bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystalline TiO2 protective layer with graded oxygen defects for efficient and stable silicon-based photocathode
Authors: Zheng Jianyun , Lyu Yanhong , Wang Ruilun , Xie Chao , Zhou Huaijuan , Jiang San Ping , Wang Shuangyin 
Published: August 2018

AbstractThe trade-offs between photoelectrode efficiency and stability significantly hinder the practical application of silicon-based photoelectrochemical devices. Here, we report a facile approach to decouple the trade-offs of silicon-based photocathodes by employing crystalline TiO2 with graded oxygen defects as protection layer. The crystalline protection layer provides high-density structure and enhances stability, and at the same time oxygen defects allow the carrier transport with low resistance as required for high efficiency. The silicon-based photocathode with black TiO2 shows a limiting current density of ~35.3 mA cm−2 and durability of over 100 h at 10 mA cm−2 in 1.0 M NaOH electrolyte, while none of photoelectrochemical behavior is observed in crystalline TiO2 protection layer. These findings have significant suggestions for further development of silicon-based, III–V compounds and other photoelectrodes and offer the possibility for achieving highly efficient and durable photoelectrochemical devices.
A terahertz-driven non-equilibrium phase transition in a room temperature atomic vapour
Authors: Wade C. G. , Marcuzzi M. , Levi E. , Kondo J. M. , Lesanovsky I. , Adams C. S. , Weatherill K. J. 
Published: August 2018

AbstractThere are few demonstrated examples of phase transitions that may be driven directly by terahertz frequency electric fields, and those that are known require field strengths exceeding 1 MV cm−1. Here we report a non-equilibrium phase transition driven by a weak (≪1 V cm−1), continuous-wave terahertz electric field. The system consists of room temperature caesium vapour under continuous optical excitation to a high-lying Rydberg state, which is resonantly coupled to a nearby level by the terahertz electric field. We use a simple model to understand the underlying physical behaviour, and we demonstrate two protocols to exploit the phase transition as a narrowband terahertz detector: the first with a fast (20 μs) non-linear response to nano-Watts of incident radiation, and the second with a linearised response and effective noise equivalent power ≤1 pW Hz−1/2. The work opens the door to a class of terahertz devices controlled with low-field intensities and operating in a room temperature environment.
Topographic precision in sensory and motor corticostriatal projections varies across cell type and cortical area
Authors: Hooks Bryan M. , Papale Andrew E. , Paletzki Ronald F. , Feroze Muhammad W. , Eastwood Brian S. , Couey Jonathan J. , Winnubst Johan , Chandrashekar Jayaram , Gerfen Charles R. 
Published: August 2018

AbstractThe striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing topographic specificity as injection sites move from sensory to motor and frontal areas. Topographic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher topographic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. As predicted by a longstanding model, corticostriatal projections of interconnected cortical areas form parallel circuits in the basal ganglia.
Predicting the evolution of Escherichia coli by a data-driven approach
Authors: Wang Xiaokang , Zorraquino Violeta , Kim Minseung , Tsoukalas Athanasios , Tagkopoulos Ilias 
Published: August 2018

AbstractA tantalizing question in evolutionary biology is whether evolution can be predicted from past experiences. To address this question, we created a coherent compendium of more than 15,000 mutation events for the bacterium Escherichia coli under 178 distinct environmental settings. Compendium analysis provides a comprehensive view of the explored environments, mutation hotspots and mutation co-occurrence. While the mutations shared across all replicates decrease with the number of replicates, our results argue that the pairwise overlapping ratio remains the same, regardless of the number of replicates. An ensemble of predictors trained on the mutation compendium and tested in forward validation over 35 evolution replicates achieves a 49.2 ± 5.8% (mean ± std) precision and 34.5 ± 5.7% recall in predicting mutation targets. This work demonstrates how integrated datasets can be harnessed to create predictive models of evolution at a gene level and elucidate the effect of evolutionary processes in well-defined environments.
Synthesis of chiral α-trifluoromethyl alcohols and ethers via enantioselective Hiyama cross-couplings of bisfunctionalized electrophiles
Authors: Varenikov Andrii , Gandelman Mark 
Published: August 2018

AbstractMethods for synthesis of chiral organic compounds bearing trifluoromethyl-substituted stereocenters are of great interest for agrochemical and pharmaceutical labs and industries in their search for new bioactive materials. We report on employment of bisfunctionalized electrophiles, bearing both a trifluoromethyl and a functional group as direct substituents of the reactive center, in cross-coupling reactions. We exemplify this concept in the asymmetric synthesis of enantioenriched α-trifluoromethyl- and perfluoroalkyl-containing benzylic and allylic ethers and alcohols by nickel-catalyzed stereoconvergent Hiyama cross-coupling reaction. Substrate electrophiles are conveniently prepared in few steps from trifluoroacetic acid. The method represents a conceptually different approach to chiral CF3-substituted alcohols and ethers and allows for a rapid catalytic preparation of a wide range of these valuable compounds in high yields and enantioselectivity.
Dendrite-targeting interneurons control synaptic NMDA-receptor activation via nonlinear α5-GABAA receptors
Authors: Schulz Jan M. , Knoflach Frederic , Hernandez Maria-Clemencia , Bischofberger Josef 
Published: August 2018

AbstractDendrite-targeting GABAergic interneurons powerfully control postsynaptic integration, synaptic plasticity, and learning. However, the mechanisms underlying the efficient GABAergic control of dendritic electrogenesis are not well understood. Using subtype-selective blockers for GABAA receptors, we show that dendrite-targeting somatostatin interneurons and NO-synthase-positive neurogliaform cells preferentially activate α5-subunit- containing GABAA receptors (α5-GABAARs), generating slow inhibitory postsynaptic currents (IPSCs) in hippocampal CA1 pyramidal cells. By contrast, only negligible contribution of these receptors could be found in perisomatic IPSCs, generated by fast-spiking parvalbumin interneurons. Remarkably, α5-GABAAR-mediated IPSCs were strongly outward-rectifying generating 4-fold larger conductances above –50 mV than at rest. Experiments and modeling show that synaptic activation of these receptors can very effectively control voltage-dependent NMDA-receptor activation as well as Schaffer-collateral evoked burst firing in pyramidal cells. Taken together, nonlinear-rectifying α5-GABAARs with slow kinetics match functional NMDA-receptor properties and thereby mediate powerful control of dendritic postsynaptic integration and action potential firing by dendrite-targeting interneurons.
Dehydrogenative reagent-free annulation of alkenes with diols for the synthesis of saturated O-heterocycles
Authors: Cai Chen-Yan , Xu Hai-Chao 
Published: August 2018

AbstractDehydrogenative annulation reactions are among the most straightforward and efficient approach for the preparation of cyclic structures. However, the applications of this strategy for the synthesis of saturated heterocycles have been rare. In addition, reported dehydrogenative bond-forming reactions commonly employ stoichiometric chemical oxidants, the use of which reduces the sustainability of the synthesis and brings safety and environmental issues. Herein, we report an organocatalyzed electrochemical dehydrogenative annulation reaction of alkenes with 1,2- and 1,3-diols for the synthesis of 1,4-dioxane and 1,4-dioxepane derivatives. The combination of electrochemistry and redox catalysis using an organic catalyst allows the electrosynthesis to proceed under transition metal- and oxidizing reagent-free conditions. In addition, the electrolytic method has a broad substrate scope and is compatible with many common functional groups, providing an efficient and straightforward access to functionalized 1,4-dioxane and 1,4-dioxepane products with diverse substitution patterns.
The complex underpinnings of genetic background effects
Authors: Mullis Martin N. , Matsui Takeshi , Schell Rachel , Foree Ryan , Ehrenreich Ian M. 
Published: August 2018

AbstractGenetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross–environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects.
Room-temperature polarized spin-photon interface based on a semiconductor nanodisk-in-nanopillar structure driven by few defects
Authors: Chen Shula , Huang Yuqing , Visser Dennis , Anand Srinivasan , Buyanova Irina A. , Chen Weimin M. 
Published: August 2018

AbstractOwing to their superior optical properties, semiconductor nanopillars/nanowires in one-dimensional (1D) geometry are building blocks for nano-photonics. They also hold potential for efficient polarized spin-light conversion in future spin nano-photonics. Unfortunately, spin generation in 1D systems so far remains inefficient at room temperature. Here we propose an approach that can significantly enhance the radiative efficiency of the electrons with the desired spin while suppressing that with the unwanted spin, which simultaneously ensures strong spin and light polarization. We demonstrate high optical polarization of 20%, inferring high electron spin polarization up to 60% at room temperature in a 1D system based on a GaNAs nanodisk-in-GaAs nanopillar structure, facilitated by spin-dependent recombination via merely 2–3 defects in each nanodisk. Our approach points to a promising direction for realization of an interface for efficient spin-photon quantum information transfer at room temperature—a key element for future spin-photonic applications.
SCFFBW7-mediated degradation of Brg1 suppresses gastric cancer metastasis
Authors: Huang Li-Yu , Zhao Junjie , Chen Hao , Wan Lixin , Inuzuka Hiroyuki , Guo Jianping , Fu Xuhong , Zhai Yangyang , Lu Zhaoning , Wang Xuefei , Han Ze-Guang , Sun Yihong , Wei Wenyi 
Published: August 2018

AbstractBrg1/SMARCA4 serves as the ATPase and the helicase catalytic subunit for the multi-component SWI/SNF chromatin remodeling complex, which plays a pivotal role in governing chromatin structure and gene transcription. However, the upstream signaling pathways regulating Brg1 protein stability and its physiological contribution to carcinogenesis remain largely elusive. Here we report that Brg1 is a bona fide ubiquitin substrate of SCFFBW7. We reveal that CK1δ phosphorylates Brg1 at Ser31/Ser35 residues to facilitate the binding of Brg1 to FBW7, leading to ubiquitination-mediated degradation. In keeping with a tumor suppressive role of FBW7 in human gastric cancer, we find an inverse correlation between FBW7 and Brg1 expression in human gastric cancer clinical samples. Mechanistically, we find that stabilization of Brg1 in gastric cancer cells suppresses E-cadherin expression, subsequently promoting gastric cancer metastasis. Hence, this previously unknown FBW7/Brg1 signaling axis provides the molecular basis and the rationale to target Brg1 in FBW7-compromised human gastric cancers.
Carboxysome encapsulation of the CO2-fixing enzyme Rubisco in tobacco chloroplasts
Authors: Long Benedict M. , Hee Wei Yih , Sharwood Robert E. , Rae Benjamin D. , Kaines Sarah , Lim Yi-Leen , Nguyen Nghiem D. , Massey Baxter , Bala Soumi , von Caemmerer Susanne , Badger Murray R. , Price G. Dean 
Published: August 2018

AbstractA long-term strategy to enhance global crop photosynthesis and yield involves the introduction of cyanobacterial CO2-concentrating mechanisms (CCMs) into plant chloroplasts. Cyanobacterial CCMs enable relatively rapid CO2 fixation by elevating intracellular inorganic carbon as bicarbonate, then concentrating it as CO2 around the enzyme Rubisco in specialized protein micro-compartments called carboxysomes. To date, chloroplastic expression of carboxysomes has been elusive, requiring coordinated expression of almost a dozen proteins. Here we successfully produce simplified carboxysomes, isometric with those of the source organism Cyanobium, within tobacco chloroplasts. We replace the endogenous Rubisco large subunit gene with cyanobacterial Form-1A Rubisco large and small subunit genes, along with genes for two key α-carboxysome structural proteins. This minimal gene set produces carboxysomes, which encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2. This result demonstrates the formation of α-carboxysomes from a reduced gene set, informing the step-wise construction of fully functional α-carboxysomes in chloroplasts.
Single crystal toroidal diamond anvils for high pressure experiments beyond 5 megabar
Authors: Jenei Zs. , O’Bannon E. F. , Weir S. T. , Cynn H. , Lipp M. J. , Evans W. J. 
Published: August 2018

AbstractStatic compression experiments over 4 Mbar are rare, yet critical for developing accurate fundamental physics and chemistry models, relevant to a range of topics including modeling planetary interiors. Here we show that focused ion beam crafted toroidal single-crystal diamond anvils with ~9.0 μm culets are capable of producing pressures over 5 Mbar. The toroidal surface prevents gasket outflow and provides a means to stabilize the central culet. We have reached a maximum pressure of ~6.15 Mbar using Re as in situ pressure marker, a pressure regime typically accessed only by double-stage diamond anvils and dynamic compression platforms. Optimizing single-crystal diamond anvil design is key for extending the pressure range over which studies can be performed in the diamond anvil cell.
Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Authors: Sena Johnny A. , Galotto Giulia , Devitt Nico P. , Connick Melanie C. , Jacobi Jennifer L. , Umale Pooja E. , Vidali Luis , Bell Callum J. 
Published: August 2018

AbstractAttaching Unique Molecular Identifiers (UMI) to RNA molecules in the first step of sequencing library preparation establishes a distinct identity for each input molecule. This makes it possible to eliminate the effects of PCR amplification bias, which is particularly important where many PCR cycles are required, for example, in single cell studies. After PCR, molecules sharing a UMI are assumed to be derived from the same input molecule. In our single cell RNA-Seq studies of Physcomitrellapatens, we discovered that reads sharing a UMI, and therefore presumed to be derived from the same mRNA molecule, frequently map to different, but closely spaced locations. This behaviour occurs in all such libraries that we have produced, and in multiple other UMI-containing RNA-Seq data sets in the public domain. This apparent paradox, that reads of identical origin map to distinct genomic coordinates may be partially explained by PCR stutter, which is often seen in low-entropy templates and those containing simple tandem repeats. In the absence of UMI this artefact is undetectable. We show that the common assumption that sequence reads having different mapping coordinates are derived from different starting molecules does not hold. Unless taken into account, this artefact is likely to result in over-estimation of certain transcript abundances, depending on the counting method employed.
Mechanistic modelling of viral spreading on empirical social network and popularity prediction
Authors: Ma Sijuan , Feng Ling , Lai Choy-Heng 
Published: August 2018

AbstractOnline social networks are becoming major platforms for people to exchange opinions and information. While spreading models have been used to study the dynamics of spreading on social networks, the actual spreading mechanism on social networks may be different from these previous models due to users’ limited attention and heterogeneous interests. The tractability of the spreading process in social networks allows us to develop a detailed and realistic model accounting for these factors. In addition, the empirical social networks have higher order correlations among node degrees, especially for directed networks like Twitter, that could affect the dynamics of spreading. Based on the analysis of the retweet process in the empirical Twitter network, we find both non-trivial correlations in network structures and non-standard spreading mechanisms for viral tweets. In particular, there is a strong evidence of information overload for retweeting behaviors that is not in line with the standard spreading model like the SIR (Susceptible, Infectious and Recovered) model, and can be described by a sublinear function. From these empirical findings, we introduce an intrinsic variable “attractiveness” to the message, describing the overall propensity for any node to retweet the message, and present the analytical equations to solve such an empirical process, validated through numerical simulations. The results from our model is consistent with findings from the empirical Twitter data. Our analysis also indicates a close relationship between the spreading sub-network structure and the final popularity of the information, leading to a method to predict the popularity of tweets more accurately than existing models.
Steroid Receptor Coactivator-2 Controls the Pentose Phosphate Pathway through RPIA in Human Endometrial Cancer Cells
Authors: Szwarc Maria M. , Kommagani Ramakrishna , Putluri Vasanta , Dubrulle Julien , Stossi Fabio , Mancini Michael A. , Coarfa Cristian , Lanz Rainer B. , Putluri Nagireddy , DeMayo Francesco J. , Lydon John P. , O’Malley Bert W. 
Published: August 2018

AbstractSteroid receptor coactivator-2 (SRC-2) is a transcriptional coregulator that modulates the activity of many transcription factors. Levels of SRC-2 are elevated in endometrial biopsies from polycystic ovary syndrome patients, a population predisposed to endometrial cancer (EC). Increased expression of SRC-2 is also detected in neoplastic endometrium suggesting a causal link between elevated SRC-2 expression and the emergence of endometrial disorders that can lead to cancer. Here, we reveal that SRC-2 knockdown reduces EC cell proliferation and anchorage-independence. Additionally, SRC-2 is required to maintain cellular glycolytic capacity and oxidative phosphorylation, processes essential for EC cell proliferation. Importantly, SRC-2 is critical for the normal performance of the pentose phosphate pathway (PPP). Perturbation of the PPP due to loss of SRC-2 expression may result from the depletion of ribose-5-P isomerase (RPIA), a key enzyme of the PPP. As with SRC-2, RPIA knockdown reduces EC cell proliferation, which is accompanied by a decrease in glycolytic capacity and oxidative phosphorylation. Glucose metabolite tracking experiments confirmed that knockdown of SRC-2 and RPIA downregulates the metabolic rate of both glycolysis and the PPP, highlighting a novel regulatory cross-talk between glycolysis and the PPP modulated by SRC-2.
Profiling the Tumour Immune Microenvironment in Pancreatic Neuroendocrine Neoplasms with Multispectral Imaging Indicates Distinct Subpopulation Characteristics Concordant with WHO 2017 Classification
Authors: Takahashi Daigoro , Kojima Motohiro , Suzuki Toshihiro , Sugimoto Motokazu , Kobayashi Shin , Takahashi Shinichiro , Konishi Masaru , Gotohda Naoto , Ikeda Masafumi , Nakatsura Tetsuya , Ochiai Atsushi , Nagino Masato 
Published: August 2018

AbstractWe successfully determined the difference of immune microenvironments between pNENs and pancreatic ductal adenocarcinomas (PDACs), and the histology-dependent variability among pNENs using multispectral fluorescent imaging system. Tumour tissue samples including 52 pNENs and 18 PDACs were investigated. The tumour-infiltrating lymphocytes (TILs), their PD-1 and PD-L1 expression in the pNENs were comprehensively and quantitatively analysed and were subsequently compared with those in PDACs. A principal component analysis revealed that the tissue immune profile is related to tumour histology, with distinct groups being observed for NETs, NECs, and PDACs. While NECs and some PDACs had hot immune microenvironments with abundant TILs, NETs had a cold immune microenvironment with few TILs. Moreover, in NETs, the numbers of intraepithelial PD-1high T cells and PD-L1high Type-II macrophages were elevated according to the grade. Univariate analysis revealed that lymph node metastasis, grade, stage, PD-1high T cells, and PD-L1high Type-II macrophages were predictors for recurrence-free survival (RFS), while grade and PD-1high T cells were prognostic factors for overall survival (OS). We also showed that PD-1high T cells and PD-L1high Type-II macrophages were associated with worse outcome in pNENs. Our results support the WHO 2017 tumour classification criteria, which distinguish between G3 NETs and NECs.