bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moulding hydrodynamic 2D-crystals upon parametric Faraday waves in shear-functionalized water surfaces
Authors: Kharbedia Mikheil , Caselli Niccolò , Herráez-Aguilar Diego , López-Menéndez Horacio , Enciso Eduardo , Santiago José A. , Monroy Francisco 
Published: February 2021

AbstractFaraday waves, or surface waves oscillating at half of the natural frequency when a liquid is vertically vibrated, are archetypes of ordering transitions on liquid surfaces. Although unbounded Faraday waves patterns sustained upon bulk frictional stresses have been reported in highly viscous fluids, the role of surface rigidity has not been investigated so far. Here, we demonstrate that dynamically frozen Faraday waves—that we call 2D-hydrodynamic crystals—do appear as ordered patterns of nonlinear gravity-capillary modes in water surfaces functionalized with soluble (bio)surfactants endowing in-plane shear stiffness. The phase coherence in conjunction with the increased surface rigidity bears the Faraday waves ordering transition, upon which the hydrodynamic crystals were reversibly molded under parametric control of their degree of order, unit cell size and symmetry. The hydrodynamic crystals here discovered could be exploited in touchless strategies of soft matter and biological scaffolding ameliorated under external control of Faraday waves coherence.
Bioinspired multisensory neural network with crossmodal integration and recognition
Authors: Tan Hongwei , Zhou Yifan , Tao Quanzheng , Rosen Johanna , van Dijken Sebastiaan 
Published: February 2021

AbstractThe integration and interaction of vision, touch, hearing, smell, and taste in the human multisensory neural network facilitate high-level cognitive functionalities, such as crossmodal integration, recognition, and imagination for accurate evaluation and comprehensive understanding of the multimodal world. Here, we report a bioinspired multisensory neural network that integrates artificial optic, afferent, auditory, and simulated olfactory and gustatory sensory nerves. With distributed multiple sensors and biomimetic hierarchical architectures, our system can not only sense, process, and memorize multimodal information, but also fuse multisensory data at hardware and software level. Using crossmodal learning, the system is capable of crossmodally recognizing and imagining multimodal information, such as visualizing alphabet letters upon handwritten input, recognizing multimodal visual/smell/taste information or imagining a never-seen picture when hearing its description. Our multisensory neural network provides a promising approach towards robotic sensing and perception.
KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation
Authors: Tran Timothy H. , Chan Albert H. , Young Lucy C. , Bindu Lakshman , Neale Chris , Messing Simon , Dharmaiah Srisathiyanarayanan , Taylor Troy , Denson John-Paul , Esposito Dominic , Nissley Dwight V. , Stephen Andrew G. , McCormick Frank , Simanshu Dhirendra K. 
Published: February 2021

AbstractThe first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation.
Neuronal fragile X mental retardation protein activates glial insulin receptor mediated PDF-Tri neuron developmental clearance
Authors: Vita Dominic J. , Meier Cole J. , Broadie Kendal 
Published: February 2021

AbstractGlia engulf and phagocytose neurons during neural circuit developmental remodeling. Disrupting this pruning process contributes to Fragile X syndrome (FXS), a leading cause of intellectual disability and autism spectrum disorder in mammals. Utilizing a Drosophila FXS model central brain circuit, we identify two glial classes responsible for Draper-dependent elimination of developmentally transient PDF-Tri neurons. We find that neuronal Fragile X Mental Retardation Protein (FMRP) drives insulin receptor activation in glia, promotes glial Draper engulfment receptor expression, and negatively regulates membrane-molding ESCRT-III Shrub function during PDF-Tri neuron clearance during neurodevelopment in Drosophila. In this context, we demonstrate genetic interactions between FMRP and insulin receptor signaling, FMRP and Draper, and FMRP and Shrub in PDF-Tri neuron elimination. We show that FMRP is required within neurons, not glia, for glial engulfment, indicating FMRP-dependent neuron-to-glia signaling mediates neuronal clearance. We conclude neuronal FMRP drives glial insulin receptor activation to facilitate Draper- and Shrub-dependent neuronal clearance during neurodevelopment in Drosophila.
Human cortical encoding of pitch in tonal and non-tonal languages
Authors: Li Yuanning , Tang Claire , Lu Junfeng , Wu Jinsong , Chang Edward F. 
Published: February 2021

AbstractLanguages can use a common repertoire of vocal sounds to signify distinct meanings. In tonal languages, such as Mandarin Chinese, pitch contours of syllables distinguish one word from another, whereas in non-tonal languages, such as English, pitch is used to convey intonation. The neural computations underlying language specialization in speech perception are unknown. Here, we use a cross-linguistic approach to address this. Native Mandarin- and English- speaking participants each listened to both Mandarin and English speech, while neural activity was directly recorded from the non-primary auditory cortex. Both groups show language-general coding of speaker-invariant pitch at the single electrode level. At the electrode population level, we find language-specific distribution of cortical tuning parameters in Mandarin speakers only, with enhanced sensitivity to Mandarin tone categories. Our results show that speech perception relies upon a shared cortical auditory feature processing mechanism, which may be tuned to the statistics of a given language.
Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery
Authors: Li Feng , Yu Wenting , Zhang Jiaojiao , Dong Yuhang , Ding Xiaohui , Ruan Xinhua , Gu Zi , Yang Dayong 
Published: February 2021

AbstractDNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity–scalability–error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity–scalability–error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.
Optimal marker gene selection for cell type discrimination in single cell analyses
Authors: Dumitrascu Bianca , Villar Soledad , Mixon Dustin G. , Engelhardt Barbara E. 
Published: February 2021

AbstractSingle-cell technologies characterize complex cell populations across multiple data modalities at unprecedented scale and resolution. Multi-omic data for single cell gene expression, in situ hybridization, or single cell chromatin states are increasingly available across diverse tissue types. When isolating specific cell types from a sample of disassociated cells or performing in situ sequencing in collections of heterogeneous cells, one challenging task is to select a small set of informative markers that robustly enable the identification and discrimination of specific cell types or cell states as precisely as possible. Given single cell RNA-seq data and a set of cellular labels to discriminate, scGeneFit selects gene markers that jointly optimize cell label recovery using label-aware compressive classification methods. This results in a substantially more robust and less redundant set of markers than existing methods, most of which identify markers that separate each cell label from the rest. When applied to a data set given a hierarchy of cell types as labels, the markers found by our method improves the recovery of the cell type hierarchy with fewer markers than existing methods using a computationally efficient and principled optimization.
E3 ligase Nedd4l promotes antiviral innate immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3
Authors: Gao Peng , Ma Xianwei , Yuan Ming , Yi Yulan , Liu Guoke , Wen Mingyue , Jiang Wei , Ji Ruihua , Zhu Lingxi , Tang Zhen , Yu Qingzhuo , Xu Jing , Yang Rui , Xia Sheng , Yang Mingjin , Pan Jianping , Yuan Hongbin , An Huazhang 
Published: February 2021

AbstractUbiquitination is one of the most prevalent protein posttranslational modifications. Here, we show that E3 ligase Nedd4l positively regulates antiviral immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3. Deficiency of Nedd4l significantly impairs type I interferon and proinflammatory cytokine production induced by virus infection both in vitro and in vivo. Nedd4l deficiency inhibits virus-induced ubiquitination of TRAF3, the binding between TRAF3 and TBK1, and subsequent phosphorylation of TBK1 and IRF3. Nedd4l directly interacts with TRAF3 and catalyzes K29-linked ubiquitination of Cys56 and Cys124, two cysteines that constitute zinc fingers, resulting in enhanced association between TRAF3 and E3 ligases, cIAP1/2 and HECTD3, and also increased K48/K63-linked ubiquitination of TRAF3. Mutation of Cys56 and Cys124 diminishes Nedd4l-catalyzed K29-linked ubiquitination, but enhances association between TRAF3 and the E3 ligases, supporting Nedd4l promotes type I interferon production in response to virus by catalyzing ubiquitination of the cysteines in TRAF3.
Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease
Authors: Hu Shixian , Uniken Venema Werna T. , Westra Harm-Jan , Vich Vila Arnau , Barbieri Ruggero , Voskuil Michiel D. , Blokzijl Tjasso , Jansen Bernadien H. , Li Yanni , Daly Mark J. , Xavier Ramnik J. , Dijkstra Gerard , Festen Eleonora A. , Weersma Rinse K. 
Published: February 2021

AbstractMore than 240 genetic risk loci have been associated with inflammatory bowel disease (IBD), but little is known about how they contribute to disease development in involved tissue. Here, we hypothesized that host genetic variation affects gene expression in an inflammation-dependent way, and investigated 299 snap-frozen intestinal biopsies from inflamed and non-inflamed mucosa from 171 IBD patients. RNA-sequencing was performed, and genotypes were determined using whole exome sequencing and genome wide genotyping. In total, 28,746 genes and 6,894,979 SNPs were included. Linear mixed models identified 8,881 independent intestinal cis-expression quantitative trait loci (cis-eQTLs) (FDR < 0.05) and interaction analysis revealed 190 inflammation-dependent intestinal cis-eQTLs (FDR < 0.05), including known IBD-risk genes and genes encoding immune-cell receptors and antibodies. The inflammation-dependent cis-eQTL SNPs (eSNPs) mainly interact with prevalence of immune cell types. Inflammation-dependent intestinal cis-eQTLs reveal genetic susceptibility under inflammatory conditions that can help identify the cell types involved in and the pathways underlying inflammation, knowledge that may guide future drug development and profile patients for precision medicine in IBD.
Stable single atomic silver wires assembling into a circuitry-connectable nanoarray
Authors: Chen Yaxin , Tang Daiming , Huang Zhiwei , Liu Xi , Chen Jun , Sekiguchi Takashi , Qu Weiye , Chen Junxiao , Xu Dongrun , Bando Yoshio , Hu Xiaolei , Wang Xiaoping , Golberg Dmitri , Tang Xingfu 
Published: February 2021

AbstractAtomic metal wires have great promise for practical applications in devices due to their unique electronic properties. Unfortunately, such atomic wires are extremely unstable. Here we fabricate stable atomic silver wires (ASWs) with appreciably unoccupied states inside the parallel tunnels of α-MnO2 nanorods. These unoccupied Ag 4d orbitals strengthen the Ag–Ag bonds, greatly enhancing the stability of ASWs while the presence of delocalized 5s electrons makes the ASWs conducting. These stable ASWs form a coherently oriented three-dimensional wire array of over 10 nm in width and up to 1 μm in length allowing us to connect it to nano-electrodes. Current-voltage characteristics of ASWs show a temperature-dependent insulator-to-metal transition, suggesting that the atomic wires could be used as thermal electrical devices.
Histamine H1 receptor deletion in cholinergic neurons induces sensorimotor gating ability deficit and social impairments in mice
Authors: Cheng Li , Xu Cenglin , Wang Lu , An Dadao , Jiang Lei , Zheng Yanrong , Xu Yixin , Wang Yi , Wang Yujing , Zhang Kuo , Wang Xiaodong , Zhang Xiangnan , Bao Aimin , Zhou Yudong , Yang Jingyu , Duan Shumin , Swaab Dick F. , Hu Weiwei , Chen Zhong 
Published: February 2021

AbstractNegative symptoms in schizophrenia strongly contribute to poor functional outcomes, however its pathogenesis is still unclear. Here, we found that histamine H1 receptor (H1R) expression in basal forebrain (BF) cholinergic neurons was decreased in patients with schizophrenia having negative symptoms. Deletion of H1R gene in cholinergic neurons in mice resulted in functional deficiency of cholinergic projections from the BF to the prefrontal cortex and in the formation of sensorimotor gating deficit, social impairment and anhedonia-like behavior. These behavioral deficits can be rescued by re-expressing H1R or by chemogenetic activation of cholinergic neurons in the BF. Direct chemogenetic inhibition of BF cholinergic neurons produced such behavioral deficits and also increased the susceptibility to hyperlocomotion. Our results suggest that the H1R deficiency in BF cholinergic neurons is critical for sensorimotor gating deficit, social impairments and anhedonia-like behavior. This finding may help to understand the genetic and biochemical bases of negative symptoms in schizophrenia.
Ultra-sensitive nanometric flat laser prints for binocular stereoscopic image
Authors: Hu Dejiao , Li Hao , Zhu Yupeng , Lei Yuqiu , Han Jing , Xian Shilin , Zheng Jiajin , Guan Bai-Ou , Cao Yaoyu , Bi Lei , Li Xiangping 
Published: February 2021

AbstractTwo-dimensional (2D) transition metal dichalcogenides (TMDs) with tantalizing layer-dependent electronic and optical properties have emerged as a paradigm for integrated flat opto-electronic devices, but their widespread applications are hampered by challenges in deterministic fabrication with demanded shapes and thicknesses, as well as light field manipulation in such atomic-thick layers with negligible thicknesses compared to the wavelength. Here we demonstrate ultra-sensitive light field manipulation in full visible ranges based on MoS2 laser prints exfoliated with nanometric precisions. The nontrivial interfacial phase shifts stemming from the unique dispersion of MoS2 layers integrated on the metallic substrate empower an ultra-sensitive resonance manipulation up to 13.95 nm per MoS2 layer across the entire visible bands, which is up to one-order-of-magnitude larger than their counterparts. The interlayer van der Waals interactions and the anisotropic thermal conductivity of layered MoS2 films endow a laser exfoliation method for on-demand patterning MoS2 with atomic thickness precision and subwavelength feature sizes. With this, nanometric flat color prints and further amplitude-modulated diffractive components for binocular stereoscopic images can be realized in a facile and lithography-free fashion. Our results with demonstrated practicality unlock the potentials of, and pave the way for, widespread applications of emerging 2D flat optics.
Dual- versus single-agent HER2 inhibition and incidence of intracranial metastatic disease: a systematic review and meta-analysis
Authors: Erickson Anders Wilder , Habbous Steven , Hoey Christianne , Jerzak Katarzyna J. , Das Sunit 
Published: February 2021

AbstractObservational studies have suggested that HER2 inhibition with trastuzumab may be associated with an increased incidence of intracranial metastatic disease (IMD) due to its ability to prolong survival. We hypothesized that prolonged survival associated with dual-agent HER2 inhibition may be associated with an even higher incidence of IMD. This study pooled estimates of IMD incidence and survival among patients with HER2-positive breast cancer receiving dual- versus single-agent HER2 targeted therapy, as well as trastuzumab versus chemotherapy, observation, or another HER2-targeted agent. We searched PubMed, EMBASE, and CENTRAL from inception to 25 March 2020. We included randomized controlled trials that reported IMD incidence for patients with HER2-positive breast cancer receiving trastuzumab as the experimental or control arm irrespective of disease stage. Among 465 records identified, 19 randomized controlled trials (32,572 patients) were included. Meta-analysis of four studies showed that dual HER2-targeted therapy was associated with improved overall survival (HR 0.76; 95% CI, 0.66–0.87) and progression-free survival (HR 0.77; 95% CI, 0.68–0.87) compared to single HER2-targeted therapy, but the risk of IMD was similar (RR 1.03; 95% CI, 0.83–1.27). Our study challenges the hypothesis that prolonged survival afforded by improved extracranial disease control is associated with increased IMD incidence.
Endocranial volume is variable and heritable, but not related to fitness, in a free-ranging primate
Authors: Colby Abigail E. , Kimock Clare M. , Higham James P. 
Published: February 2021

AbstractLarge relative brain size is a defining characteristic of the order Primates. Arguably, this can be attributed to selection for behavioral aptitudes linked to a larger brain size. In order for selection of a trait to occur, the trait must vary, that variation must be heritable, and enhance fitness. In this study, we use a quantitative genetic approach to investigate the production and maintenance of variation in endocranial volume in a population of free-ranging rhesus macaques. We measured the endocranial volume and body mass proxies of 542 rhesus macaques from Cayo Santiago. We investigated variation in endocranial volume within and between sexes. Using a genetic pedigree, we estimated heritability of absolute and relative endocranial volume, and selection gradients of both traits as well as estimated body mass in the sample. Within this population, both absolute and relative endocranial volume display variation and sexual dimorphism. Both absolute and relative endocranial volume are highly heritable, but we found no evidence of selection on absolute or relative endocranial volume. These findings suggest that endocranial volume is not undergoing selection, or that we did not detect it because selection is neither linear nor quadratic, or that we lacked sufficient sample sizes to detect it.
Syntenin-knock out reduces exosome turnover and viral transduction
Authors: Kashyap Rudra , Balzano Marielle , Lechat Benoit , Lambaerts Kathleen , Egea-Jimenez Antonio Luis , Lembo Frédérique , Fares Joanna , Meeussen Sofie , Kügler Sebastian , Roebroek Anton , David Guido , Zimmermann Pascale 
Published: February 2021

AbstractExosomal transfers represent an important mode of intercellular communication. Syntenin is a small scaffold protein that, when binding ALIX, can direct endocytosed syndecans and syndecan cargo to budding endosomal membranes, supporting the formation of intraluminal vesicles that compose the source of a major class of exosomes. Syntenin, however, can also support the recycling of these same components to the cell surface. Here, by studying mice and cells with syntenin-knock out, we identify syntenin as part of dedicated machinery that integrates both the production and the uptake of secreted vesicles, supporting viral/exosomal exchanges. This study significantly extends the emerging role of heparan sulfate proteoglycans and syntenin as key components for macromolecular cargo internalization into cells.
Probing the floral developmental stages, bisexuality and sex reversions in castor (Ricinus communis L.)
Authors: Parvathy Sujatha Thankeswaran , Prabakaran Amala Joseph , Jayakrishna Thadakamalla 
Published: February 2021

AbstractCastor (Ricinus communis L) is an ideal model species for sex mechanism studies in monoecious angiosperms, due to wide variations in sex expression. Sex reversion to monoecy in pistillate lines, along with labile sex expression, negatively influences hybrid seed purity. The study focuses on understanding the mechanisms of unisexual flower development, sex reversions and sex variations in castor, using various genotypes with distinct sex expression pattern. Male and female flowers had 8 and 12 developmental stages respectively, were morphologically similar till stage 4, with an intermediate bisexual state and were intermediate between type 1 and type 2 flowers. Pistil abortion was earlier than stamen inhibition. Sex alterations occurred at floral and inflorescence level. While sex-reversion was unidirectional towards maleness via bisexual stage, at high day temperatures (Tmax > 38 °C), femaleness was restored with subsequent drop in temperatures. Temperature existing for 2–3 weeks during floral meristem development, influences sexuality of the flower. We report for first time that unisexuality is preceded by bisexuality in castor flowers which alters with genotype and temperature, and sex reversions as well as high sexual polymorphisms in castor are due to alterations in floral developmental pathways. Differentially expressed (male-abundant or male-specific) genes Short chain dehydrogenase reductase 2a (SDR) and WUSCHEL are possibly involved in sex determination of castor.