnetic domains in a ferromagnetic metallic glass
Authors: Shen L. Q. , Luo P. , Hu Y. C. , Bai H. Y. , Sun Y. H. , Sun B. A. , Liu Y. H. , Wang W. H. 
Published: October 2018

AbstractPlastic deformation of metallic glasses (MGs) has long been considered to be confined to nanoscale shear bands, but recently an affected zone around the shear band was found. Yet, due to technical limitations, the shear-band affected zone (SBAZ), which is critical for understanding shear banding and design of ductile MGs, has yet to be precisely identified. Here, by using magnetic domains as a probe with sufficiently high sensitivity and spatial resolution, we unveil the structure of SBAZs in detail. We demonstrate that shear banding is accompanied by a micrometer-scale SBAZ with a gradient in the strain field, and multiple shear bands interact through the superimposition of SBAZs. There also exists an ultra-long-range gradual elastic stress field extending hundreds of micrometers away from the shear band. Our findings provide a comprehensive picture on shear banding and are important for elucidating the micro-mechanisms of plastic deformation in glasses.
Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1
Authors: Kato Kazuki , Nishimasu Hiroshi , Oikawa Daisuke , Hirano Seiichi , Hirano Hisato , Kasuya Go , Ishitani Ryuichiro , Tokunaga Fuminori , Nureki Osamu 
Published: October 2018

AbstractENPP1 (Ecto-nucleotide pyrophosphatase phosphodiesterase 1), a type II transmembrane glycoprotein, hydrolyzes ATP to produce AMP and diphosphate, thereby inhibiting bone mineralization. A recent study showed that ENPP1 also preferentially hydrolyzes 2′3′-cGAMP (cyclic GMP-AMP) but not its linkage isomer 3′3′-cGAMP, and negatively regulates the cGAS-STING pathway in the innate immune system. Here, we present the high-resolution crystal structures of ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG. The structures revealed that the adenine and guanine bases of the dinucleotides are recognized by nucleotide- and guanine-pockets, respectively. Furthermore, the structures indicate that 2′3′-cGAMP, but not 3′3′-cGAMP, binds to the active site in a conformation suitable for catalysis, thereby explaining the specific degradation of 2′3′-cGAMP by ENPP1. Our findings provide insights into how ENPP1 hydrolyzes both ATP and cGAMP to participate in the two distinct biological processes.