bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy
Authors: Mitra Jaba , Makurath Monika A. , Ngo Thuy T. M. , Troitskaia Alice , Chemla Yann R. , Ha Taekjip 
Published: April 2019

Significance
G-quadruplex (GQ)–forming G4 DNA, made of four repeats of guanines, is implicated in many important processes. Telomeric GQs are being studied extensively as anticancer drug targets. Because many nucleic acid-processing enzymes can exert piconewton forces and can be functionally regulated by tension on DNA, we used a single-molecule instrument combining fluorescence with mechanical manipulation to study the dynamics of human telomeric DNA under physiological levels of tension. We observed extreme mechanical diversity with at least six different interconverting species that differ in mechanical responses. Such extreme mechanical diversity may induce differential interactions with helicases and polymerases and modulate processes such as replication and transcription. Our comparative analysis further revealed the effects of sequence changes and ionic conditions.
Cone photoreceptor classification in the living human eye from photostimulation-induced phase dynamics
Authors: Zhang Furu , Kurokawa Kazuhiro , Lassoued Ayoub , Crowell James A. , Miller Donald T. 
Published: April 2019

Significance
The three spectral types of cone photoreceptors underlie color perception and are largely responsible for inherited and acquired color vision anomalies. In vivo mapping of the trichromatic cone mosaic by imaging provides the most direct and quantitative means to assess the role of photoreceptors in color vision, but remains challenging because cone reflections only weakly differentiate cone types. Here, we show a noninvasive light microscopy modality that reveals the cell’s spectral type, using the optical phase change that arises within the cell when stimulated with light. Our procedure is orders of magnitude faster and more accurate than prior approaches and makes in vivo cone classification promising for a much wider range of color vision applications.
Relative interfacial cleavage energetics of protein complexes revealed by surface collisions
Authors: Harvey Sophie R. , Seffernick Justin T. , Quintyn Royston S. , Song Yang , Ju Yue , Yan Jing , Sahasrabuddhe Aniruddha N. , Norris Andrew , Zhou Mowei , Behrman Edward J. , Lindert Steffen , Wysocki Vicki H. 
Published: April 2019

Significance
There is a large gap between the number of protein complex structures currently solved and the number of functionally relevant structures. Mass spectrometry-based approaches for biomacromolecule structural characterization are growing, are beginning to fill critical gaps, and complement other structural biology tools. We have shown for several examples that collision of protein complex ions with a surface yields products that are reflective of substructure. We present here a computational model that predicts the relative appearance energy at which a globular protein complex dissociates. This appearance energy prediction can provide structural information when a high-resolution structure has not or cannot be obtained and in the future has potential to be used to select the best-fit candidate computational models, dramatically increasing the structural information obtained.
Hierarchy of clinical manifestations in SAVI N153S and V154M mouse models
Authors: Motwani Mona , Pawaria Sudesh , Bernier Jennifer , Moses Stephanie , Henry Kate , Fang Terry , Burkly Linda , Marshak-Rothstein Ann , Fitzgerald Katherine A. 
Published: April 2019

Significance
STING is a key driver of monogenic interferonopathies that include STING-associated vasculopathy with onset in infancy (SAVI). Defining the molecular mechanisms and the contribution of individual cell types to disease could unveil new therapeutic targets for management of SAVI and related autoimmune diseases. Here we compare and contrast murine models representative of the two most common mutations and identify a hierarchy of lymphoid abnormalities that depend on T cell-intrinsic expression of the SAVI mutation. Although clinical manifestations result from hyperactivation of STING, they occur independently of type I interferon and necroptosis. These murine models facilitate a dissection of the role of STING in specific tissues and provide tools for evaluating STING inhibitors for the treatment of SAVI patients.
EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation
Authors: Ramakrishna Priya , Ruiz Duarte Paola , Rance Graham A. , Schubert Martin , Vordermaier Vera , Vu Lam Dai , Murphy Evan , Vilches Barro Amaya , Swarup Kamal , Moirangthem Kamaljit , Jørgensen Bodil , van de Cotte Brigitte , Goh Tatsuaki , Lin Zhefeng , Voβ Ute , Beeckman Tom , Bennett Malcolm J. , Gevaert Kris , Maizel Alexis , De Smet Ive 
Published: April 2019

Significance
Organ formation is an essential process in plants and animals, driven by cell division and cell identity establishment. Root branching where lateral roots form along the primary root axis increases the root system and aids the capture of water and nutrients. We have discovered that tight control of the cell width is necessary to coordinate asymmetric cell divisions in cells that give rise to a new lateral root organ. Although biomechanical processes have been shown to play a role in plant organogenesis, including lateral root formation, our data give mechanistic insights into cell size control during lateral root initiation.
Expectation propagation for Poisson data
Authors: Zhang Chen , Arridge Simon , Jin Bangti 
Published: April 2019

AbstractThe Poisson distribution arises naturally when dealing with data involving counts, and it has found many applications in inverse problems and imaging. In this work, we develop an approximate Bayesian inference technique based on expectation propagation for approximating the posterior distribution formed from the Poisson likelihood function and a Laplace type prior distribution, e.g. the anisotropic total variation prior. The approach iteratively yields a Gaussian approximation, and at each iteration, it updates the Gaussian approximation to one factor of the posterior distribution by moment matching. We derive explicit update formulas in terms of one-dimensional integrals, and also discuss stable and efficient quadrature rules for evaluating these integrals. The method is showcased on two-dimensional PET images.
Many-body perturbation theory calculations using the yambo code
Authors: Sangalli D , Ferretti A , Miranda H , Attaccalite C , Marri I , Cannuccia E , Melo P , Marsili M , Paleari F , Marrazzo A , Prandini G , Bonfà P , Atambo M O , Affinito F , Palummo M , Molina-Sánchez A , Hogan C , Grüning M , Varsano D , Marini A 
Published: April 2019

Abstract

yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo’s capabilities include the calculation of linear response quantities (both independent-particle and including electron–hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron–phonon interactions to the implementation of a real-time propagation scheme for simulating linear and non-linear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools.
Rangeland vegetation dynamics in the Altai mountain region of Mongolia, Russia, Kazakhstan and China: effects of climate, topography, and socio-political context for livestock herding practices
Authors: Iegorova Liza V , Gibbs James P , Mountrakis Giorgos , Bastille-Rousseau Guillaume , Paltsyn Mikhail Yu , Ayatkhan Atay , Baylagasov Leonid V , Robertus Yury V , Chelyshev Andrey V 
Published: April 2019

Abstract
Discriminating between climate- and human-induced variation in rangeland quality poses a major challenge for developing policy to sustain herder livelihoods and alleviate herder poverty. We contrasted changes in rangeland vegetation cover across a region—the Altai Mountains of central Asia (China, Kazakhstan, Russia and Mongolia)—that juxtaposes strongly contrasting social, political and economic conditions across a community of herders of shared cultural background (all of Kazakh origin). Our analysis focused on a satellite-derived vegetation index (Normalized Difference Vegetation Index—NDVI) from the Advanced Very High Resolution Radiometer sensor during the period 1982–2013, which included the breakup of the Soviet Union in 1990 and heralded a transition away from pervasive state control on herding practices in many parts of the region. Grassland cover increased with decreasing elevation and increasing precipitation. Grassland also decreased under increased livestock density but was largely unresponsive to the dramatic changes that occurred in the sociopolitical context for grazing practices. Average NDVI values and duration of growing season were greater after the Soviet Union’s collapse across the region, trends that precipitation and temperature data indicate were most likely driven by a changing climate. We conclude that rangeland policy development to assure sustainability of herder livelihoods in the Altai Mountain region should focus on climate change adaptation measures rather than modifying herders’ grazing practices.
The service-stock trap: analysis of the environmental impacts and productivity of the service sector in Hungary
Authors: Dombi Mihály 
Published: April 2019

Abstract
Urbanization and the emerging share of the service sector in economic output may support the sustainability transition due to lower material input and emissions, while further accelerating the economic growth at the same time. Nevertheless, there are significant barriers to the transition. In this study, the service sector of Hungary and its four commercial sub-sectors have been analyzed with regard to their material requirement (input flows and stock) and greenhouse gas emissions (GHG) emissions utilizing EXIOBASE v3. General policy implications are also provided with special regard to costs, possible taxes and productivity of resources. The share of direct and indirect GHG emissions and material input generated by the sector was stable and moderate. A permanently improving trend is present in GHG, and material input intensity. Material stock accumulation in the service sector (capital stock), however, shows an ascending trend, and it has increased from 42% in 1995 to be 55% in 2015. Material input productivity of investments into services has increased until the economic crisis, then it starts to decline or stagnate; while overall stock productivity has decreased in two sub-sectors, and slow improvement was observable in sub-sectors of transportation and information and communication technology (ICT). Stock productivity of ICT and machinery capital stock was decreased dramatically in all sub-sectors. Four economic sub-sectors of the commercial services analyzed in this study have increased their capital stock from 130 to 288 Mt between 2000 and 2015. The exponential trend in material stock accumulation is an environmental issue with rising scientific concern and awareness, since it constitutes the basis of crucial waste management, resource scarcity and resource use challenges in the future. The current study indicates general reinforcement of the environmental pressure of material stock accumulation by the service sector. This phenomena was defined as the ‘service-stock trap’, which refers to the sign of a trade-off between the descending flow-type environmental impacts and ascending impacts of capital stock accumulation during the economic transition towards a service-based economy. As a promising way out of the trap, the resource tax was discussed in detail, which seems to be suitable for forming investment decisions of the business actors.
Ten years of AoB PLANTS the open access journal for plant scientists: inception and progress since 2009
Authors: Jackson Michael B 
Published: April 2019

Abstract
AoB PLANTS is a not-for-profit, open access, plant science journal and one of three peer-reviewed journals owned and managed by the Annals of Botany Company. This article explains events and thinking that led to the starting of AoB PLANTS and how the unique features of the Journal came to be formalized prior to its launch in September 2009. The article also describes how the Journal’s management developed over the first 10 years and summarizes the Journal’s achievements in a decade where open access journals have proliferated despite subscription journals continuing to dominate the publishing of peer-reviewed botanical science.
Figure and caption extraction from biomedical documents
Authors: Li Pengyuan , Jiang Xiangying , Shatkay Hagit 
Published: April 2019

Abstract

Motivation
Figures and captions convey essential information in biomedical documents. As such, there is a growing interest in mining published biomedical figures and in utilizing their respective captions as a source of knowledge. Notably, an essential step underlying such mining is the extraction of figures and captions from publications. While several PDF parsing tools that extract information from such documents are publicly available, they attempt to identify images by analyzing the PDF encoding and structure and the complex graphical objects embedded within. As such, they often incorrectly identify figures and captions in scientific publications, whose structure is often non-trivial. The extraction of figures, captions and figure-caption pairs from biomedical publications is thus neither well-studied nor yet well-addressed.

Results
We introduce a new and effective system for figure and caption extraction, PDFigCapX. Unlike existing methods, we first separate between text and graphical contents, and then utilize layout information to effectively detect and extract figures and captions. We generate files containing the figures and their associated captions and provide those as output to the end-user.
We test our system both over a public dataset of computer science documents previously used by others, and over two newly collected sets of publications focusing on the biomedical domain. Our experiments and results comparing PDFigCapX to other state-of-the-art systems show a significant improvement in performance, and demonstrate the effectiveness and robustness of our approach.

Availability and implementation
Our system is publicly available for use at: https://www.eecis.udel.edu/~compbio/PDFigCapX. The two new datasets are available at: https://www.eecis.udel.edu/~compbio/PDFigCapX/Downloads
Impact of 10-Valent Pneumococcal Conjugate Vaccine Introduction on Pneumococcal Carriage and Antibiotic Susceptibility Patterns Among Children Aged &lt;5 Years and Adults With Human Immunodeficiency Virus Infection: Kenya, 2009–2013
Authors: Kobayashi Miwako , Bigogo Godfrey , Kim Lindsay , Mogeni Ondari D , Conklin Laura M , Odoyo Arthur , Odiembo Herine , Pimenta Fabiana , Ouma Dominic , Harris Aaron M , Odero Kennedy , Milucky Jennifer L , Ouma Alice , Aol George , Audi Allan , Onyango Clayton , Cosmas Leonard , Jagero Geofrey , Farrar Jennifer L , da Gloria Carvalho Maria , Whitney Cynthia G , Breiman Robert F , Lessa Fernanda C 
Published: April 2019

Abstract

Background
Kenya introduced 10-valent pneumococcal conjugate vaccine (PCV10) among children &lt;1 year in 2011 with catch-up vaccination among children 1–4 years in some areas. We assessed changes in pneumococcal carriage and antibiotic susceptibility patterns in children &lt;5 years and adults.

Methods
During 2009–2013, we performed annual cross-sectional pneumococcal carriage surveys in 2 sites: Kibera (children &lt;5 years) and Lwak (children &lt;5 years, adults). Only Lwak had catch-up vaccination. Nasopharyngeal and oropharyngeal (adults only) swabs underwent culture for pneumococci; isolates were serotyped. Antibiotic susceptibility testing was performed on isolates from 2009 and 2013; penicillin nonsusceptible pneumococci (PNSP) was defined as penicillin-intermediate or -resistant. Changes in pneumococcal carriage by age (&lt;1 year, 1–4 years, adults), site, and human immunodeficiency virus (HIV) status (adults only) were calculated using modified Poisson regression, with 2009–2010 as baseline.

Results
We enrolled 2962 children (2073 in Kibera, 889 in Lwak) and 2590 adults (2028 HIV+, 562 HIV−). In 2013, PCV10-type carriage was 10.3% (Lwak) to 14.6% (Kibera) in children &lt;1 year and 13.8% (Lwak) to 18.7% (Kibera) in children 1–4 years. This represents reductions of 60% and 63% among children &lt;1 year and 52% and 60% among children 1–4 years in Kibera and Lwak, respectively. In adults, PCV10-type carriage decreased from 12.9% to 2.8% (HIV+) and from 11.8% to 0.7% (HIV−). Approximately 80% of isolates were PNSP, both in 2009 and 2013.

Conclusions
PCV10-type carriage declined in children &lt;5 years and adults post–PCV10 introduction. However, PCV10-type and PNSP carriage persisted in children regardless of catch-up vaccination.
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer
Authors: Wang Ying , Wang Yueqian , Wang Shuangkuai , Tong Yuantao , Jin Ling , Zong Hui , Zheng Rongbin , Yang Jinxuan , Zhang Zeyu , Ouyang En , Zhou Mengyan , Zhang Xiaoyan 
Published: April 2019

Abstract
Gastrointestinal (GI) cancer is common, characterized by high mortality, and includes oesophagus, gastric, liver, bile duct, pancreas, rectal and colon cancers. The insufficient specificity and sensitivity of biomarkers is still a key clinical hindrance for GI cancer diagnosis and successful treatment. The emergence of `precision medicine’, `basket trial’ and `field cancerization’ concepts calls for an urgent need and importance for the understanding of how organ system cancers occur at the molecular levels. Knowledge from both the literature and data available in public databases is informative in elucidating the molecular alterations underlying GI cancer. Currently, most available cancer databases have not offered a comprehensive discovery of gene-disease associations, molecular alterations and clinical information by integrated text mining and data mining in GI cancer. We develop GIDB, a panoptic knowledge database that attempts to automate the curation of molecular signatures using natural language processing approaches and multidimensional analyses. GIDB covers information on 8730 genes with both literature and data supporting evidence, 248 miRNAs, 58 lncRNAs, 320 copy number variations, 49 fusion genes and 2381 semantic networks. It presents a comprehensive database, not only in parallelizing supporting evidence and data integration for signatures associated with GI cancer but also in providing the timeline feature of major molecular discoveries. It highlights the most comprehensive overview, research hotspots and the development of historical knowledge of genes in GI cancer. Furthermore, GIDB characterizes genomic abnormalities in multilevel analysis, including simple somatic mutations, gene expression, DNA methylation and prognosis. GIDB offers a user-friendly interface and two customizable online tools (Heatmap and Network) for experimental researchers and clinicians to explore data and help them shorten the learning curve and broaden the scope of knowledge. More importantly, GIDB is an ongoing research project that will continue to be updated and improve the automated method for reducing manual work.
Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations
Authors: Matyášek Roman , Kuderová Alena , Kutílková Eva , Kučera Marek , Kovařík Aleš 
Published: April 2019

AbstractThe intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300–1250 bp) and R2 (290–643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
A Micro-Scale Approach to Ethnic Minority Concentration in the Residential Environment and Voting for the Radical Right in The Netherlands
Authors: Janssen Heleen J , van Ham Maarten , Kleinepier Tom , Nieuwenhuis Jaap 
Published: April 2019

Abstract
Existing empirical research on the link between ethnic minority concentration in residential environments and voting for the radical right is inconclusive, mainly due to major differences between studies in the spatial scale at which minority concentration is measured. We examined whether the presence of non-western ethnic minorities in the residential environment, measured at four spatial scales, is related to individuals’ intention to vote for the Dutch Party for Freedom (Dutch acronym PVV). We combined individual level survey data and register data, and we used multi-level structural equation models to examine possible mediation by anti-immigrant attitudes and political dissatisfaction. The models show different effects at different scales. At the micro scale (100 by 100 meter grids) we find a curvilinear effect: individuals with 30–50 per cent non-western minorities in their direct living environment are most likely to report to vote for the PVV. At higher spatial scales (up to municipal level) we find that the higher the proportion of non-western minorities, the more likely individuals are to report to vote for the PVV. These effects can however not be explained by anti-immigrant attitudes or political dissatisfaction. We even find that at the micro scale the presence of non-western minorities is related to less anti-immigrant attitudes.