bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy Partitioning During Subcritical Mode I Crack Propagation Through a Heterogeneous Interface
Authors: Jestin Camille , Lengliné Olivier , Schmittbuhl Jean 
Published: January 2019

AbstractThe energy budget during the propagation of tensile fractures typically includes two major energy dissipation modes: the fracture energy to create a new interface and the radiated energy. Since seismic hazard is related to the amount of seismic energy released, it is important to evaluate precisely the energy budget during fracture propagation and see in particular if it is constant or not. However, two aspects are typically limiting a precise estimate of the energy budget: first, the measurement of the nonseismic energy release and second, the rock heterogeneity‐like asperities or barriers. We conducted here laboratory experiments, using an analog material (Polymethyl methacrylate (PMMA)), of a stable mode I interfacial crack propagation close to brittle‐creep transition through a heterogeneous interface for different macroscopic rupture velocities to evaluate carefully their energy budget. Both acoustic and optical advances of the crack front were measured simultaneously, providing precise estimates of both types of dissipated energy. We computed the radiation efficiency ηR (ratio of the radiated energy to the available energy for driving the fracture) and observed a nonlinear increase of ηR with the average fracture propagation velocity v over 2 orders of magnitude independently of the initial quenched disorder. The experimental observations are supported by a model based on the fluctuations of the local rupture velocity induced by the crack front pinning on local asperities which leads to ηR ∝ v0.55. We discuss implications for slow shear rupture modes, seismicity rate evolution, and induced seismicity.
Anomalous scaling of flexural phonon damping in nanoresonators with confined fluid
Authors: De Subhadeep , Aluru Narayana R. 
Published: January 2019

AbstractVarious one and two-dimensional (1D and 2D) nanomaterials and their combinations are emerging as next-generation sensors because of their unique opto-electro-mechanical properties accompanied by large surface-to-volume ratio and high quality factor. Though numerous studies have demonstrated an unparalleled sensitivity of these materials as resonant nanomechanical sensors under vacuum isolation, an assessment of their performance in the presence of an interacting medium like fluid environment is scarce. Here, we report the mechanical damping behavior of a 1D single-walled carbon nanotube (SWCNT) resonator operating in the fundamental flexural mode and interacting with a fluid environment, where the fluid is placed either inside or outside of the SWCNT. A scaling study of dissipation shows an anomalous behavior in case of interior fluid where the dissipation is found to be extremely low and scaling inversely with the fluid density. Analyzing the sources of dissipation reveals that (i) the phonon dissipation remains unaltered with fluid density and (ii) the anomalous dissipation scaling in the fluid interior case is solely a characteristic of the fluid response under confinement. Using linear response theory, we construct a fluid damping kernel which characterizes the hydrodynamic force response due to the resonant motion. The damping kernel-based analysis shows that the unexpected behavior stems from time dependence of the hydrodynamic response under nanoconfinement. Our systematic dissipation analysis helps us to infer the origin of the intrinsic dissipation. We also emphasize on the difference in dissipative response of the fluid under nanoconfinement when compared to a fluid exterior case. Our finding highlights a unique feature of confined fluid–structure interaction and evaluates its effect on the performance of high-frequency nanoresonators.
Self-powered smart patch for sweat conductivity monitoring
Authors: Ortega Laura , Llorella Anna , Esquivel Juan Pablo , Sabaté Neus 
Published: January 2019

AbstractA self-powered skin patch for the measurement of sweat conductivity is presented. The key component of the patch consists of a paper battery that is activated upon absorption of sweat. This body fluid acts as the battery electrolyte, the conductivity of which has a direct impact on the battery-generated output power and voltage. This particular behaviour enables the operation of a very simple and robust conductivity sensor in direct current mode without needing an external power source. The device presented in this paper takes advantage of this new measurement method to develop a sweat patch for screening cystic fibrosis that operates with an extremely simple electronic circuit that minimizes its cost and environmental impact. The patch provides an unambiguous digital result that can be read in an electrochromic display and yields 95% sensitivity and 100% specificity when tested with artificial eccrine perspiration samples.
Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns
Authors: Tully Benjamin J. 
Published: January 2019

AbstractDespite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.
Activity in perceptual classification networks as a basis for human subjective time perception
Authors: Roseboom Warrick , Fountas Zafeirios , Nikiforou Kyriacos , Bhowmik David , Shanahan Murray , Seth Anil K. 
Published: January 2019

AbstractDespite being a fundamental dimension of experience, how the human brain generates the perception of time remains unknown. Here, we provide a novel explanation for how human time perception might be accomplished, based on non-temporal perceptual classification processes. To demonstrate this proposal, we build an artificial neural system centred on a feed-forward image classification network, functionally similar to human visual processing. In this system, input videos of natural scenes drive changes in network activation, and accumulation of salient changes in activation are used to estimate duration. Estimates produced by this system match human reports made about the same videos, replicating key qualitative biases, including differentiating between scenes of walking around a busy city or sitting in a cafe or office. Our approach provides a working model of duration perception from stimulus to estimation and presents a new direction for examining the foundations of this central aspect of human experience.
Negative longitudinal magnetoresistance in gallium arsenide quantum wells
Authors: Xu Jing , Ma Meng K. , Sultanov Maksim , Xiao Zhi-Li , Wang Yong-Lei , Jin Dafei , Lyu Yang-Yang , Zhang Wei , Pfeiffer Loren N. , West Ken W. , Baldwin Kirk W. , Shayegan Mansour , Kwok Wai-Kwong 
Published: January 2019

AbstractNegative longitudinal magnetoresistances (NLMRs) have been recently observed in a variety of topological materials and often considered to be associated with Weyl fermions that have a defined chirality. Here we report NLMRs in non-Weyl GaAs quantum wells. In the absence of a magnetic field the quantum wells show a transition from semiconducting-like to metallic behaviour with decreasing temperature. We observe pronounced NLMRs up to 9 Tesla at temperatures above the transition and weak NLMRs in low magnetic fields at temperatures close to the transition and below 5 K. The observed NLMRs show various types of magnetic field behaviour resembling those reported in topological materials. We attribute them to microscopic disorder and use a phenomenological three-resistor model to account for their various features. Our results showcase a contribution of microscopic disorder in the occurrence of unusual phenomena. They may stimulate further work on tuning electronic properties via disorder/defect nano-engineering.
Tip60- and sirtuin 2-regulated MARCKS acetylation and phosphorylation are required for diabetic embryopathy
Authors: Yang Penghua , Xu Cheng , Reece E. Albert , Chen Xi , Zhong Jianxiang , Zhan Min , Stumpo Deborah J. , Blackshear Perry J. , Yang Peixin 
Published: January 2019

AbstractFailure of neural tube closure results in severe birth defects and can be induced by high glucose levels resulting from maternal diabetes. MARCKS is required for neural tube closure, but the regulation and of its biological activity and function have remained elusive. Here, we show that high maternal glucose induced MARCKS acetylation at lysine 165 by the acetyltransferase Tip60, which is a prerequisite for its phosphorylation, whereas Sirtuin 2 (SIRT2) deacetylated MARCKS. Phosphorylated MARCKS dissociates from organelles, leading to mitochondrial abnormalities and endoplasmic reticulum stress. Phosphorylation dead MARCKS (PD-MARCKS) reversed maternal diabetes-induced cellular organelle stress, apoptosis and delayed neurogenesis in the neuroepithelium and ameliorated neural tube defects. Restoring SIRT2 expression in the developing neuroepithelium exerted identical effects as those of PD-MARCKS. Our studies reveal a new regulatory mechanism for MARCKS acetylation and phosphorylation that disrupts neurulation under diabetic conditions by diminishing the cellular organelle protective effect of MARCKS.
Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations
Authors: Layeghifard Mehdi , Li Hannah , Wang Pauline W. , Donaldson Sylva L. , Coburn Bryan , Clark Shawn T. , Caballero Julio Diaz , Zhang Yu , Tullis D. Elizabeth , Yau Yvonne C. W. , Waters Valerie , Hwang David M. , Guttman David S. 
Published: January 2019

AbstractOver 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading to respiratory failure. The decline in CF lung function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach to identify key members of the microbiota. We used two CF sputum microbiome data sets that were longitudinally collected through periods spanning baseline health and PEs. Key taxa were defined based on three strategies: overall relative abundance, prevalence, and co-occurrence network interconnectedness. We measured the association between changes in the abundance of the key taxa and changes in patient clinical status over time via change-point detection, and found that taxa with the highest level of network interconnectedness tracked changes in patient health significantly better than taxa with the highest abundance or prevalence. We also cross-sectionally stratified all samples into the clinical states and identified key taxa associated with each state. We found that network interconnectedness most strongly delineated the taxa among clinical states, and that anaerobic bacteria were over-represented during PEs. Many of these anaerobes are oropharyngeal bacteria that have been previously isolated from the respiratory tract, and/or have been studied for their role in CF. The observed shift in community structure, and the association of anaerobic taxa and PEs lends further support to the growing consensus that anoxic conditions and the subsequent growth of anaerobic microbes are important predictors of PEs.
Multi-loop node line states in ternary MgSrSi-type crystals
Authors: Lian Jinling , Yu Lixian , Liang Qi-Feng , Zhou Jian , Yu Rui , Weng Hongming 
Published: January 2019

AbstractNode line band-touchings protected by mirror symmetry (named as m-NLs), the product of inversion and time reversal symmetry S = PT (named as s-NLs), or nonsymmorphic symmetry are nontrivial topological objects of topological semimetals in the Brillouin Zone. In this work, we screened a family of MgSrSi-type crystals using first principles calculations, and discovered that more than 70 members are node-line semimetals. A new type of multi-loop structure was found in AsRhTi that a s-NL touches robustly with a m-NL at some “nexus point”, and in the meanwhile a second m-NL crosses with the s-NL to form a Hopf-link. Unlike the previously proposed Hopf-link formed by two s-NLs or two m-NLs, a Hopf-link formed by a s-NL and a m-NL requires a minimal three-band model to characterize its essential electronic structure. The associated topological surface states on different surfaces of AsRhTi crystal were also obtained. Even more complicated and exotic multi-loop structure of NLs were predicted in AsFeNb and PNiNb. Our work may shed light on search for exotic multi-loop node-line semimetals in real materials.
Autophagy–lysosome pathway alterations and alpha-synuclein up-regulation in the subtype of neuronal ceroid lipofuscinosis, CLN5 disease
Authors: Adams Jessie , Feuerborn Melissa , Molina Joshua A. , Wilden Alexa R. , Adhikari Babita , Budden Theodore , Lee Stella Y. 
Published: January 2019

AbstractNeuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative lysosomal storage disorders. CLN5 deficiency causes a subtype of NCL, referred to as CLN5 disease. CLN5 is a soluble lysosomal protein with an unclear function in the cell. Increased levels of the autophagy marker protein LC3-II have been reported in several subtypes of NCLs. In this report, we examine whether autophagy is altered in CLN5 disease. We found that the basal level of LC3-II was elevated in both CLN5 disease patient fibroblasts and CLN5-deficient HeLa cells. Further analysis using tandem fluorescent mRFP-GFP-LC3 showed the autophagy flux was increased. We found the alpha-synuclein (α-syn) gene SNCA was highly up-regulated in CLN5 disease patient fibroblasts. The aggregated form of α-syn is well known for its role in the pathogenicity of Parkinson’s disease. Higher α-syn protein levels confirmed the SNCA up-regulation in both patient cells and CLN5 knockdown HeLa cells. Furthermore, α-syn was localized to the vicinity of lysosomes in CLN5 deficient cells, indicating it may have a lysosome-related function. Intriguingly, knocking down SNCA reversed lysosomal perinuclear clustering caused by CLN5 deficiency. These results suggest α-syn may affect lysosomal clustering in non-neuronal cells, similar to its role in presynaptic vesicles in neurons.
Polymorphisms in MDM2 and TP53 Genes and Risk of Developing Therapy-Related Myeloid Neoplasms
Authors: Cabezas Maria , García-Quevedo Lydia , Alonso Cintia , Manubens Marta , Álvarez Yolanda , Barquinero Joan Francesc , Ramón y Cajal Santiago , Ortega Margarita , Blanco Adoración , Caballín María Rosa , Armengol Gemma 
Published: January 2019

AbstractOne of the most severe complications after successful cancer therapy is the development of therapy-related myeloid neoplasms (t-MN). Constitutional genetic variation is likely to impact on t-MN risk. We aimed to evaluate if polymorphisms in the p53 pathway can be useful for predicting t-MN susceptibility. First, an association study revealed that the Pro variant of theTP53Arg72Pro polymorphism and the G allele of theMDM2SNP309 were associated with t-MN risk. The Arg variant ofTP53is more efficient at inducing apoptosis, whereas the Pro variant is a more potent inductor of cell cycle arrest and DNA repair. As regardsMDM2SNP309, the G allele is associated with attenuation of the p53 apoptotic response. Second, to evaluate the biological effect of theTP53polymorphism, we established Jurkat isogenic cell lines expressing p53Arg or p53Pro. Jurkat p53Arg cells presented higher DNA damage and higher apoptotic potential than p53Pro cells, after treatment with chemotherapy agents. Only p53Pro cells presented t(15;17) translocation and del(5q). We suggest that failure to repair DNA lesions in p53Arg cells would lead them to apoptosis, whereas some p53Pro cells, prone to cell cycle arrest and DNA repair, could undergo misrepair, generating chromosomal abnormalities typical of t-MN.
Downregulation of pectin biosynthesis gene GAUT4 leads to reduced ferulate and lignin-carbohydrate cross-linking in switchgrass
Authors: Li Mi , Yoo Chang Geun , Pu Yunqiao , Biswal Ajaya K. , Tolbert Allison K. , Mohnen Debra , Ragauskas Arthur J. 
Published: January 2019

AbstractKnockdown (KD) expression of GAlactUronosylTransferase 4 (GAUT4) in switchgrass improves sugar yield and ethanol production from the biomass. The reduced recalcitrance of GAUT4-KD transgenic biomass is associated with reduced cell wall pectic homogalacturonan and rhamnogalacturonan II content and cross-linking, and the associated increases in accessibility of cellulose to enzymatic deconstruction. To further probe the molecular basis for the reduced recalcitrance of GAUT4-KD biomass, potential recalcitrance-related factors including the physicochemical properties of lignin and hemicellulose are investigated. We show that the transgenic switchgrass have a lower abundance of ferulate and lignin-carbohydrate complex cross-linkages, reduced amounts of residual arabinan and xylan in lignin-enriched fractions after enzymatic hydrolysis, and greater coalescence and migration of lignin after hydrothermal pretreatment in comparison to the wild-type switchgrass control. The results reveal the roles of both decreased lignin-polymer and pectin cross-links in the reduction of recalcitrance in PvGAUT4-KD switchgrass.
Representing dynamic biological networks with multi-scale probabilistic models
Authors: Groß Alexander , Kracher Barbara , Kraus Johann M. , Kühlwein Silke D. , Pfister Astrid S. , Wiese Sebastian , Luckert Katrin , Pötz Oliver , Joos Thomas , Van Daele Dries , De Raedt Luc , Kühl Michael , Kestler Hans A. 
Published: January 2019

AbstractDynamic models analyzing gene regulation and metabolism face challenges when adapted to modeling signal transduction networks. During signal transduction, molecular reactions and mechanisms occur in different spatial and temporal frames and involve feedbacks. This impedes the straight-forward use of methods based on Boolean networks, Bayesian approaches, and differential equations. We propose a new approach, ProbRules, that combines probabilities and logical rules to represent the dynamics of a system across multiple scales. We demonstrate that ProbRules models can represent various network motifs of biological systems. As an example of a comprehensive model of signal transduction, we provide a Wnt network that shows remarkable robustness under a range of phenotypical and pathological conditions. Its simulation allows the clarification of controversially discussed molecular mechanisms of Wnt signaling by predicting wet-lab measurements. ProbRules provides an avenue in current computational modeling by enabling systems biologists to integrate vast amounts of available data on different scales.
The dietary flavonoid isoliquiritigenin is a potent cytotoxin for human neuroblastoma cells
Authors: Alshangiti Amnah M. , Togher Katie L. , Hegarty Shane V. , Sullivan Aideen M. , O’Keeffe Gerard W. 
Published: January 2019

AbstractNeuroblastoma (NB) is the most common extracranial solid tumor of early childhood; it accounts for approximately 8–10% of all childhood cancers and is the most common cancer in children in the first year of life. Patients in the high-risk group have a poor prognosis, with relapses being common and often refractory to drug treatment in those that survive. Moreover, the drug treatment itself can lead to a range of long-term sequelae. Therefore, there is a critical need to identify new therapeutics for NB. Isoliquiritigenin (ISLQ) is a naturally-occurring, dietary chalcone-type flavonoid with a range of biological effects that depend on the cell type and context. ISLQ has potential as an anticancer agent. Here we show that ISLQ has potent cytotoxic effects on SK-N-BE(2) and IMR-32 human NB cells, which carry amplification of the MYCN gene, the main prognostic marker of poor survival in NB. ISLQ was found to increase cellular reactive oxygen species (ROS). The cytotoxic effect of ISLQ was blocked by small molecule inhibitors of oxidative stress-induced cell death, and by the antioxidant N-acetyl-l-cysteine (NAC). Combined treatment of either SK-N-B-E(2) or IMR-32 cells with ISLQ and the anticancer agent cisplatin resulted in loss of cell viability that was greater than that induced by cisplatin alone. This study provides proof-of-principle that ISLQ is a potent cytotoxin for MYCN-amplified human NB cells. This is an important first step in rationalizing the further study of ISLQ as a potential adjunct therapy for high-risk NB.
Wide-area photometric and astrometric (Gaia DR2) study of the young cluster NGC 6530
Authors: Damiani F. , Prisinzano L. , Micela G. , Sciortino S. 
Published: January 2019

Context. NGC 6530 is a young cluster, with a complex morphology and star-formation history. We present a statistical study of its global properties, using a new, large list of candidate members down to masses of 0.2−0.4 M⊙ and Gaia DR2 astrometry.
Aims. We consider a larger sky region compared to previous studies, to investigate the entire cluster until its periphery, including any diffuse population all around the main cluster. We study the distribution of extinction and age across the different regions, and obtain constraints on the star-formation history. We also study the dynamics of cluster members.
Methods. Cluster membership was determined on the basis of literature X-ray data, Hα emission, near-IR and UV excesses from the VPHAS+ and UKIDSS photometric surveys and published near-IR catalogs, and Gaia DR2 astrometry; moreover, we used a method for photometric selection of M-type pre-main-sequence cluster members, which we recently developed and used for other star-formation regions. The list of candidates includes nearly 3700 stars, of which we estimate approximately 2700 to be genuine NGC 6530 members.
Results. Using Gaia parallaxes, the cluster distance is found to be 1325 pc, with errors of 0.5% (statistical) and 8.5% (systematic), in agreement with previous determinations. The cluster morphology and boundaries are established with great confidence, from the agreement between the subsamples of members selected using different criteria. There is no diffuse population of members around the cluster, but there are minor condensations of true members in addition to the two main groups in the cluster core and in the Hourglass nebula. Two such subgroups are spatially associated with the stars 7 Sgr (F2II-III) and HD 164536 (O7.5V). There is a definite pattern of sequential star formation across the cluster, within an age range from less than 0.5 Myr to ∼5 Myr. Extinction is spatially non-uniform, with part of the population still embedded or obscured by thick dust. The precise Gaia proper motion data indicate that the NGC 6530 parent cloud collided with the Galactic plane around 4 Myr ago, and we suggest that event as the trigger of the bulk of star formation in NGC 6530. The internal cluster dynamics is also partially resolved by the Gaia data, indicating expansion of the main cluster population with respect to its center.