bluuebunny/crossref_metadata_2025_split huggingface dataset:
In V4, pair-wise synchrony and correlations depend on the structure of the population code
Authors: Koren Veronika , Andrei Ariana R. , Hu Ming , Dragoi Valentin , Obermayer Klaus 
Published: May 2019

AbstractIn visual areas of primates, neurons activate in parallel while the animal is engaged in a behavioral task. In this study, we examine the structure of the population code while the animal performs delayed match to sample task on complex natural images. The macaque monkeys visualized two consecutive stimuli that were either the same or different, while recorded with laminar arrays across the cortical depth in cortical areas V1 and V4. We decoded correct choice behavior from neural populations of simultaneously recorded units. Utilizing decoding weights, we divide neurons in most informative and less informative, and show that most informative neurons in V4, but not in V1, are more strongly synchronized, coupled and correlated than less informative neurons. As neurons are divided in two coding pools according to their coding preference, in V4, but not in V1, spiking synchrony, coupling and correlations within the coding pool are stronger than across coding pools.HighlightsIn a match-to-sample visual task, responses of neural populations in V1 and in V4 predict the stimulus class better than chance.In V4, informative neurons are more strongly coupled, correlated and synchronized than less informative neurons.In V4, neurons are more strongly coupled, correlated and synchronized within coding pools compared to across coding pools.Correlations within coding pools harm the performance of the classifier in both V1 and V4.
Insulin-like growth factor 1 is related to the expression of plumage traits in a passerine species
Authors: Mahr Katharina , Vincze Orsolya , Tóth Zsófia , Hoi Herbert , Lendvai Ádám Z. 
Published: May 2019

AbstractAvian plumage colors and ornaments are ideal models to study the endocrine mechanisms linking sexually selected traits and individual parameters of quality and condition. The insulin-like growth factor 1 (IGF-1), an evolutionarily highly conserved peptide hormone, represents a link between body condition and the individual capacity to grow elaborated ornamental features, due to its regulatory role in cell proliferation and differentiation and its high sensitivity to the nutritional state of individuals. We investigated whether IGF-1 levels during molting affect the expression of multiple ornaments in a sexually dichromatic passerine species, the bearded reedling (Panurus biarmicus). We collected blood samples of males and females shortly before the molting completed and measured the size and colors of ornamental traits. Our results indicate that in males, structural plumage colors, the size of the melanin based ornament (beard) and tail length are independent traits. IGF-1 levels predict the length of the tail and the expression of male structural plumage components (UV-coloration), but not the melanin based ornament. In females plumage color and tail length were independent traits, which were not related to IGF-1 levels. Overall, our results indicate for the first time that IGF-1 could play a role in the development of secondary sexual characters in a passerine species.
Cross-species cortical alignment identifies different types of neuroanatomical reorganization in the temporal lobe of higher primates
Authors: Eichert Nicole , Robinson Emma C. , Bryant Katherine L. , Jbabdi Saad , Jenkinson Mark , Li Longchuan , Krug Kristine , Watkins Kate E. , Mars Rogier B. 
Published: May 2019

AbstractEvolutionary modifications of the temporo-parietal cortex are considered to be a critical adaptation of the human brain. Cortical adaptations, however, can affect different aspects of brain architecture, including areal expansion or changes in connectivity profiles. We propose to distinguishing different types of brain reorganization using a computational neuroanatomy approach. We investigate the extent to which between-species alignment based on cortical myelin can predict changes in connectivity patterns across macaque, chimpanzee and human. We show that expansion and relocation of brain areas are sufficient to predict terminations of several white matter tracts in temporo-parietal cortex, including the middle and superior longitudinal fasciculus, but not of the arcuate fasciculus. This demonstrates that the arcuate fasciculus underwent additional evolutionary modifications affecting the connectivity pattern of the temporal lobe. The presented approach can flexibly be extended to include other features of cortical organization and other species, allowing direct tests of comparative hypotheses of brain organization.
SciBet: a portable and fast single cell type identifier
Authors: Li Chenwei , Liu Baolin , Kang Boxi , Liu Zedao , Liu Yedan , Chen Changya , Ren Xianwen , Zhang Zemin 
Published: May 2019

ABSTRACTFast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a Bayesian classifier that accurately predicts cell identity for newly sequenced cells or cell clusters. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. This user-friendly and cross-platform tool can be widely useful for single cell type identification.
Spatiotemporal patterns of urbanization in three Swiss urban agglomerations: insights from landscape metrics, growth modes and fractal analysis
Authors: Bosch Martí , Chenal Jérôme 
Published: May 2019

AbstractUrbanization is currently a global phenomenon that has become the most important form of landscape change and is increasingly affecting biodiversity and ecosystem functions. In order to evaluate the impacts of urbanization and inform urban planning, it is important to understand the spatiotemporal patterns of land use change associated to urbanization. This paper exploits three different frameworks, namely landscape metrics, urban growth modes and fractal analysis to characterize the spatiotemporal patterns of urbanization of the Swiss urban agglomerations of Zurich, Bern and Lausanne. The land use inventory provided by the Swiss Federal Statistical Office was used to assemble four temporal snapshots from 1980 to 2016 at the extent of the urban agglomerations. The time series of landscape metrics generally supports the diffusion and coalescence model of urban growth, with Zurich exhibiting most characteristics of coalescence while Bern and Lausanne seem to be at the transition between diffusion and coalescence. Nevertheless, the analysis of the urban growth modes suggest that leapfrog development occurs at all periods, which contributes to an increasing fragmentation of natural patches and maintains the fractal configuration of the landscape. The discussion reviews potential explanations for the observed landscape changes, and concludes with some planning implications.
A single bacterial genus maintains root development in a complex microbiome
Authors: Finkel Omri M. , Salas-González Isai , Castrillo Gabriel , Conway Jonathan M. , Law Theresa F. , Teixeira Paulo José Pereira Lima , Wilson Ellie D. , Fitzpatrick Connor R. , Jones Corbin D. , Dangl Jeffery L. 
Published: May 2019

AbstractPlants grow within a complex web of species interacting with each other and with the plant. Many of these interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development. To understand how microbe-microbe interactions influence root development in Arabidopsis, we established a model system for plant-microbe-microbe-environment interactions. We inoculated seedlings with a 185-member bacterial synthetic community (SynCom), manipulated the abiotic environment, and measured bacterial colonization of the plant. This enabled classification of the SynCom into four modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying microbe-microbe interactions that determine root phenotypes. These interactions primarily involve a single bacterial genus, Variovorax, which completely reverts severe root growth inhibition (RGI) induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulate plant hormone levels to balance this ecologically realistic root community’s effects on root development. We identify a novel auxin degradation operon in the Variovorax genome that is necessary and sufficient for RGI reversion. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the root’s developmental program. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising new ecological strategy towards the development of more resilient and productive crops.
The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans
Authors: Roberts Buceta Paloma M. , Romanelli-Cedrez Laura , Babcock Shannon J. , Xun Helen , VonPaige Miranda L. , Higley Thomas W. , Schlatter Tyler D. , Davis Dakota C. , Drexelius Julia A. , Culver John C. , Carrera Inés , Shepherd Jennifer N. , Salinas Gustavo 
Published: May 2019

ABSTRACTA key metabolic adaptation for some species that face hypoxia as part of their life-cycle involves an alternative electron transport chain in which rhodoquinone (RQ) is required for fumarate reduction and ATP production. RQ biosynthesis in bacteria and protists requires ubiquinone (Q) as a precursor. In contrast, Q is not a precursor for RQ biosynthesis in animals such as parasitic helminths, and this pathway has remained elusive. We used Caenorhabditis elegans as a model animal to elucidate several key steps in RQ biosynthesis. Through RNA interference and a series of mutants, we found that arylamine metabolites from the kynurenine pathway are essential precursors for RQ biosynthesis de novo. Deletion of kynu-1, which encodes a kynureninase that converts L-kynurenine (KYN) into anthranilic acid (AA), and 3-hydroxykynurenine (HKYN) into 3-hydroxyanthranilic acid (3HAA), completely abolishes RQ biosynthesis, but does not affect Q levels. Deletion of kmo-1, which encodes a kynurenine 3-monooxygenase that converts KYN to HKYN, drastically reduces RQ, but not Q levels. Knockdown of the Q biosynthetic genes, coq-5 and coq-6, affects both Q and RQ levels demonstrating that common enzymes are used in both biosynthetic pathways. Our study reveals that two pathways for RQ biosynthesis have independently evolved. In contrast to bacteria, where amination is the last step in RQ biosynthesis, worms begin with the arylamine precursor, AA or 3HAA. Since RQ is absent in mammalian hosts of helminths, inhibition of RQ biosynthesis may have broad implications for targeting parasitic infections which cause important neglected tropical diseases.
Molecular basis for feedback inhibition of Notch signaling by the Notch regulated ankyrin repeat protein NRARP
Authors: Jarrett Sanchez M. , Seegar Tom C. M. , Andrews Mark , Adelmant Guillaume , Marto Jarrod A. , Aster Jon C. , Blacklow Stephen C. 
Published: May 2019

AbstractThe Notch regulated ankyrin repeat protein (NRARP) is a negative feedback regulator of Notch signaling in higher organisms. The molecular basis for NRARP function, however, has remained elusive. Mass spectrometry-based proteomic studies show that human NRARP associates with the core Notch transcriptional activation complex (NTC), containing the RBPJ transcription factor, the Notch intracellular domain (NICD), and a Mastermind-like co-activator. Binding of NRARP is direct, requires both RBPJ and NICD, and is independent of Mastermind-like proteins or DNA. The X-ray structure of an NRARP/RBPJ/NOTCH1/DNA complex, determined to 3.75 Å resolution, reveals a non-canonical mode of binding in which NRARP extends the NOTCH1 ankyrin-repeat stack by three additional repeats. Mutations of NRARP residues at the binding interface disrupt entry into complexes and suppress feedback inhibition in signaling assays. These studies establish the structural basis for NTC engagement by NRARP and provide insight into its mechanism of feedback inhibition of Notch signaling.
Motility of Enzyme-Powered Vesicles
Authors: Ghosh Subhadip , Mohajerani Farzad , Son Seoyoung , Velegol Darrell , Butler Peter J. , Sen Ayusman 
Published: May 2019

AbstractAutonomous nanovehicles powered by energy derived from chemical catalysis have potential applications as active delivery agents. For in vivo applications, it is necessary that the engine and its fuel, as well as the chassis itself, be biocompatible. Enzyme molecules have been shown to generate mechanical force through substrate turnover and are attractive candidates as engines; phospholipid vesicles are biocompatible and can serve as cargo containers. Herein, we describe the autonomous movement of vesicles with membrane-bound enzymes in the presence of the substrate. We find that the motility of the vesicles increases with increasing enzymatic turnover rate. The enhanced diffusion of these enzyme-powered systems was further substantiated in real time by tracking the motion of the vesicles using optical microscopy. The membrane-bound protocells that move by transducing chemical energy into mechanical motion serve as models for motile living cells and are key to the elucidation of the fundamental mechanisms governing active membrane dynamics and cellular movement.
“For Table of Contents Only”
Disease Resistance Genetics and Genomics in Octoploid Strawberry
Authors: Barbey Christopher , Lee Seonghee , Verma Sujeet , Bird Kevin A. , Yocca Alan E. , Edger Patrick P. , Knapp Steven J. , Whitaker Vance M. , Folta Kevin M. 
Published: May 2019

ABSTRACTOctoploid strawberry (Fragaria × ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, eQTL analysis and RenSeq analysis in cultivars. Octoploid fruit transcript expression quantitative trait loci (eQTL) were identified for 77 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. × ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance towards exploiting variation for strawberry cultivar improvement.
Iron-deficiency and estrogen are associated with ischemic stroke by up-regulating transferrin to induce hypercoagulability
Authors: Tang Xiaopeng , Fang Mingqian , Cheng Ruomei , Zhang Zhiye , Wang Yuming , Shen Chuanbin , Han Yajun , Lu Qiumin , Du Yingrong , Liu Yingying , Sun Zhaohui , Zhu Liping , Mwangi James , Xue Min , Long Chengbo , Lai Ren 
Published: May 2019

SummaryIn the accompanying manuscript, transferrin has been demonstrated to maintain coagulation balance by interacting with clotting factors, suggesting that elevated transferrin causes thromboembolic diseases and factors up-regulating transferrin is associated with thrombosis. Here we show that transferrin and transferrin-thrombin/FXIIa complexes are elevated in plasma and cerebrospinal fluid of ischemic stroke (IS) patients with iron-deficiency anemia (IDA) history, IDA patients and venous thromboembolism patients using combined oral contraceptives (CC) as well as ID mice, suggesting an association of transferrin up-regulation with ID and CC. ID and estrogen up-regulated transferrin through hypoxia and estrogen response elements located at transferrin gene enhancer and promoter region, respectively. ID, exogenous transferrin/estrogen administration or transferrin over-expression promoted hypercoagulability and aggravated IS, while anti-transferrin antibody, transferrin knockdown or designed peptide inhibitors interfering transferrin-thrombin/FXIIa interaction exerted anti-IS effects invivo. Collectively, the results reveal that factors (i.e., ID and CC) up-regulating transferrin are risk factors of thromboembolic diseases.
Regulation of KRAS4A/B splicing in cancer stem cells by the RBM39 splicing complex
Authors: Chen Wei-Ching , To Minh D. , Westcott Peter M.K. , Delrosario Reyno , Kim Il-Jin , Philips Mark , Tran Quan , Bayani Nora , Balmain Allan 
Published: May 2019

AbstractThe KRAS oncogene is expressed as major KRAS4B and minor KRAS4A splice isoforms, the distinct functions of which in cancer are unknown. We demonstrate here that KRAS4A is enriched in cancer stem-like cells, and is activated by hypoxia, whereas KRAS4B is more widely expressed and responds to ER stress. Mice completely lacking either isoform are viable but resistant to lung cancer development, as are Kras4A/B double heterozygous mice expressing both isoforms, but in which splice regulation has been uncoupled. Splicing of KRAS4A, but not KRAS4B, in human tumor cells can be inhibited by treatment with the splice inhibitor indisulam, or by CRISPR/Cas inhibition of the RBM39 splicing complex. Our data suggest that control of KRAS4A/B splicing is a targetable vulnerability in KRAS mutant tumors.
BOLD and EEG Signal Variability at Rest Differently Relate to Aging in the Human Brain
Authors: Kumral D. , Şansal F. , Cesnaite E. , Mahjoory K. , Al E. , Gaebler M. , Nikulin V. V. , Villringer A. 
Published: May 2019

AbstractVariability of neural activity is regarded as a crucial feature of healthy brain function, and several neuroimaging approaches have been employed to assess it noninvasively. Studies on the variability of both evoked brain response and spontaneous brain signals have shown remarkable changes with aging but it is unclear if the different measures of brain signal variability – identified with either hemodynamic or electrophysiological methods – reflect the same underlying physiology. In this study, we aimed to explore age differences of spontaneous brain signal variability with two different imaging modalities (EEG, fMRI) in healthy younger (25±3 years, N=135) and older (67±4 years, N=54) adults. Consistent with the previous studies, we found lower blood oxygenation level dependent (BOLD) variability in the older subjects as well as less signal variability in the amplitude of low-frequency oscillations (1–12 Hz), measured in source space. These age-related reductions were mostly observed in the areas that overlap with the default mode network. Moreover, age-related increases of variability in the amplitude of beta-band frequency EEG oscillations (15–25 Hz) were seen predominantly in temporal brain regions. There were significant sex differences in EEG signal variability in various brain regions while no significant sex differences were observed in BOLD signal variability. Bivariate and multivariate correlation analyses revealed no significant associations between EEG- and fMRI-based variability measures. In summary, we show that both BOLD and EEG signal variability reflect aging-related processes but are likely to be dominated by different physiological origins, which relate differentially to age and sex.
miR-26a regulates extracellular vesicle secretion from prostate cancer cells via targeting SHC4, PFDN4 and CHORDC1
Authors: Urabe Fumihiko , Kosaka Nobuyoshi , Sawa Yurika , Yamamoto Tomofumi , Yamamoto Yusuke , Ito Kagenori , Kimura Takahiro , Egawa Shin , Ochiya Takahiro 
Published: May 2019

AbstractExtracellular vesicles (EVs) are known to be involved in intercellular communication during cancer progression; thus, elucidating the detailed mechanism will contribute to the development of a novel strategy for EV-targeted cancer treatment. However, the biogenesis of EVs in cancer cells is not completely understood. MicroRNAs (miRNAs) regulate a variety of physiological and pathological phenomena; thus, miRNAs could regulate EV secretion. Here, we performed high-throughput miRNA-based screening to identify the regulators of EV secretion using an ExoScreen assay. By using this miRNA-based screening, we identified miR-26a, which was reported as a tumor suppressive miRNA, as a miRNA involved in EV secretion from prostate cancer (PCa) cells. In addition, we found that the SHC4, PFDN4, and CHORDC1 genes regulate EV secretion in PCa cells. Suppression of these genes by siRNAs significantly inhibited the secretion of EVs in PCa cells. Furthermore, the progression of PCa cells was inhibited in an in vivo study. On the other hand, injection of EVs isolated from PCa cells partially rescued this suppressive effect on tumor growth. Taken together, our findings suggest that miR-26a regulates EV secretion via targeting SHC4, PFDN4, and CHORDC1 in PCa cells, resulting in the suppression of PCa progression.
RNF152 Negatively Regulates mTOR Signalling and Blocks Cell Proliferation in the Floor Plate
Authors: Kadoya Minori , Sasai Noriaki 
Published: May 2019

AbstractThe neural tube is composed of a number of neural progenitors and postmitotic neurons distributed in a quantitatively and spatially precise manner. The floor plate, located in the ventral-most region of the neural tube, has a lot of unique characteristics, including a low cell proliferation rate. The mechanisms by which this region-specific proliferation rate is regulated remain elusive.Here we show that the activity of the mTOR signalling pathway, which regulates the proliferation of the neural progenitor cells, is significantly lower in the floor plate than in other domains of the embryonic neural tube. We identified the forkhead-type transcription factor FoxA2 as a negative regulator of mTOR signalling in the floor plate. We demonstrate that FoxA2 transcriptionally induces the expression of the E3 ubiquitin ligase RNF152, which together with its substrate RagA, regulates cell proliferation via the mTOR pathway. Silencing of RNF152 led to the aberrant upregulation of the mTOR signal and aberrant cell division in the floor plate. Taken together, the present findings suggest that floor plate cell number is controlled by the negative regulation of mTOR signalling through the activity of FoxA2 and its downstream effector RNF152.