bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gas phase synthesis of [4]-helicene
Authors: Zhao Long , Kaiser Ralf I. , Xu Bo , Ablikim Utuq , Lu Wenchao , Ahmed Musahid , Evseev Mikhail M. , Bashkirov Eugene K. , Azyazov Valeriy N. , Zagidullin Marsel V. , Morozov Alexander N. , Howlader A. Hasan , Wnuk Stanislaw F. , Mebel Alexander M. , Joshi Dharati , Veber Gregory , Fischer Felix R. 
Published: April 2019

AbstractA synthetic route to racemic helicenes via a vinylacetylene mediated gas phase chemistry involving elementary reactions with aryl radicals is presented. In contrast to traditional synthetic routes involving solution chemistry and ionic reaction intermediates, the gas phase synthesis involves a targeted ring annulation involving free radical intermediates. Exploiting the simplest helicene as a benchmark, we show that the gas phase reaction of the 4-phenanthrenyl radical ([C14H9]•) with vinylacetylene (C4H4) yields [4]-helicene (C18H12) along with atomic hydrogen via a low-barrier mechanism through a resonance-stabilized free radical intermediate (C18H13). This pathway may represent a versatile mechanism to build up even more complex polycyclic aromatic hydrocarbons such as [5]- and [6]-helicene via stepwise ring annulation through bimolecular gas phase reactions in circumstellar envelopes of carbon-rich stars, whereas secondary reactions involving hydrogen atom assisted isomerization of thermodynamically less stable isomers of [4]-helicene might be important in combustion flames as well.
MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression
Authors: Jiang Yao , Zhang Yanqiong , Leung Janet Y. , Fan Cheng , Popov Konstantin I. , Su Siyuan , Qian Jiayi , Wang Xiaodong , Holtzhausen Alisha , Ubil Eric , Xiang Yang , Davis Ian , Dokholyan Nikolay V. , Wu Gang , Perou Charles M. , Kim William Y. , Earp H. Shelton , Liu Pengda 
Published: April 2019

AbstractAkt plays indispensable roles in cell proliferation, survival and metabolism. Mechanisms underlying posttranslational modification-mediated Akt activation have been extensively studied yet the Akt interactome is less understood. Here, we report that SAV1, a Hippo signaling component, inhibits Akt, a function independent of its role in Hippo signaling. Binding to a proline-tyrosine motif in the Akt-PH domain, SAV1 suppresses Akt activation by blocking Akt’s movement to plasma membrane. We further identify cancer-associated SAV1 mutations with impaired ability to bind Akt, leading to Akt hyperactivation. We also determine that MERTK phosphorylates Akt1-Y26, releasing SAV1 binding and allowing Akt responsiveness to canonical PI-3K pathway activation. This work provides a mechanism underlying MERTK-mediated Akt activation and survival signaling in kidney cancer. Akt activation drives oncogenesis and therapeutic resistance; this mechanism of Akt regulation by MERTK/SAV1 provides yet another complexity in an extensively studied pathway, and may yield prognostic information and therapeutic targets.
Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism
Authors: Tsutsumi Kenta , Yonehara Ryo , Ishizaka-Ikeda Etsuko , Miyazaki Naoyuki , Maeda Shintaro , Iwasaki Kenji , Nakagawa Atsushi , Yamashita Eiki 
Published: April 2019

AbstractIn Pseudomonas aeruginosa, MexAB–OprM plays a central role in multidrug resistance by ejecting various drug compounds, which is one of the causes of serious nosocomial infections. Although the structures of the components of MexAB–OprM have been solved individually by X-ray crystallography, no structural information for fully assembled pumps from P. aeruginosa were previously available. In this study, we present the structure of wild-type MexAB–OprM in the presence or absence of drugs at near-atomic resolution. The structure reveals that OprM does not interact with MexB directly, and that it opens its periplasmic gate by forming a complex. Furthermore, we confirm the residues essential for complex formation and observed a movement of the drug entrance gate. Based on these results, we propose mechanisms for complex formation and drug efflux.
Zero-temperature glass transition in two dimensions
Authors: Berthier Ludovic , Charbonneau Patrick , Ninarello Andrea , Ozawa Misaki , Yaida Sho 
Published: April 2019

AbstractLiquids cooled towards the glass transition temperature transform into amorphous solids that have a wide range of applications. While the nature of this transformation is understood rigorously in the mean-field limit of infinite spatial dimensions, the problem remains wide open in physical dimensions. Nontrivial finite-dimensional fluctuations are hard to control analytically, and experiments fail to provide conclusive evidence regarding the nature of the glass transition. Here, we develop Monte Carlo methods for two-dimensional glass-forming liquids that allow us to access equilibrium states at sufficiently low temperatures to directly probe the glass transition in a regime inaccessible to experiments. We find that the liquid state terminates at a thermodynamic glass transition which occurs at zero temperature and is associated with an entropy crisis and a diverging static correlation length. Our results thus demonstrate that a thermodynamic glass transition can occur in finite dimensional glass-formers.
The compressive strength of crumpled matter
Authors: Croll Andrew B. , Twohig Timothy , Elder Theresa 
Published: April 2019

AbstractCrumpling a sheet creates a unique, stiff and lightweight structure. Use of crumples in engineering design is limited because there are not simple, physically motivated structure-property relations available for crumpled materials; one cannot trust a crumple. On the contrary, we demonstrate that an empirical model reliably predicts the reaction of a crumpled sheet to a compressive force. Experiments show that the prediction is quantitative over 50 orders of magnitude in force, for purely elastic and highly plastic polymer films. Our data does not match recent theoretical predictions based on the dominance of building-block structures (bends, folds, d-cones, and ridges). However, by directly measuring substructures, we show clearly that the bending in the stretching ridge is responsible for the strength of both elastic and plastic crumples. Our simple, predictive model may open the door to the engineering use of a vast range of materials in this state of crumpled matter.
In vivo topology converts competition for cell-matrix adhesion into directional migration
Authors: Bajanca Fernanda , Gouignard Nadège , Colle Charlotte , Parsons Maddy , Mayor Roberto , Theveneau Eric 
Published: April 2019

AbstractWhen migrating in vivo, cells are exposed to numerous conflicting signals: chemokines, repellents, extracellular matrix, growth factors. The roles of several of these molecules have been studied individually in vitro or in vivo, but we have yet to understand how cells integrate them. To start addressing this question, we used the cephalic neural crest as a model system and looked at the roles of its best examples of positive and negative signals: stromal-cell derived factor 1 (Sdf1/Cxcl12) and class3-Semaphorins. Here we show that Sdf1 and Sema3A antagonistically control cell-matrix adhesion via opposite effects on Rac1 activity at the single cell level. Directional migration at the population level emerges as a result of global Semaphorin-dependent confinement and broad activation of adhesion by Sdf1 in the context of a biased Fibronectin distribution. These results indicate that uneven in vivo topology renders the need for precise distribution of secreted signals mostly dispensable.
Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics
Authors: Shen Xiaotao , Wang Ruohong , Xiong Xin , Yin Yandong , Cai Yuping , Ma Zaijun , Liu Nan , Zhu Zheng-Jiang 
Published: April 2019

AbstractLarge-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.
Reduced nitrogenase efficiency dominates response of the globally important nitrogen fixer Trichodesmium to ocean acidification
Authors: Luo Ya-Wei , Shi Dalin , Kranz Sven A. , Hopkinson Brian M. , Hong Haizheng , Shen Rong , Zhang Futing 
Published: April 2019

AbstractThe response of the prominent marine dinitrogen (N2)-fixing cyanobacteria Trichodesmium to ocean acidification (OA) is critical to understanding future oceanic biogeochemical cycles. Recent studies have reported conflicting findings on the effect of OA on growth and N2 fixation of Trichodesmium. Here, we quantitatively analyzed experimental data on how Trichodesmium reallocated intracellular iron and energy among key cellular processes in response to OA, and integrated the findings to construct an optimality-based cellular model. The model results indicate that Trichodesmium growth rate decreases under OA primarily due to reduced nitrogenase efficiency. The downregulation of the carbon dioxide (CO2)-concentrating mechanism under OA has little impact on Trichodesmium, and the energy demand of anti-stress responses to OA has a moderate negative effect. We predict that if anthropogenic CO2 emissions continue to rise, OA could reduce global N2 fixation potential of Trichodesmium by 27% in this century, with the largest decrease in iron-limiting regions.
Ca2+-dependent regulation of sodium channels NaV1.4 and NaV1.5 is controlled by the post-IQ motif
Authors: Yoder Jesse B. , Ben-Johny Manu , Farinelli Federica , Srinivasan Lakshmi , Shoemaker Sophie R. , Tomaselli Gordon F. , Gabelli Sandra B. , Amzel L. Mario 
Published: April 2019

AbstractSkeletal muscle voltage-gated Na+ channel (NaV1.4) activity is subject to calmodulin (CaM) mediated Ca2+-dependent inactivation; no such inactivation is observed in the cardiac Na+ channel (NaV1.5). Taken together, the crystal structures of the NaV1.4 C-terminal domain relevant complexes and thermodynamic binding data presented here provide a rationale for this isoform difference. A Ca2+-dependent CaM N-lobe binding site previously identified in NaV1.5 is not present in NaV1.4 allowing the N-lobe to signal other regions of the NaV1.4 channel. Consistent with this mechanism, removing this binding site in NaV1.5 unveils robust Ca2+-dependent inactivation in the previously insensitive isoform. These findings suggest that Ca2+-dependent inactivation is effected by CaM’s N-lobe binding outside the NaV C-terminal while CaM’s C-lobe remains bound to the NaV C-terminal. As the N-lobe binding motif of NaV1.5 is a mutational hotspot for inherited arrhythmias, the contributions of mutation-induced changes in CDI to arrhythmia generation is an intriguing possibility.
Role of fluid cohesiveness in safe swallowing
Authors: Nishinari Katsuyoshi , Turcanu Mihaela , Nakauma Makoto , Fang Yapeng 
Published: April 2019

AbstractIn patients with dysphagia, it has been a practice to thicken fluid food to prevent aspiration—the transport of a bolus into the trachea instead of the oesophagus. In these patients, aspiration is a risk behaviour and is closely related to pneumonia (caused by the aspiration of oral bacteria into the lungs). Since excessive thickening of fluids can cause adverse effects, such as lowering the palatability of food, subsequent reduction of liquid intake, dehydration and malnutrition, identifying the optimum thickening level is vital. Thickening might not only increase fluid viscosity, but could also modify its cohesiveness, which is another key factor affecting aspiration. Even though cohesiveness is more of a concept than a well-defined measurable parameter, this property describes the degree of coherency provided by the internal structure of a material against its fractional breakup. In fluids, this concept is less explored than in solids, powders and granules, and during the last decade few scientists have tackled this topic. Although the role of cohesiveness in the swallowing of heterogeneous solid foods is briefly overviewed, the aim of the present paper is to introduce the concept of cohesiveness for a relatively homogeneous fluid bolus and its effect on swallowing. Cohesiveness is highly correlated with the extensibility and yield stress of the fluid, suggesting that a high cohesiveness could have an important role in preventing aspiration.
A 204-subject multimodal neuroimaging dataset to study language processing
Authors: Schoffelen Jan-Mathijs , Oostenveld Robert , Lam Nietzsche H. L. , Uddén Julia , Hultén Annika , Hagoort Peter 
Published: April 2019

AbstractThis dataset, colloquially known as the Mother Of Unification Studies (MOUS) dataset, contains multimodal neuroimaging data that has been acquired from 204 healthy human subjects. The neuroimaging protocol consisted of magnetic resonance imaging (MRI) to derive information at high spatial resolution about brain anatomy and structural connections, and functional data during task, and at rest. In addition, magnetoencephalography (MEG) was used to obtain high temporal resolution electrophysiological measurements during task, and at rest. All subjects performed a language task, during which they processed linguistic utterances that either consisted of normal or scrambled sentences. Half of the subjects were reading the stimuli, the other half listened to the stimuli. The resting state measurements consisted of 5 minutes eyes-open for the MEG and 7 minutes eyes-closed for fMRI. The neuroimaging data, as well as the information about the experimental events are shared according to the Brain Imaging Data Structure (BIDS) format. This unprecedented neuroimaging language data collection allows for the investigation of various aspects of the neurobiological correlates of language.
Geo-referenced population-specific microsatellite data across American continents, the MacroPopGen Database
Authors: Lawrence Elizabeth R. , Benavente Javiera N. , Matte Jean-Michel , Marin Kia , Wells Zachery R. R. , Bernos Thaïs A. , Krasteva Nia , Habrich Andrew , Nessel Gabrielle A. , Koumrouyan Ramela Arax , Fraser Dylan J. 
Published: April 2019

AbstractPopulation genetic data from nuclear DNA has yet to be synthesized to allow broad scale comparisons of intraspecific diversity versus species diversity. The MacroPopGen database collates and geo-references vertebrate population genetic data across the Americas from 1,308 nuclear microsatellite DNA studies, 897 species, and 9,090 genetically distinct populations where genetic differentiation (FST) was measured. Caribbean populations were particularly distinguished from North, Central, and South American populations, in having higher differentiation (FST = 0.12 vs. 0.07–0.09) and lower mean numbers of alleles (MNA = 4.11 vs. 4.84–5.54). While mammalian populations had lower MNA (4.86) than anadromous fish, reptiles, amphibians, freshwater fish, and birds (5.34–7.81), mean heterozygosity was largely similar across groups (0.57–0.63). Mean FST was consistently lowest in anadromous fishes (0.06) and birds (0.05) relative to all other groups (0.09–0.11). Significant differences in Family/Genera variance among continental regions or taxonomic groups were also observed. MacroPopGen can be used in many future applications including latitudinal analyses, spatial analyses (e.g. central-margin), taxonomic comparisons, regional assessments of anthropogenic impacts on biodiversity, and conservation of wild populations.
Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research
Authors: Fox Ramos Alexander E. , Le Pogam Pierre , Fox Alcover Charlotte , Otogo N’Nang Elvis , Cauchie Gaëla , Hazni Hazrina , Awang Khalijah , Bréard Dimitri , Echavarren Antonio M. , Frédérich Michel , Gaslonde Thomas , Girardot Marion , Grougnet Raphaël , Kirillova Mariia S. , Kritsanida Marina , Lémus Christelle , Le Ray Anne-Marie , Lewin Guy , Litaudon Marc , Mambu Lengo , Michel Sylvie , Miloserdov Fedor M. , Muratore Michael E. , Richomme-Peniguel Pascal , Roussi Fanny , Evanno Laurent , Poupon Erwan , Champy Pierre , Beniddir Mehdi A. 
Published: April 2019

AbstractThis Data Descriptor announces the submission to public repositories of the monoterpene indole alkaloid database (MIADB), a cumulative collection of 172 tandem mass spectrometry (MS/MS) spectra from multiple research projects conducted in eight natural product chemistry laboratories since the 1960s. All data have been annotated and organized to promote reuse by the community. Being a unique collection of these complex natural products, these data can be used to guide the dereplication and targeting of new related monoterpene indole alkaloids within complex mixtures when applying computer-based approaches, such as molecular networking. Each spectrum has its own accession number from CCMSLIB00004679916 to CCMSLIB00004680087 on the GNPS. The MIADB is available for download from MetaboLights under the identifier: MTBLS142 (https://www.ebi.ac.uk/metabolights/MTBLS142).
MarTurtSI, a global database of stable isotope analyses of marine turtles
Authors: Figgener Christine , Bernardo Joseph , Plotkin Pamela T. 
Published: April 2019

AbstractMarine turtles are both flagship species of conservation concern and indicators of ocean health. As highly migratory species, and despite substantial research effort focusing on nesting females and satellite tagging studies, we still know little about the trophic ecology and habitat use of immature stages and males. Consequently, marine turtle biologists began using stable isotope analyses in the last decade to elucidate various aspects of trophic ecology, including habitat use and trophic position. This has resulted in a burgeoning but largely disconnected literature of mostly single-species case studies. Here we comprehensively synthesize this body of work into a unified data repository, the MarTurtSI database. MarTurtSI contains stable isotope data from six of seven marine turtle species ranging from juveniles to adults, in different developmental, feeding, and breeding habitats across multiple ocean basins. MarTurtSI will be curated and updated with the aim of enabling continued comprehensive and global investigations into the trophic ecology of marine turtles especially in the face of climate change and other conservation challenges.
Comparison of lower extremity joint mechanics between healthy active young and middle age people in walking and running gait
Authors: Jin Li , Hahn Michael E. 
Published: April 2019

AbstractProgression of age can influence gait characteristics. Previous research has investigated lower extremity joint mechanics between young and elderly people in locomotion, however little is known about whether differences exist between young and middle age people. Ten young healthy subjects (22.8 ± 5.3 years) and ten middle age healthy subjects (50.7 ± 6.0 years) engaged in treadmill walking (from 0.8 to 2.0 m/s) and running (from 1.8 to 3.8 m/s). The middle age group had higher ankle plantar flexor moment angular impulse (p = 0.002), total support moment impulse (p = 0.016), and hip stance positive work (p = 0.029) across walking speeds. Additionally, the middle age group had higher knee flexion angle at ground contact in walking (p = 0.005) and running (p = 0.037). These findings indicate that moderate age affects changes in ankle and hip kinetic characteristics in walking, and knee kinematic patterns in both walking and running.
The influence of gaze direction on food preferences
Authors: Madipakkam Apoorva Rajiv , Bellucci Gabriele , Rothkirch Marcus , Park Soyoung Q. 
Published: April 2019

AbstractIn our information-rich environment, the gaze direction of another indicates their current focus of attention. Following the gaze of another, results in gaze-evoked shifts in joint attention, a phenomenon critical for the functioning of social cognition. Previous research in joint attention has shown that objects that are attended by another are more liked than ignored objects. Here, we investigated this effect of gaze-cueing on participants’ preferences for unknown food items. Participants provided their willingness to pay (WTP), taste and health preferences for food items before and after a standard gaze-cueing paradigm. We observed a significant effect of gaze-cueing on participants’ WTP bids. Specifically, participants were willing to pay more money for the food items that were looked at by another person. In contrast, there was a decrease in preference for the food items that were ignored by another person. Interestingly, this increase in WTP occurred without participants’ awareness of the contingency between the cue and target. These results highlight the influence of social information on human choice behavior and lay the foundation for experiments in neuromarketing and consumer decision making.
3D Structure and Processing Methods Direct the Biological Attributes of ECM-Based Cardiac Scaffolds
Authors: Efraim Yael , Schoen Beth , Zahran Sharbel , Davidov Tzila , Vasilyev Gleb , Baruch Limor , Zussman Eyal , Machluf Marcelle 
Published: April 2019

AbstractHigh hopes are held for cardiac regenerative therapy, driving a vast research effort towards the development of various cardiac scaffolds using diverse technologies and materials. Nevertheless, the role of factors such as fabrication process and structure in determining scaffold’s characteristics is yet to be discovered. In the present study, the effects of 3D structure and processing method on cardiac scaffolds are addressed using three distinct scaffolds made through different production technologies from the same biomaterial: decellularized porcine cardiac extracellular matrix (pcECM). pcECM patch, injectable pcECM hydrogel, and electrospun pcECM scaffolds were all proven as viable prospective therapies for MI, thus generally preserving pcECM beneficial properties. Yet, as we demonstrate, minor differences in scaffolds composition and micro-morphology as well as substantial differences in their mechanical properties, which arise from their production process, highly affect the interactions of the scaffold with both proliferating cells and functional cells. Hence, the rates of cell attachment, survival, and proliferation significantly vary between the different scaffolds. Moreover, major differences in cell morphology and alignment as well as in matrix remodeling are obtained. Overall, the effects revealed herein can guide a more rational scaffold design for the improved cellular or acellular treatment of different cardiac disease scenarios.