bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease
Authors: Alkallas Rached , Fish Lisa , Goodarzi Hani , Najafabadi Hamed S. 
Published: October 2017

AbstractThe abundance of mRNA is mainly determined by the rates of RNA transcription and decay. Here, we present a method for unbiased estimation of differential mRNA decay rate from RNA-sequencing data by modeling the kinetics of mRNA metabolism. We show that in all primary human tissues tested, and particularly in the central nervous system, many pathways are regulated at the mRNA stability level. We present a parsimonious regulatory model consisting of two RNA-binding proteins and four microRNAs that modulate the mRNA stability landscape of the brain, which suggests a new link between RBFOX proteins and Alzheimer’s disease. We show that downregulation of RBFOX1 leads to destabilization of mRNAs encoding for synaptic transmission proteins, which may contribute to the loss of synaptic function in Alzheimer’s disease. RBFOX1 downregulation is more likely to occur in older and female individuals, consistent with the association of Alzheimer’s disease with age and gender.
Entanglement between more than two hundred macroscopic atomic ensembles in a solid
Authors: Zarkeshian P. , Deshmukh C. , Sinclair N. , Goyal S. K. , Aguilar G. H. , Lefebvre P. , Puigibert M. Grimau , Verma V. B. , Marsili F. , Shaw M. D. , Nam S. W. , Heshami K. , Oblak D. , Tittel W. , Simon C. 
Published: October 2017

AbstractThere are both fundamental and practical motivations for studying whether quantum entanglement can exist in macroscopic systems. However, multiparty entanglement is generally fragile and difficult to quantify. Dicke states are multiparty entangled states where a single excitation is delocalized over many systems. Building on previous work on quantum memories for photons, we create a Dicke state in a solid by storing a single photon in a crystal that contains many large atomic ensembles with distinct resonance frequencies. The photon is re-emitted at a well-defined time due to an interference effect analogous to multi-slit diffraction. We derive a lower bound for the number of entangled ensembles based on the contrast of the interference and the single-photon character of the input, and we experimentally demonstrate entanglement between over two hundred ensembles, each containing a billion atoms. We also illustrate the fact that each individual ensemble contains further entanglement.
Experimental certification of millions of genuinely entangled atoms in a solid
Authors: Fröwis Florian , Strassmann Peter C. , Tiranov Alexey , Gut Corentin , Lavoie Jonathan , Brunner Nicolas , Bussières Félix , Afzelius Mikael , Gisin Nicolas 
Published: October 2017

AbstractQuantum theory predicts that entanglement can also persist in macroscopic physical systems, albeit difficulties to demonstrate it experimentally remain. Recently, significant progress has been achieved and genuine entanglement between up to 2900 atoms was reported. Here, we demonstrate 16 million genuinely entangled atoms in a solid-state quantum memory prepared by the heralded absorption of a single photon. We develop an entanglement witness for quantifying the number of genuinely entangled particles based on the collective effect of directed emission combined with the non-classical nature of the emitted light. The method is applicable to a wide range of physical systems and is effective even in situations with significant losses. Our results clarify the role of multipartite entanglement in ensemble-based quantum memories and demonstrate the accessibility to certain classes of multipartite entanglement with limited experimental control.
A conserved KLF-autophagy pathway modulates nematode lifespan and mammalian age-associated vascular dysfunction
Authors: Hsieh Paishiun N. , Zhou Guangjin , Yuan Yiyuan , Zhang Rongli , Prosdocimo Domenick A. , Sangwung Panjamaporn , Borton Anna H. , Boriushkin Evgenii , Hamik Anne , Fujioka Hisashi , Fealy Ciaran E. , Kirwan John P. , Peters Maureen , Lu Yuan , Liao Xudong , Ramírez-Bergeron Diana , Feng Zhaoyang , Jain Mukesh K. 
Published: October 2017

AbstractLoss of protein and organelle quality control secondary to reduced autophagy is a hallmark of aging. However, the physiologic and molecular regulation of autophagy in long-lived organisms remains incompletely understood. Here we show that the Kruppel-like family of transcription factors are important regulators of autophagy and healthspan in C. elegans, and also modulate mammalian vascular age-associated phenotypes. Kruppel-like family of transcription factor deficiency attenuates autophagy and lifespan extension across mechanistically distinct longevity nematode models. Conversely, Kruppel-like family of transcription factor overexpression extends nematode lifespan in an autophagy-dependent manner. Furthermore, we show the mammalian vascular factor Kruppel-like family of transcription factor 4 has a conserved role in augmenting autophagy and improving vessel function in aged mice. Kruppel-like family of transcription factor 4 expression also decreases with age in human vascular endothelium. Thus, Kruppel-like family of transcription factors constitute a transcriptional regulatory point for the modulation of autophagy and longevity in C. elegans with conserved effects in the murine vasculature and potential implications for mammalian vascular aging.
Poverty eradication in a carbon constrained world
Authors: Hubacek Klaus , Baiocchi Giovanni , Feng Kuishuang , Patwardhan Anand 
Published: October 2017

Abstract
The UN Framework Convention on Climate Change aims to keep warming below 2 °C while recognizing developing countries’ right to eradicate extreme poverty. Poverty eradication is also the first of the Sustainable Development Goals. This paper investigates potential consequences for climate targets of achieving poverty eradication. We find that eradicating extreme poverty, i.e., moving people to an income above $1.9 purchasing power parity (PPP) a day, does not jeopardize the climate target even in the absence of climate policies and with current technologies. On the other hand, bringing everybody to a still modest expenditure level of at least $2.97 PPP would have long-term consequences on achieving emission targets. Compared to the reference mitigation pathway, eradicating extreme poverty increases the effort by 2.8% whereas bringing everybody to at least $2.97 PPP would increase the required mitigation rate by 27%. Given that the top 10% global income earners are responsible for 36% of the current carbon footprint of households; the discourse should address income distribution and the carbon intensity of lifestyles.
Observation of spin-orbit effects with spin rotation symmetry
Authors: Humphries Alisha M. , Wang Tao , Edwards Eric R. J. , Allen Shane R. , Shaw Justin M. , Nembach Hans T. , Xiao John Q. , Silva T. J. , Fan Xin 
Published: October 2017

AbstractThe spin–orbit interaction enables interconversion between a charge current and a spin current. It is usually believed that in a nonmagnetic metal (NM) or at a NM/ferromagnetic metal (FM) bilayer interface, the symmetry of spin–orbit effects requires that the spin current, charge current, and spin orientation are all orthogonal to each other. Here we demonstrate the presence of spin–orbit effects near the NM/FM interface that exhibit a very different symmetry, hereafter referred to as spin-rotation symmetry, from the conventional spin Hall effect while the spin polarization is rotating about the magnetization. These results imply that a perpendicularly polarized spin current can be generated with an in-plane charge current simply by use of a FM/NM bilayer with magnetization collinear to the charge current. The ability to generate a spin current with arbitrary polarization using typical magnetic materials will benefit the development of magnetic memories.
Understanding seed-mediated growth of gold nanoclusters at molecular level
Authors: Yao Qiaofeng , Yuan Xun , Fung Victor , Yu Yong , Leong David Tai , Jiang De-en , Xie Jianping 
Published: October 2017

AbstractThe continuous development of total synthesis chemistry has allowed many organic and biomolecules to be produced with known synthetic history–that is, a complete set of step reactions in their synthetic routes. Here, we extend such molecular-level precise reaction routes to nanochemistry, particularly to a seed-mediated synthesis of inorganic nanoparticles. By systematically investigating the time−dependent abundance of 35 intermediate species in total, we map out relevant step reactions in a model size growth reaction from molecularly pure Au25 to Au44 nanoparticles. The size growth of Au nanoparticles involves two different size−evolution processes (monotonic LaMer growth and volcano-shaped aggregative growth), which are driven by a sequential 2-electron boosting of the valence electron count of Au nanoparticles. Such fundamental findings not only provide guiding principles to produce other sizes of Au nanoparticles (e.g., Au38), but also represent molecular-level insights on long-standing puzzles in nanochemistry, including LaMer growth, aggregative growth, and digestive ripening.
Actomyosin polarisation through PLC-PKC triggers symmetry breaking of the mouse embryo
Authors: Zhu Meng , Leung Chuen Yan , Shahbazi Marta N. , Zernicka-Goetz Magdalena 
Published: October 2017

AbstractEstablishment of cell polarity in the mammalian embryo is fundamental for the first cell fate decision that sets aside progenitor cells for both the new organism and the placenta. Yet the sequence of events and molecular mechanism that trigger this process remain unknown. Here, we show that de novo polarisation of the mouse embryo occurs in two distinct phases at the 8-cell stage. In the first phase, an apical actomyosin network is formed. This is a pre-requisite for the second phase, in which the Par complex localises to the apical domain, excluding actomyosin and forming a mature apical cap. Using a variety of approaches, we also show that phospholipase C-mediated PIP2 hydrolysis is necessary and sufficient to trigger the polarisation of actomyosin through the Rho-mediated recruitment of myosin II to the apical cortex. Together, these results reveal the molecular framework that triggers de novo polarisation of the mouse embryo.
Cancer-associated fibroblasts induce metalloprotease-independent cancer cell invasion of the basement membrane
Authors: Glentis Alexandros , Oertle Philipp , Mariani Pascale , Chikina Aleksandra , El Marjou Fatima , Attieh Youmna , Zaccarini Francois , Lae Marick , Loew Damarys , Dingli Florent , Sirven Philemon , Schoumacher Marie , Gurchenkov Basile G. , Plodinec Marija , Vignjevic Danijela Matic 
Published: October 2017

AbstractAt the stage of carcinoma in situ, the basement membrane (BM) segregates tumor cells from the stroma. This barrier must be breached to allow dissemination of the tumor cells to adjacent tissues. Cancer cells can perforate the BM using proteolysis; however, whether stromal cells play a role in this process remains unknown. Here we show that an abundant stromal cell population, cancer-associated fibroblasts (CAFs), promote cancer cell invasion through the BM. CAFs facilitate the breaching of the BM in a matrix metalloproteinase-independent manner. Instead, CAFs pull, stretch, and soften the BM leading to the formation of gaps through which cancer cells can migrate. By exerting contractile forces, CAFs alter the organization and the physical properties of the BM, making it permissive for cancer cell invasion. Blocking the ability of stromal cells to exert mechanical forces on the BM could therefore represent a new therapeutic strategy against aggressive tumors.
NatD promotes lung cancer progression by preventing histone H4 serine phosphorylation to activate Slug expression
Authors: Ju Junyi , Chen Aiping , Deng Yexuan , Liu Ming , Wang Ying , Wang Yadong , Nie Min , Wang Chao , Ding Hong , Yao Bing , Gui Tao , Li Xinyu , Xu Zhen , Ma Chi , Song Yong , Kvansakul Marc , Zen Ke , Zhang Chen-Yu , Luo Cheng , Fang Ming , Huang David C. S. , Allis C. David , Tan Renxiang , Zeng Changjiang Kathy , Wei Jiwu , Zhao Quan 
Published: October 2017

AbstractN-α-acetyltransferase D (NatD) mediates N-α-terminal acetylation (Nt-acetylation) of histone H4 known to be involved in cell growth. Here we report that NatD promotes the migratory and invasive capabilities of lung cancer cells in vitro and in vivo. Depletion of NatD suppresses the epithelial-to-mesenchymal transition (EMT) of lung cancer cells by directly repressing the expression of transcription factor Slug, a key regulator of EMT. We found that Nt-acetylation of histone H4 antagonizes histone H4 serine 1 phosphorylation (H4S1ph), and that downregulation of Nt-acetylation of histone H4 facilitates CK2α binding to histone H4 in lung cancer cells, resulting in increased H4S1ph and epigenetic reprogramming to suppress Slug transcription to inhibit EMT. Importantly, NatD is commonly upregulated in primary human lung cancer tissues where its expression level correlates with Slug expression, enhanced invasiveness, and poor clinical outcomes. These findings indicate that NatD is a crucial epigenetic modulator of cell invasion during lung cancer progression.
Spontaneous jumping, bouncing and trampolining of hydrogel drops on a heated plate
Authors: Pham Jonathan T. , Paven Maxime , Wooh Sanghyuk , Kajiya Tadashi , Butt Hans-Jürgen , Vollmer Doris 
Published: October 2017

AbstractThe contact between liquid drops and hot solid surfaces is of practical importance for industrial processes, such as thermal spraying and spray cooling. The contact and bouncing of solid spheres is also an important event encountered in ball milling, powder processing, and everyday activities, such as ball sports. Using high speed video microscopy, we demonstrate that hydrogel drops, initially at rest on a surface, spontaneously jump upon rapid heating and continue to bounce with increasing amplitudes. Jumping is governed by the surface wettability, surface temperature, hydrogel elasticity, and adhesion. A combination of low-adhesion impact behavior and fast water vapor formation supports continuous bouncing and trampolining. Our results illustrate how the interplay between solid and liquid characteristics of hydrogels results in intriguing dynamics, as reflected by spontaneous jumping, bouncing, trampolining, and extremely short contact times.
Evidence of indirect gap in monolayer WSe2
Authors: Hsu Wei-Ting , Lu Li-Syuan , Wang Dean , Huang Jing-Kai , Li Ming-Yang , Chang Tay-Rong , Chou Yi-Chia , Juang Zhen-Yu , Jeng Horng-Tay , Li Lain-Jong , Chang Wen-Hao 
Published: October 2017

AbstractMonolayer transition metal dichalcogenides, such as MoS2 and WSe2, have been known as direct gap semiconductors and emerged as new optically active materials for novel device applications. Here we reexamine their direct gap properties by investigating the strain effects on the photoluminescence of monolayer MoS2 and WSe2. Instead of applying stress, we investigate the strain effects by imaging the direct exciton populations in monolayer WSe2–MoS2 and MoSe2–WSe2 lateral heterojunctions with inherent strain inhomogeneity. We find that unstrained monolayer WSe2 is actually an indirect gap material, as manifested in the observed photoluminescence intensity–energy correlation, from which the difference between the direct and indirect optical gaps can be extracted by analyzing the exciton thermal populations. Our findings combined with the estimated exciton binding energy further indicate that monolayer WSe2 exhibits an indirect quasiparticle gap, which has to be reconsidered in further studies for its fundamental properties and device applications.
Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras
Authors: Peeters Ken , Van Leemputte Frederik , Fischer Baptiste , Bonini Beatriz M. , Quezada Hector , Tsytlonok Maksym , Haesen Dorien , Vanthienen Ward , Bernardes Nuno , Gonzalez-Blas Carmen Bravo , Janssens Veerle , Tompa Peter , Versées Wim , Thevelein Johan M. 
Published: October 2017

AbstractYeast and cancer cells share the unusual characteristic of favoring fermentation of sugar over respiration. We now reveal an evolutionary conserved mechanism linking fermentation to activation of Ras, a major regulator of cell proliferation in yeast and mammalian cells, and prime proto-oncogene product. A yeast mutant (tps1∆) with overactive influx of glucose into glycolysis and hyperaccumulation of Fru1,6bisP, shows hyperactivation of Ras, which causes its glucose growth defect by triggering apoptosis. Fru1,6bisP is a potent activator of Ras in permeabilized yeast cells, likely acting through Cdc25. As in yeast, glucose triggers activation of Ras and its downstream targets MEK and ERK in mammalian cells. Biolayer interferometry measurements show that physiological concentrations of Fru1,6bisP stimulate dissociation of the pure Sos1/H-Ras complex. Thermal shift assay confirms direct binding to Sos1, the mammalian ortholog of Cdc25. Our results suggest that the Warburg effect creates a vicious cycle through Fru1,6bisP activation of Ras, by which enhanced fermentation stimulates oncogenic potency.
Heading representations in primates are compressed by saccades
Authors: Bremmer Frank , Churan Jan , Lappe Markus 
Published: October 2017

AbstractPerceptual illusions help to understand how sensory signals are decoded in the brain. Here we report that the opposite approach is also applicable, i.e., results from decoding neural activity from monkey extrastriate visual cortex correctly predict a hitherto unknown perceptual illusion in humans. We record neural activity from monkey medial superior temporal (MST) and ventral intraparietal (VIP) area during presentation of self-motion stimuli and concurrent reflexive eye movements. A heading-decoder performs veridically during slow eye movements. During fast eye movements (saccades), however, the decoder erroneously reports compression of heading toward straight ahead. Functional equivalents of macaque areas MST and VIP have been identified in humans, implying a perceptual correlate (illusion) of this perisaccadic decoding error. Indeed, a behavioral experiment in humans shows that perceived heading is perisaccadically compressed toward the direction of gaze. Response properties of primate areas MST and VIP are consistent with being the substrate of the newly described visual illusion.
Highly compressed water structure observed in a perchlorate aqueous solution
Authors: Lenton Samuel , Rhys Natasha H. , Towey James J. , Soper Alan K. , Dougan Lorna 
Published: October 2017

AbstractThe discovery by the Phoenix Lander of calcium and magnesium perchlorates in Martian soil samples has fueled much speculation that flows of perchlorate brines might be the cause of the observed channeling and weathering in the surface. Here, we study the structure of a mimetic of Martian water, magnesium perchlorate aqueous solution at its eutectic composition, using neutron diffraction in combination with hydrogen isotope labeling and empirical potential structure refinement. We find that the tetrahedral structure of water is heavily perturbed, the effect being equivalent to pressurizing pure water to pressures of order 2 GPa or more. The Mg2+ and ClO4− ions appear charge-ordered, confining the water on length scales of order 9 Å, preventing ice formation at low temperature. This may explain the low evaporation rates and high deliquescence of these salt solutions, which are essential for stability within the low relative humidity environment of the Martian atmosphere.
Kif2 localizes to a subdomain of cortical endoplasmic reticulum that drives asymmetric spindle position
Authors: Costache Vlad , Hebras Celine , Pruliere Gerard , Besnardeau Lydia , Failla Margaux , Copley Richard R. , Burgess David , Chenevert Janet , McDougall Alex 
Published: October 2017

AbstractAsymmetric positioning of the mitotic spindle is a fundamental process responsible for creating sibling cell size asymmetry; however, how the cortex causes the depolymerization of astral microtubules during asymmetric spindle positioning has remained elusive. Early ascidian embryos possess a large cortical subdomain of endoplasmic reticulum (ER) that causes asymmetric spindle positioning driving unequal cell division. Here we show that the microtubule depolymerase Kif2 localizes to this subdomain of cortical ER. Rapid live-cell imaging reveals that microtubules are less abundant in the subdomain of cortical ER. Inhibition of Kif2 function prevents the development of mitotic aster asymmetry and spindle pole movement towards the subdomain of cortical ER, whereas locally increasing microtubule depolymerization causes exaggerated asymmetric spindle positioning. This study shows that the microtubule depolymerase Kif2 is localized to a cortical subdomain of endoplasmic reticulum that is involved in asymmetric spindle positioning during unequal cell division.
Cubic gauche polymeric nitrogen under ambient conditions
Authors: Benchafia El Mostafa , Yao Zhenhua , Yuan Gu , Chou Tsengmin , Piao Hong , Wang Xianqin , Iqbal Zafar 
Published: October 2017

AbstractThe long-sought cubic gauche phase of polymeric nitrogen (cg-PN) with nitrogen-nitrogen single bonds has been synthesized together with a related phase by a radio-frequency plasma reaction under near-ambient conditions. Here, we report the synthesis of polymeric nitrogen using a mixture of nitrogen and argon flowing over bulk β-sodium azide or β-sodium azide dispersed on 100 nm long multiwall carbon nanotubes. The cg-PN phase is identified by Raman and attenuated total reflection-Fourier transform infrared spectroscopy, and powder X-ray diffraction. The synthesis of the cubic gauche allotrope of high energy density polymeric nitrogen under near-ambient conditions should therefore enable its optimized production and applications as a “green” energetic material and a potential catalyst for different chemical reactions.
CCDC88B is required for pathogenesis of inflammatory bowel disease
Authors: Fodil Nassima , Moradin Neda , Leung Vicki , Olivier Jean-Frederic , Radovanovic Irena , Jeyakumar Thiviya , Flores Molina Manuel , McFarquhar Ashley , Cayrol Romain , Bozec Dominique , Shoukry Naglaa H. , Kubo Michiaki , Dimitrieva Julia , Louis Edouard , Theatre Emilie , Dahan Stephanie , Momozawa Yukihide , Georges Michel , Yeretssian Garabet , Gros Philippe 
Published: October 2017

AbstractInflammatory bowel disease (IBD) involves interaction between host genetic factors and environmental triggers. CCDC88B maps within one IBD risk locus on human chromosome 11q13. Here we show that CCDC88B protein increases in the colon during intestinal injury, concomitant with an influx of CCDC88B+lymphoid and myeloid cells. Loss of Ccdc88b protects against DSS-induced colitis, with fewer pathological lesions and reduced intestinal inflammation in Ccdc88b-deficient mice. In a T cell transfer model of colitis, Ccdc88b mutant CD4+ T cells do not induce colitis in immunocompromised hosts. Expression of human CCDC88B RNA and protein is higher in IBD patient colons than in control colon tissue. In human CD14+ myeloid cells, CCDC88B is regulated by cis-acting variants. In a cohort of patients with Crohn’s disease, CCDC88B expression correlates positively with disease risk. These findings suggest that CCDC88B has a critical function in colon inflammation and the pathogenesis of IBD.