bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haploinsufficiency in the ANKS1B gene encoding AIDA-1 leads to a neurodevelopmental syndrome
Authors: Carbonell Abigail U. , Cho Chang Hoon , Tindi Jaafar O. , Counts Pamela A. , Bates Juliana C. , Erdjument-Bromage Hediye , Cvejic Svetlana , Iaboni Alana , Kvint Ifat , Rosensaft Jenny , Banne Ehud , Anagnostou Evdokia , Neubert Thomas A. , Scherer Stephen W. , Molholm Sophie , Jordan Bryen A. 
Published: August 2019

AbstractNeurodevelopmental disorders, including autism spectrum disorder, have complex polygenic etiologies. Single-gene mutations in patients can help define genetic factors and molecular mechanisms underlying neurodevelopmental disorders. Here we describe individuals with monogenic heterozygous microdeletions in ANKS1B, a predicted risk gene for autism and neuropsychiatric diseases. Affected individuals present with a spectrum of neurodevelopmental phenotypes, including autism, attention-deficit hyperactivity disorder, and speech and motor deficits. Neurons generated from patient-derived induced pluripotent stem cells demonstrate loss of the ANKS1B-encoded protein AIDA-1, a brain-specific protein highly enriched at neuronal synapses. A transgenic mouse model of Anks1b haploinsufficiency recapitulates a range of patient phenotypes, including social deficits, hyperactivity, and sensorimotor dysfunction. Identification of the AIDA-1 interactome using quantitative proteomics reveals protein networks involved in synaptic function and the etiology of neurodevelopmental disorders. Our findings formalize a link between the synaptic protein AIDA-1 and a rare, previously undefined genetic disease we term ANKS1B haploinsufficiency syndrome.
Rapid fabrication of vascularized and innervated cell-laden bone models with biomimetic intrafibrillar collagen mineralization
Authors: Thrivikraman Greeshma , Athirasala Avathamsa , Gordon Ryan , Zhang Limin , Bergan Raymond , Keene Douglas R. , Jones James M. , Xie Hua , Chen Zhiqiang , Tao Jinhui , Wingender Brian , Gower Laurie , Ferracane Jack L. , Bertassoni Luiz E. 
Published: August 2019

AbstractBone tissue, by definition, is an organic–inorganic nanocomposite, where metabolically active cells are embedded within a matrix that is heavily calcified on the nanoscale. Currently, there are no strategies that replicate these definitive characteristics of bone tissue. Here we describe a biomimetic approach where a supersaturated calcium and phosphate medium is used in combination with a non-collagenous protein analog to direct the deposition of nanoscale apatite, both in the intra- and extrafibrillar spaces of collagen embedded with osteoprogenitor, vascular, and neural cells. This process enables engineering of bone models replicating the key hallmarks of the bone cellular and extracellular microenvironment, including its protein-guided biomineralization, nanostructure, vasculature, innervation, inherent osteoinductive properties (without exogenous supplements), and cell-homing effects on bone-targeting diseases, such as prostate cancer. Ultimately, this approach enables fabrication of bone-like tissue models with high levels of biomimicry that may have broad implications for disease modeling, drug discovery, and regenerative engineering.
The antimicrobial peptide thanatin disrupts the bacterial outer membrane and inactivates the NDM-1 metallo-β-lactamase
Authors: Ma Bo , Fang Chao , Lu Linshan , Wang Mingzhi , Xue Xiaoyan , Zhou Ying , Li Mingkai , Hu Yue , Luo Xiaoxing , Hou Zheng 
Published: August 2019

AbstractNew Delhi metallo-β-lactamase-1 (NDM-1) is the most prevalent type of metallo-β-lactamase and hydrolyzes almost all clinically used β-lactam antibiotics. Here we show that the antimicrobial peptide thanatin disrupts the outer membrane of NDM-1-producing bacteria by competitively displacing divalent cations on the outer membrane and inducing the release of lipopolysaccharides. In addition, thanatin inhibits the enzymatic activity of NDM-1 by displacing zinc ions from the active site, and reverses carbapenem resistance in NDM-1-producing bacteria in vitro and in vivo. Thus, thanatin’s dual mechanism of action may be useful for combating infections caused by NDM-1-producing pathogens.
Direct atomic insight into the role of dopants in phase-change materials
Authors: Zhu Min , Song Wenxiong , Konze Philipp M. , Li Tao , Gault Baptiste , Chen Xin , Shen Jiabin , Lv Shilong , Song Zhitang , Wuttig Matthias , Dronskowski Richard 
Published: August 2019

AbstractDoping is indispensable to tailor phase-change materials (PCM) in optical and electronic data storage. Very few experimental studies, however, have provided quantitative information on the distribution of dopants on the atomic-scale. Here, we present atom-resolved images of Ag and In dopants in Sb2Te-based (AIST) PCM using electron microscopy and atom-probe tomography. Combing these with DFT calculations and chemical-bonding analysis, we unambiguously determine the dopants’ role upon recrystallization. Composition profiles corroborate the substitution of Sb by In and Ag, and the segregation of excessive Ag into grain boundaries. While In is bonded covalently to neighboring Te, Ag binds ionically. Moreover, In doping accelerates the crystallization and hence operation while Ag doping limits the random diffusion of In atoms and enhances the thermal stability of the amorphous phase.
Structural basis for the target specificity of actin histidine methyltransferase SETD3
Authors: Dai Shaobo , Horton John R. , Woodcock Clayton B. , Wilkinson Alex W. , Zhang Xing , Gozani Or , Cheng Xiaodong 
Published: August 2019

AbstractSETD3 is an actin histidine-N3 methyltransferase, whereas other characterized SET-domain enzymes are protein lysine methyltransferases. We report that in a pre-reactive complex SETD3 binds the N3-protonated form (N3-H) of actin His73, and in a post-reactive product complex, SETD3 generates the methylated histidine in an N1-protonated (N1-H) and N3-methylated form. During the reaction, the imidazole ring of His73 rotates ~105°, which shifts the proton from N3 to N1, thus ensuring that the target atom N3 is deprotonated prior to the methyl transfer. Under the conditions optimized for lysine deprotonation, SETD3 has weak lysine methylation activity on an actin peptide in which the target His73 is substituted by a lysine. The structure of SETD3 with Lys73-containing peptide reveals a bent conformation of Lys73, with its side chain aliphatic carbons tracing along the edge of imidazole ring and the terminal ε-amino group occupying a position nearly identical to the N3 atom of unmethylated histidine.
3D non-isothermal phase-field simulation of microstructure evolution during selective laser sintering
Authors: Yang Yangyiwei , Ragnvaldsen Olav , Bai Yang , Yi Min , Xu Bai-Xiang 
Published: August 2019

AbstractDuring selective laser sintering (SLS), the microstructure evolution and local temperature variation interact mutually. Application of conventional isothermal sintering model is thereby insufficient to describe SLS. In this work, we construct our model from entropy level, and derive the non-isothermal kinetics for order parameters along with the heat transfer equation coupled with microstructure evolution. Influences from partial melting and laser-powder interaction are also addressed. We then perform 3D finite element non-isothermal phase-field simulations of the SLS single scan. To confront the high computation cost, we propose a novel algorithm analogy to minimum coloring problem and manage to simulate a system of 200 grains with grain tracking algorithm using as low as 8 non-conserved order parameters. Specifically, applying the model to SLS of the stainless steel 316L powder, we identify the influences of laser power and scan speed on microstructural features, including the porosity, surface morphology, temperature profile, grain geometry, and densification. We further validate the first-order kinetics of the transient porosity during densification, and demonstrate the applicability of the developed model in predicting the linkage of densification factor to the specific energy input during SLS.
Evaluating relevance and redundancy to quantify how binary node metadata interplay with the network structure
Authors: Cinelli Matteo , Ferraro Giovanna , Iovanella Antonio 
Published: August 2019

AbstractNetworks are real systems modelled through mathematical objects made up of nodes and links arranged into peculiar and deliberate (or partially deliberate) topologies. Studying these real-world topologies allows for several properties of interest to be revealed. In real networks, nodes are also identified by a certain number of non-structural features or metadata. Given the current possibility of collecting massive quantity of such metadata, it becomes crucial to identify automatically which are the most relevant for the observed structure. We propose a new method that, independently from the network size, is able to not only report the relevance of binary node metadata, but also rank them. Such a method can be applied to networks from any domain, and we apply it in two heterogeneous cases: a temporal network of technology transfer and a protein-protein interaction network. Together with the relevance of node metadata, we investigate the redundancy of these metadata displaying by the results on a Redundancy-Relevance diagram, which is able to highlight the differences among vectors of metadata from both a structural and a non-structural point of view. The obtained results provide insights of a practical nature into the importance of the observed node metadata for the actual network structure.
Electro-haptic enhancement of speech-in-noise performance in cochlear implant users
Authors: Fletcher Mark D. , Hadeedi Amatullah , Goehring Tobias , Mills Sean R. 
Published: August 2019

AbstractCochlear implant (CI) users receive only limited sound information through their implant, which means that they struggle to understand speech in noisy environments. Recent work has suggested that combining the electrical signal from the CI with a haptic signal that provides crucial missing sound information (“electro-haptic stimulation”; EHS) could improve speech-in-noise performance. The aim of the current study was to test whether EHS could enhance speech-in-noise performance in CI users using: (1) a tactile signal derived using an algorithm that could be applied in real time, (2) a stimulation site appropriate for a real-world application, and (3) a tactile signal that could readily be produced by a compact, portable device. We measured speech intelligibility in multi-talker noise with and without vibro-tactile stimulation of the wrist in CI users, before and after a short training regime. No effect of EHS was found before training, but after training EHS was found to improve the number of words correctly identified by an average of 8.3%-points, with some users improving by more than 20%-points. Our approach could offer an inexpensive and non-invasive means of improving speech-in-noise performance in CI users.
Strong genetic isolation of the black-lipped pearl oyster (Pinctada margaritifera) in the Marquesas archipelago (French Polynesia)
Authors: Reisser Céline , Lo Cédrik , Schikorski David , Sham Koua Manaarii , Planes Serge , Ky Chin-Long 
Published: August 2019

AbstractThe French Polynesian islands are internationally known for their black pearls, produced by culture of the black lipped pearl oysterPinctada margaritifera. The ongoing development of hatcheries forP.margaritiferain French Polynesia poses new challenges for the industry, particularly regarding the maintenance of genetic diversity in the hatchery stocks. This emphasizes the necessity to characterize the genetic diversity and differentiation within natural and exploited populations, to carefully select putative parental populations. The present study aimed at validating the phylogenetic status and investigating genetic attributes of populations from the only two non-exploited archipelagos of French Polynesia, the Marquesas archipelago, and the Australes archipelago, never analysed before. We found that individuals from both archipelagos belonged toP.margaritiferaspecies. However, while the Australes population was genetically similar to non-exploited populations of the Tuamotu, the Marquesas populations were highly differentiated from the rest of the populations. This differentiation cannot not be only attributed to geographic distance and aquaculture status, but likely to hydrodynamic barriers allowing vicariant events to take place. Our results add up to other studies describing the Marquesas archipelago as a hotspot for biodiversity and differentiation, with some of the highest levels of endemism and vicariance found among marine species worldwide and provide precious information on available genetic resources for the implementation ofP.margaritiferaselective breeding and its genetic conservation in French Polynesia.
Efficient Alpha Radiation Detector using Low Temperature Hydrothermally Grown ZnO:Ga Nanorod Scintillator
Authors: Sahani R. M. , Kumari Chandni , Pandya Arun , Dixit Ambesh 
Published: August 2019

AbstractWe report efficient detection of alpha radiation on highly textured and vertically aligned along (002) Gallium-doped Zinc Oxide (ZnO:Ga) nanorods on a glass substrate with an average diameter ~150 ± 10 nm. Photoluminescence measurement showed near band emission 393 nm, in agreement with the bandgap value ~3.22 eV, measured by UV-Vis spectroscopy. The developed ZnO:Ga nanorod scintillator is coupled with a commercially available photomultiplier tube and 1K Multichannel Analyser to fabricate an alpha radiation detector. The performance of the alpha radiation detector is evaluated using various activities alpha radiation sources. A large pulse height spectrum is recorded by the detector for different alpha sources against the background spectrum. The calculated detection efficiency and Minimum Detectable Activity (MDA) showed that the detector is highly sensitive to alpha radiation. The repeatability and reproducibility of the performance are studied by evaluating the response of a single scintillator for numerous exposures and by studying inter-batch response variations, respectively. The response is repeatable within ±1% whereas reproducibility varies from ±20% for extremely low activity alpha sources to ±5% for high activity alpha sources. The performance of ZnO:Ga nanorod scintillator grown on glass substrate demonstrates that it can be a promising material system for the detection of alpha radiation.
The role of ESCO2, SALL4 and TBX5 genes in the susceptibility to thalidomide teratogenesis
Authors: Gomes Julia do Amaral , Kowalski Thayne Woycinck , Fraga Lucas Rosa , Macedo Gabriel S. , Sanseverino Maria Teresa Vieira , Schuler-Faccini Lavínia , Vianna Fernanda Sales Luiz 
Published: August 2019

AbstractThalidomide is widely used for several diseases; however, it causes malformations in embryos exposed during pregnancy. The complete understanding of the mechanisms by which thalidomide affects the embryo development has not yet been obtained. The phenotypic similarity makes TE a phenocopy of syndromes caused by mutations in ESCO2, SALL4 and TBX5 genes. Recently, SALL4 and TBX5 were demonstrated to be thalidomide targets. To understand if these genes act in the TE development, we sequenced them in 27 individuals with TE; we verified how thalidomide affect them in human pluripotent stem cells (hPSCs) through a differential gene expression (DGE) analysis from GSE63935; and we evaluated how these genes are functionally related through an interaction network analysis. We identified 8 variants in ESCO2, 15 in SALL4 and 15 in TBX5. We compared allelic frequencies with data from ExAC, 1000 Genomes and ABraOM databases; eight variants were significantly different (p < 0.05). Eleven variants in SALL4 and TBX5 were previously associated with cardiac diseases or malformations; however, in TE sample there was no association. Variant effect prediction tools showed 97% of the variants with potential to influence in these genes regulation. DGE analysis showed a significant reduction of ESCO2 in hPSCs after thalidomide exposure.
Dual-active antifungal agents containing strobilurin and SDHI-based pharmacophores
Authors: Zuccolo Marco , Kunova Andrea , Musso Loana , Forlani Fabio , Pinto Andrea , Vistoli Giulio , Gervasoni Silvia , Cortesi Paolo , Dallavalle Sabrina 
Published: August 2019

AbstractCrop disease management often implies repeated application of fungicides. However, the increasing emergence of fungicide-resistant pathogens requires their rotation or combined use. Tank-mix combinations using fungicides with different modes of action are often hard to manage by farmers. An alternative and unexploited strategy are bifunctional fungicides, i.e. compounds resulting from conjugation of the pharmacophores of fungicides with different mechanisms of action. In this paper we describe a new approach to antifungal treatments based on the synthesis of dual agents, obtained by merging the strobilurin and succinate dehydrogenase inhibitor pharmacophores into a new entity. The compounds were tested against important fungal plant pathogens and showed good inhibition of Pyricularia oryzae and Sclerotinia sclerotiorum with activity comparable to commercial fungicides. The inhibition of the cytochrome bc1 and the succinate dehydrogenase enzyme activity confirmed that the new molecules are endowed with a dual mechanism of action. These results were further supported by molecular modelling which showed that selected compounds form stable complexes with both cytochrome b subunit and succinate dehydrogenase enzyme. This work can be considered an important first step towards the development of novel dual-action agents with optimized structure and improved interaction with the targets.
DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture
Authors: Sharma Alok , Vans Edwin , Shigemizu Daichi , Boroevich Keith A. , Tsunoda Tatsuhiko 
Published: August 2019

AbstractIt is critical, but difficult, to catch the small variation in genomic or other kinds of data that differentiates phenotypes or categories. A plethora of data is available, but the information from its genes or elements is spread over arbitrarily, making it challenging to extract relevant details for identification. However, an arrangement of similar genes into clusters makes these differences more accessible and allows for robust identification of hidden mechanisms (e.g. pathways) than dealing with elements individually. Here we propose, DeepInsight, which converts non-image samples into a well-organized image-form. Thereby, the power of convolution neural network (CNN), including GPU utilization, can be realized for non-image samples. Furthermore, DeepInsight enables feature extraction through the application of CNN for non-image samples to seize imperative information and shown promising results. To our knowledge, this is the first work to apply CNN simultaneously on different kinds of non-image datasets: RNA-seq, vowels, text, and artificial.
Water versus Asphaltenes; Liquid–Liquid and Solid–Liquid Molecular Interactions Unravel the Mechanisms behind an Improved Oil Recovery Methodology
Authors: Joonaki Edris , Buckman Jim , Burgass Rod , Tohidi Bahman 
Published: August 2019

AbstractUnderstanding of possible molecular interactions at liquid-liquid and solid-liquid interfaces can shed lights onto the nature’s design and authorise fine manipulation aptitude in biological, manufacturing, microfluidic and oil recovery applications. Of particular interest is the capability to control the aggregation of organic and biological macromolecules, which typically poses significant challenges for oil industry and human life, respectively. Following asphaltene aggregation phenomenon through π-stacking and hydrogen bonding interactions, asphaltene aggregates can form a thin layer at the crude oil-brine interface through noncovalent interactions such as -O-H···O hydrogen bonds and/or alter the wettability state of the solid surface from initially water-wet into mixed-oil wetting. Here, we probe the impact of water with variety of salinities and ion types on formation of water in oil micro-emulsions, asphaltene deposition, and induced water wettability transition at micro scale. For the first time we investigate the influence of water in oil micro-emulsions on asphaltene aggregation and deposition phenomena at elevated pressure and temperature conditions. We also monitor the micro-wettability alterations of gold surface of the QCM owing to ion valency/concentration changes using state of the art ESEM imaging facility. Our results depict that owing to the substitution of divalent cations with monovalent ones, asphaltene deposition is repelled and the solid surface becomes more hydrophilic, proposing a generalizable strategy to control wettability and an elucidation for the profitability of so-called low salinity water flooding, an enhanced oil recovery methodology. For the biological applications, this study provides insights into the potential roles of ions and hydrogen bonds in the protein deposition in tissues and self-assembly interactions and efficiency of drugs against protein aggregation drivers.
Parenting Stress Undermines Mother-Child Brain-to-Brain Synchrony: A Hyperscanning Study
Authors: Azhari A. , Leck W. Q. , Gabrieli G. , Bizzego A. , Rigo P. , Setoh P. , Bornstein M. H. , Esposito G. 
Published: August 2019

AbstractSynchrony refers to the coordinated interplay of behavioural and physiological signals that reflect the bi-directional attunement of one partner to the other’s psychophysiological, cognitive, emotional, and behavioral state. In mother-child relationships, a synchronous pattern of interaction indicates parental sensitivity. Parenting stress has been shown to undermine mother-child behavioural synchrony. However, it has yet to be discerned whether parenting stress affects brain-to-brain synchrony during everyday joint activities. Here, we show that greater parenting stress is associated with less brain-to-brain synchrony in the medial left cluster of the prefrontal cortex when mother and child engage in a typical dyadic task of watching animation videos together. This brain region overlaps with the inferior frontal gyrus, the frontal eye field, and the dorsolateral prefrontal cortex, which are implicated in inference of mental states and social cognition. Our result demonstrates the adverse effect of parenting stress on mother-child attunement that is evident at a brain-to-brain level. Mother-child brain-to-brain asynchrony may underlie the robust association between parenting stress and poor dyadic co-regulation. We anticipate our study to form the foundation for future investigations into mechanisms by which parenting stress impairs the mother-child relationship.
Insects to feed insects - feeding Aedes mosquitoes with flies for laboratory rearing
Authors: Bimbilé Somda Nanwintoum Séverin , Maïga Hamidou , Mamai Wadaka , Yamada Hanano , Ali Adel , Konczal Anna , Gnankiné Olivier , Diabaté Abdoulaye , Sanon Antoine , Dabiré Kounbobr Roch , Gilles Jérémie R. L. , Bouyer Jérémy 
Published: August 2019

AbstractThe black soldier fly, yellow mealworm and house fly are known for their wide distribution, ease of breeding, and environmental and nutritional attributes. Diets based on these fly proteins for the rearing of mosquito larvae are more accessible and affordable when compared to the reference IAEA diet which consists largely of costly livestock products such as bovine liver powder. Following a step-by-step assessment, we developed diet mixtures based on insect meal for the optimal mass production of Aedes albopictus and Ae. aegypti. Based on the assessed parameters including mosquito egg hatch, body size, flight ability, longevity and diet cost reduction, two mixtures are recommended: 1/2 tuna meal (TM) + 7/20 black soldier fly (BSF) + 3/20 brewer’s yeast and 1/2 TM + 1/2 BSF. These findings, which could be adapted to other mosquito species, provide alternative protein sources for mass rearing insects for genetic control strategies.