bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder
Authors: Griesi-Oliveira K. , Fogo M. S. , Pinto B. G. G. , Alves A. Y. , Suzuki A. M. , Morales A. G. , Ezquina S. , Sosa O. J. , Sutton G. J. , Sunaga-Franze D. Y. , Bueno A. P. , Seabra G. , Sardinha L. , Costa S. S. , Rosenberg C. , Zachi E. C. , Sertie A. L. , Martins-de-Souza D. , Reis E. M. , Voineagu I. , Passos-Bueno M. R. 
Published: February 2020

AbstractEvaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons—which has an expression profile more closely related to fetal brain—while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column
Authors: Luo Elaine , Eppley John M , Romano Anna E , Mende Daniel R , DeLong Edward F 
Published: February 2020

Abstract
Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses are essential elements of these communities, influencing the productivity, diversity, and evolution of cellular hosts. To further explore the natural history and ecology of open-ocean viruses, we surveyed the spatiotemporal dynamics of double-stranded DNA (dsDNA) viruses in both virioplankton and bacterioplankton size fractions in the North Pacific Subtropical Gyre, one of the largest biomes on the planet. Assembly and clustering of viral genomes revealed a peak in virioplankton diversity at the base of the euphotic zone, where virus populations and host species richness both reached their maxima. Simultaneous characterization of both extracellular and intracellular viruses suggested depth-specific reproductive strategies. In particular, analyses indicated elevated lytic interactions in the mixed layer, more temporally variable temperate phage interactions at the base of the euphotic zone, and increased lysogeny in the mesopelagic ocean. Furthermore, the depth variability of auxiliary metabolic genes suggested habitat-specific strategies for viral influence on light-energy, nitrogen, and phosphorus acquisition during host infection. Most virus populations were temporally persistent over several years in this environment at the 95% nucleic acid identity level. In total, our analyses revealed variable distributional patterns and diverse reproductive and metabolic strategies of virus populations in the open-ocean water column.
Conversion of p–n conduction type by spinodal decomposition in Zn-Sb-Bi phase-change alloys
Authors: Wang Guoxiang , Shi Haizhou , Lotnyk Andriy , Shi Daotian , Wang Rongping 
Published: February 2020

AbstractPhase-change films with multiple resistance levels are promising for increasing the storage density in phase-change memory technology. Diffusion-dominated Zn2Sb3 films undergo transitions across three states, from high through intermediate to low resistance, upon annealing. The properties of the Zn2Sb3 material can be further optimized by doping with Bi. Based on scanning transmission electron microscopy combined with electrical transport measurements, at a particular Bi concentration, the conduction of Zn-Sb-Bi compounds changes from p- to n-type, originating from spinodal decomposition. Simultaneously, the change in the temperature coefficient of resistivity shows a metal-to-insulator transition. Further analysis of microstructure characteristics reveals that the distribution of the Bi-Sb phase may be the origin of the driving force for the p–n conduction and metal-to-insulator transitions and therefore may provide us with another way to improve multilevel data storage. Moreover, the Bi doping promotes the thermoelectric properties of the studied alloys, leading to higher values of the power factor compared to known reported structures. The present study sheds valuable light on the spinodal decomposition process caused by Bi doping, which can also occur in a wide variety of chalcogenide-based phase-change materials. In addition, the study provides a new strategy for realizing novel p–n heterostructures for multilevel data storage and thermoelectric applications.
Post-functionalization of dibenzothiophene to functionalized biphenyls via a photoinduced thia-Baeyer-Villiger oxidation
Authors: Ma Xiaofeng , Liu Yazhou , Du Le , Zhou Jingwei , Markó István E. 
Published: February 2020

AbstractThe Baeyer-Villiger reaction is used extensively in organic chemistry. Sila- and bora-variants have also been documented widely, with these processes underpinning, for example, the Fleming-Tamao oxidation and hydroborative alkene hydration, respectively. By contrast, the development of thia-Baeyer-Villiger reactions involving sulfoxides has long been considered unlikely because competitive oxidation to the sulfone occurs exclusively. Here, we disclose a photoinduced thia-Baeyer-Villiger-type oxidations; specifically, we find that exposure of dibenzothiophene (DBT) derivatives to an iron porphyrin catalyst under Ultraviolet irradiation in the presence oft-BuOOH generates sulfinic esters in up to 87% yield. The produced sulfinic esters are transformed to a variety of biphenyl substrates including biphenyl sulfoxides, sulfones and sulfonamides in 1-2 steps. These results provide a mild process for the selective functionalization of sulfur compounds, and offer a biomimetic approach to convert DBT into 2-hydroxybiphenyl under controllable stepwise pathway. Based upon experimental evidences and DFT calculation, a mechanism is proposed.
Evolutionary games with environmental feedbacks
Authors: Tilman Andrew R. , Plotkin Joshua B. , Akçay Erol 
Published: February 2020

AbstractStrategic interactions arise in all domains of life. This form of competition often plays out in dynamically changing environments. The strategies employed in a population may alter the state of the environment, which may in turn feedback to change the incentive structure of strategic interactions. Feedbacks between strategies and the environment are common in social-ecological systems, evolutionary-ecological systems, and even psychological-economic systems. Here we develop a framework of ‘eco-evolutionary game theory’ that enables the study of strategic and environmental dynamics with feedbacks. We consider environments governed either by intrinsic growth, decay, or tipping points. We show how the joint dynamics of strategies and the environment depend on the incentives for individuals to lead or follow behavioral changes, and on the relative speed of environmental versus strategic change. Our analysis unites dynamical phenomena that occur in settings as diverse as human decision-making, plant nutrient acquisition, and resource harvesting. We discuss implications in fields ranging from ecology to economics.
Insights into the aetiology of snoring from observational and genetic investigations in the UK Biobank
Authors: Campos Adrián I. , García-Marín Luis M. , Byrne Enda M. , Martin Nicholas G. , Cuéllar-Partida Gabriel , Rentería Miguel E. 
Published: February 2020

AbstractAlthough snoring is common in the general population, its aetiology has been largely understudied. Here we report a genetic study on snoring (n ~ 408,000; snorers ~ 152,000) using data from the UK Biobank. We identify 42 genome-wide significant loci, with an SNP-based heritability estimate of ~10% on the liability scale. Genetic correlations with body mass index, alcohol intake, smoking, schizophrenia, anorexia nervosa and neuroticism are observed. Gene-based associations identify 173 genes, including DLEU7, MSRB3 and POC5, highlighting genes expressed in the brain, cerebellum, lungs, blood and oesophagus. We use polygenic scores (PGS) to predict recent snoring and probable obstructive sleep apnoea (OSA) in an independent Australian sample (n ~ 8000). Mendelian randomization analyses suggest a potential causal relationship between high BMI and snoring. Altogether, our results uncover insights into the aetiology of snoring as a complex sleep-related trait and its role in health and disease beyond it being a cardinal symptom of OSA.
Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma
Authors: Kalaora Shelly , Lee Joo Sang , Barnea Eilon , Levy Ronen , Greenberg Polina , Alon Michal , Yagel Gal , Bar Eli Gitit , Oren Roni , Peri Aviyah , Patkar Sushant , Bitton Lital , Rosenberg Steven A. , Lotem Michal , Levin Yishai , Admon Arie , Ruppin Eytan , Samuels Yardena 
Published: February 2020

AbstractPredicting the outcome of immunotherapy treatment in melanoma patients is challenging. Alterations in genes involved in antigen presentation and the interferon gamma (IFNγ) pathway play an important role in the immune response to tumors. We describe here that the overexpression of PSMB8 and PSMB9, two major components of the immunoproteasome, is predictive of better survival and improved response to immune-checkpoint inhibitors of melanoma patients. We study the mechanism underlying this connection by analyzing the antigenic peptide repertoire of cells that overexpress these subunits using HLA peptidomics. We find a higher response of patient-matched tumor infiltrating lymphocytes against antigens diferentially presented after immunoproteasome overexpression. Importantly, we find that PSMB8 and PSMB9 expression levels are much stronger predictors of melanoma patientsʼ immune response to checkpoint inhibitors than the tumors’ mutational burden. These results suggest that PSMB8 and PSMB9 expression levels can serve as important biomarkers for stratifying melanoma patients for immune-checkpoint treatment.
CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG
Authors: Liu Zhihui , Zhang Xiyuan , Lei Haiyan , Lam Norris , Carter Sakereh , Yockey Oliver , Xu Max , Mendoza Arnulfo , Hernandez Edjay R. , Wei Jun S. , Khan Javed , Yohe Marielle E. , Shern Jack F. , Thiele Carol J. 
Published: February 2020

AbstractEmbryonal rhabdomyosarcoma (ERMS) is a childhood cancer that expresses myogenic master regulatory factor MYOD but fails to differentiate. Here, we show that the zinc finger transcription factor CASZ1 up-regulates MYOD signature genes and induces skeletal muscle differentiation in normal myoblasts and ERMS. The oncogenic activation of the RAS-MEK pathway suppresses CASZ1 expression in ERMS. ChIP-seq, ATAC-seq and RNA-seq experiments reveal that CASZ1 directly up-regulates skeletal muscle genes and represses non-muscle genes through affecting regional epigenetic modifications, chromatin accessibility and super-enhancer establishment. Next generation sequencing of primary RMS tumors identified a single nucleotide variant in the CASZ1 coding region that potentially contributes to ERMS tumorigenesis. Taken together, loss of CASZ1 activity, due to RAS-MEK signaling or genetic alteration, impairs ERMS differentiation, contributing to RMS tumorigenesis.
Room-temperature terahertz anomalous Hall effect in Weyl antiferromagnet Mn3Sn thin films
Authors: Matsuda Takuya , Kanda Natsuki , Higo Tomoya , Armitage N. P. , Nakatsuji Satoru , Matsunaga Ryusuke 
Published: February 2020

AbstractAntiferromagnetic spin motion at terahertz (THz) frequencies attracts growing interests for fast spintronics, however, their smaller responses to external field inhibit device application. Recently the noncollinear antiferromagnet Mn3Sn, a Weyl semimetal candidate, was reported to show large anomalous Hall effect (AHE) at room temperature comparable to ferromagnets. Dynamical aspect of such large responses is an important issue to be clarified for future THz data processing. Here the THz anomalous Hall conductivity in Mn3Sn thin films is investigated by polarization-resolved spectroscopy. Large anomalous Hall conductivity $${\mathrm{Re}}\;\sigma _{xy}\left( \omega \right) \sim 20\;{\mathrm{\Omega }}^{ - 1}{\mathrm{cm}}^{ - 1}$$
Re

σ

x
y

ω

~
20

Ω

−
1

cm

−
1

at THz frequencies is clearly observed as polarization rotation. A peculiar temperature dependence corresponding to the breaking/recovery of symmetry in the spin texture is also discussed. Observation of the THz AHE at room temperature demonstrates the ultrafast readout for the antiferromagnetic spintronics using Mn3Sn, and will also open new avenue for studying nonequilibrium dynamics in Weyl antiferromagnets.
In vitro self-replication and multicistronic expression of large synthetic genomes
Authors: Libicher K. , Hornberger R. , Heymann M. , Mutschler H. 
Published: February 2020

AbstractThe generation of a chemical system capable of replication and evolution is a key objective of synthetic biology. This could be achieved by in vitro reconstitution of a minimal self-sustaining central dogma consisting of DNA replication, transcription and translation. Here, we present an in vitro translation system, which enables self-encoded replication and expression of large DNA genomes under well-defined, cell-free conditions. In particular, we demonstrate self-replication of a multipartite genome of more than 116 kb encompassing the full set of Escherichia coli translation factors, all three ribosomal RNAs, an energy regeneration system, as well as RNA and DNA polymerases. Parallel to DNA replication, our system enables synthesis of at least 30 encoded translation factors, half of which are expressed in amounts equal to or greater than their respective input levels. Our optimized cell-free expression platform could provide a chassis for the generation of a partially self-replicating in vitro translation system.
Controlled division of cell-sized vesicles by low densities of membrane-bound proteins
Authors: Steinkühler Jan , Knorr Roland L. , Zhao Ziliang , Bhatia Tripta , Bartelt Solveig M. , Wegner Seraphine , Dimova Rumiana , Lipowsky Reinhard 
Published: February 2020

AbstractThe proliferation of life on earth is based on the ability of single cells to divide into two daughter cells. During cell division, the plasma membrane undergoes a series of morphological transformations which ultimately lead to membrane fission. Here, we show that analogous remodeling processes can be induced by low densities of proteins bound to the membranes of cell-sized lipid vesicles. Using His-tagged fluorescent proteins, we are able to precisely control the spontaneous curvature of the vesicle membranes. By fine-tuning this curvature, we obtain dumbbell-shaped vesicles with closed membrane necks as well as neck fission and complete vesicle division. Our results demonstrate that the spontaneous curvature generates constriction forces around the membrane necks and that these forces can easily cover the force range found in vivo. Our approach involves only one species of membrane-bound proteins at low densities, thereby providing a simple and extendible module for bottom-up synthetic biology.
Inflammation mobilizes copper metabolism to promote colon tumorigenesis via an IL-17-STEAP4-XIAP axis
Authors: Liao Yun , Zhao Junjie , Bulek Katarzyna , Tang Fangqiang , Chen Xing , Cai Gang , Jia Shang , Fox Paul L. , Huang Emina , Pizarro Theresa T. , Kalady Matthew F. , Jackson Mark W. , Bao Shideng , Sen Ganes C. , Stark George R. , Chang Christopher J. , Li Xiaoxia 
Published: February 2020

AbstractCopper levels are known to be elevated in inflamed and malignant tissues. But the mechanism underlying this selective enrichment has been elusive. In this study, we report a axis by which inflammatory cytokines, such as IL-17, drive cellular copper uptake via the induction of a metalloreductase, STEAP4. IL-17-induced elevated intracellular copper level leads to the activation of an E3-ligase, XIAP, which potentiates IL-17-induced NFκB activation and suppresses the caspase 3 activity. Importantly, this IL-17-induced STEAP4-dependent cellular copper uptake is critical for colon tumor formation in a murine model of colitis-associated tumorigenesis and STEAP4 expression correlates with IL-17 level and XIAP activation in human colon cancer. In summary, this study reveals a IL-17-STEAP4-XIAP axis through which the inflammatory response induces copper uptake, promoting colon tumorigenesis.
Self-assembled conjoined-cages
Authors: Samantray Sagarika , Krishnaswamy Shobhana , Chand Dillip K. 
Published: February 2020

AbstractA self-assembled coordination cage usually possesses one well-defined three-dimensional (3D) cavity whereas infinite number of 3D-cavities are crafted in a designer metal-organic framework. Construction of a discrete coordination cage possessing multiple number of 3D-cavities is a challenging task. Here we report the peripheral decoration of a trinuclear [Pd3L6] core with one, two and three units of a [Pd2L4] entity for the preparation of multi-3D-cavity conjoined-cages of [Pd4(La)2(Lb)4], [Pd5(Lb)4(Lc)2] and [Pd6(Lc)6] formulations, respectively. Formation of the tetranuclear and pentanuclear complexes is attributed to the favorable integrative self-sorting of the participating components. Cage-fusion reactions and ligand-displacement-induced cage-to-cage transformation reactions are carried out using appropriately chosen ligand components and cages prepared in this work. The smaller [Pd2L4] cavity selectively binds one unit of NO3−, F−, Cl− or Br− while the larger [Pd3L6] cavity accommodates up to four DMSO molecules. Designing aspects of our conjoined-cages possess enough potential to inspire construction of exotic molecular architectures.
Optoacoustic brain stimulation at submillimeter spatial precision
Authors: Jiang Ying , Lee Hyeon Jeong , Lan Lu , Tseng Hua-an , Yang Chen , Man Heng-Ye , Han Xue , Cheng Ji-Xin 
Published: February 2020

AbstractLow-intensity ultrasound is an emerging modality for neuromodulation. Yet, transcranial neuromodulation using low-frequency piezo-based transducers offers poor spatial confinement of excitation volume, often bigger than a few millimeters in diameter. In addition, the bulky size limits their implementation in a wearable setting and prevents integration with other experimental modalities. Here, we report spatially confined optoacoustic neural stimulation through a miniaturized Fiber-Optoacoustic Converter (FOC). The FOC has a diameter of 600 μm and generates omnidirectional ultrasound wave locally at the fiber tip through the optoacoustic effect. We show that the acoustic wave generated by FOC can directly activate individual cultured neurons and generate intracellular Ca2+ transients. The FOC activates neurons within a radius of 500 μm around the fiber tip, delivering superior spatial resolution over conventional piezo-based low-frequency transducers. Finally, we demonstrate direct and spatially confined neural stimulation of mouse brain and modulation of motor activity in vivo.
Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
Authors: VanBuren Robert , Man Wai Ching , Wang Xuewen , Pardo Jeremy , Yocca Alan E. , Wang Hao , Chaluvadi Srinivasa R. , Han Guomin , Bryant Douglas , Edger Patrick P. , Messing Joachim , Sorrells Mark E. , Mockler Todd C. , Bennetzen Jeffrey L. , Michael Todd P. 
Published: February 2020

AbstractTeff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling
Authors: Zhuang Youwen , Liu Heng , Edward Zhou X. , Kumar Verma Ravi , de Waal Parker W. , Jang Wonjo , Xu Ting-Hai , Wang Lei , Meng Xing , Zhao Gongpu , Kang Yanyong , Melcher Karsten , Fan Hao , Lambert Nevin A. , Eric Xu H. , Zhang Cheng 
Published: February 2020

AbstractFormylpeptide receptors (FPRs) as G protein-coupled receptors (GPCRs) can recognize formylpeptides derived from pathogens or host cells to function in host defense and cell clearance. In addition, FPRs, especially FPR2, can also recognize other ligands with a large chemical diversity generated at different stages of inflammation to either promote or resolve inflammation in order to maintain a balanced inflammatory response. The mechanism underlying promiscuous ligand recognition and activation of FPRs is not clear. Here we report a cryo-EM structure of FPR2-Gisignaling complex with a peptide agonist. The structure reveals a widely open extracellular region with an amphiphilic environment for ligand binding. Together with computational docking and simulation, the structure suggests a molecular basis for the recognition of formylpeptides and a potential mechanism of receptor activation, and reveals conserved and divergent features in Gicoupling. Our results provide a basis for understanding the molecular mechanism of the functional promiscuity of FPRs.