bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of a large bandwidth 2 × 2 interferometric switching cell based on a sub-wavelength grating
Authors: Brunetti Giuseppe , Marocco Giovanna , Benedetto Alessandro Di , Giorgio Agostino , Armenise Mario Nicola , Ciminelli Caterina 
Published: June 2021

Abstract
In the last few decades, increasing research effort has focused on the design of telecommunication payload systems with advanced features and lower costs in space applications. In this context, photonic solutions have already proven the potential to achieve additional functionalities, such as multiplexing or switching of RF or microwave signals, with consequent additional benefits in terms of size and mass reduction. In this paper, we report on the design of a 2 × 2 switching cell based on a thermo-optic interferometric configuration, whose key element is a sub-wavelength grating. We have theoretically demonstrated a broadband operation, with better performance in terms of operating wavelength range and compactness with respect to the existing interferometric cells. The switching cell shows a worst extinction ratio of about 13 dB, insertion loss of less than 2 dB, crosstalk of 12 dB, over a bandwidth of 150 nm, within a footprint as small as 240 µm × 9 µm. To demonstrate its potential use as a routing fabric in flexible telecommunication satellite payloads, as an example, the designed switching cell has been used as a building block of an 8 × 8 dilated Banyan matrix, where large bandwidth (150 nm), low crosstalk (−38 dB), small footprint (≈1620 µm × 576 µm) and relatively low power consumption (276 mW) have been achieved.
Increased seminal root number associated with domestication improves nitrogen and phosphorus acquisition in maize seedlings
Authors: Perkins Alden C , Lynch Jonathan P 
Published: June 2021

AbstractBackground and AimsDomesticated maize (Zea mays ssp. mays) generally forms between two and six seminal roots, while its wild ancestor, Mexican annual teosinte (Zea mays ssp. parviglumis), typically lacks seminal roots. Maize also produces larger seeds than teosinte, and it generally has higher growth rates as a seedling. Maize was originally domesticated in the tropical soils of southern Mexico, but it was later brought to the Mexican highlands before spreading to other parts of the continent, where it experienced different soil resource constraints. The aims of this study were to understand the impacts of increased seminal root number on seedling nitrogen and phosphorus acquisition and to model how differences in maize and teosinte phenotypes might have contributed to increased seminal root number in domesticated maize.MethodsSeedling root system architectural models of a teosinte accession and a maize landrace were constructed by parameterizing the functional–structural plant model OpenSimRoot using plants grown in mesocosms. Seedling growth was simulated in a low-phosphorus environment, multiple low-nitrogen environments, and at variable planting densities. Models were also constructed to combine individual components of the maize and teosinte phenotypes.Key ResultsSeminal roots contributed ~35 % of the nitrogen and phosphorus acquired by maize landrace seedlings in the first 25 d after planting. Increased seminal root number improved plant nitrogen acquisition under low-nitrogen environments with varying precipitation patterns, fertilization rates, soil textures and planting densities. Models suggested that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves.ConclusionsSeminal roots can improve the acquisition of both nitrogen and phosphorus in maize seedlings, and the increase in seed size associated with maize domestication may have facilitated increased seminal root number.
Fast food in the city? Nomadic flying-foxes commute less and hang around for longer in urban areas
Authors: Meade Jessica , Martin John M , Welbergen Justin A 
Published: June 2021

AbstractUrbanization creates novel ecological spaces where some species thrive. Geographical urbanization promotes human–wildlife conflict; however, we know relatively little about the drivers of biological urbanization, which poses impediments for sound wildlife management and conservation action. Flying-foxes are extremely mobile and move nomadically in response to flowering resources, but are now increasingly found in urban areas, for reasons that are poorly understood. To investigate the mechanisms behind flying-fox urbanization, we examined the movement of 99 satellite tracked grey-headed flying-foxes (Pteropus poliocephalus) over 1 year in urban versus non-urban environments. We found that tracked individuals preferentially visited major-urban roosts, exhibited higher fidelity to major-urban roosts, and foraged over shorter distances when roosting in major-urban areas. In contrast to other colonial species, there were no density-dependent effects of colony size on foraging distance, suggesting that at a landscape scale, flying-foxes distribute themselves across roosts in an ideal-free manner, minimizing competition over urban and non-urban foraging resources. Yet, males consistently foraged over shorter distances than females, suggesting that at a local scale foraging distances reflect competitive inequalities between individuals. Overall, our study supports the hypothesis that flying-fox urbanization is driven by increased spatiotemporal availability of food resources in urban areas; however, unlike in other species, it is likely a consequence of increased urban visitation by nomadic individuals rather than a subset of the population becoming “urban residents” per se. We discuss the implications of the movement behavior we report for the conservation and management of highly mobile species.
Improving sequence-based modeling of protein families using secondary-structure quality assessment
Authors: Malbranke Cyril , Bikard David , Cocco Simona , Monasson Rémi 
Published: June 2021

Abstract

Motivation
Modeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for structure and function predictions, as well as for protein design. In particular, direct coupling analysis, a method to infer effective pairwise interactions between residues, was shown to capture important structural constraints and to successfully generate functional protein sequences. Building on this and other graphical models, we introduce a new framework to assess the quality of the secondary structures of the generated sequences with respect to reference structures for the family.

Results
We introduce two scoring functions characterizing the likeliness of the secondary structure of a protein sequence to match a reference structure, called Dot Product and Pattern Matching. We test these scores on published experimental protein mutagenesis and design dataset, and show improvement in the detection of nonfunctional sequences. We also show that use of these scores help rejecting nonfunctional sequences generated by graphical models (Restricted Boltzmann Machines) learned from homologous sequence alignments.

Availability and implementation
Data and code available at https://github.com/CyrilMa/ssqa

Supplementary information
Supplementary data are available at Bioinformatics online.
Methylation-eQTL analysis in cancer research
Authors: Liu Yusha , Baggerly Keith A , Orouji Elias , Manyam Ganiraju , Chen Huiqin , Lam Michael , Davis Jennifer S , Lee Michael S , Broom Bradley M , Menter David G , Rai Kunal , Kopetz Scott , Morris Jeffrey S 
Published: June 2021

AbstractMotivationDNA methylation is a key epigenetic factor regulating gene expression. While promoter methylation has been well studied, recent publications have revealed that functionally important methylation also occurs in intergenic and distal regions, and varies across genes and tissue types. Given the growing importance of inter-platform integrative genomic analyses, there is an urgent need to develop methods to discover and characterize gene-level relationships between methylation and expression.ResultsWe introduce a novel sequential penalized regression approach to identify methylation-expression quantitative trait loci (methyl-eQTLs), a term that we have coined to represent, for each gene and tissue type, a sparse set of CpG loci best explaining gene expression and accompanying weights indicating direction and strength of association. Using TCGA and MD Anderson colorectal cohorts to build and validate our models, we demonstrate our strategy better explains expression variability than current commonly used gene-level methylation summaries. The methyl-eQTLs identified by our approach can be used to construct gene-level methylation summaries that are maximally correlated with gene expression for use in integrative models, and produce a tissue-specific summary of which genes appear to be strongly regulated by methylation. Our results introduce an important resource to the biomedical community for integrative genomics analyses involving DNA methylation.Availability and implementationWe produce an R Shiny app (https://rstudio-prd-c1.pmacs.upenn.edu/methyl-eQTL/) that interactively presents methyl-eQTL results for colorectal, breast and pancreatic cancer. The source R code for this work is provided in the Supplementary Material.Supplementary informationSupplementary data are available at Bioinformatics online.
Thyroid Hormone Transporter Deficiency in Mice Impacts Multiple Stages of GABAergic Interneuron Development
Authors: Mayerl Steffen , Chen Jiesi , Salveridou Eva , Boelen Anita , Darras Veerle M , Heuer Heike 
Published: June 2021

Abstract
Cortical interneuron neurogenesis is strictly regulated and depends on the presence of thyroid hormone (TH). In particular, inhibitory interneurons expressing the calcium binding protein Parvalbumin are highly sensitive toward developmental hypothyroidism. Reduced numbers of Parvalbumin-positive interneurons are observed in mice due to the combined absence of the TH transporters Mct8 and Oatp1c1. To unravel if cortical Parvalbumin-positive interneurons depend on cell-autonomous action of Mct8/Oatp1c1, we compared Mct8/Oatp1c1 double knockout (dko) mice to conditional knockouts with abolished TH transporter expression in progenitors of Parvalbumin-positive interneurons. These conditional knockouts exhibited a transient delay in the appearance of Parvalbumin-positive interneurons in the early postnatal somatosensory cortex while cell numbers remained permanently reduced in Mct8/Oatp1c1 dko mice. Using fluorescence in situ hybridization on E12.5 embryonic brains, we detected reduced expression of sonic hedgehog signaling components in Mct8/Oatp1c1 dko embryos only. Moreover, we revealed spatially distinct expression patterns of both TH transporters at brain barriers at E12.5 by immunofluorescence. At later developmental stages, we uncovered a sequential expression of first Oatp1c1 in individual interneurons and then Mct8 in Parvalbumin-positive subtypes. Together, our results point to multiple cell-autonomous and noncell-autonomous mechanisms that depend on proper TH transport during cortical interneuron development.
Modified scoping review of the enablers and barriers to implementing primary health care in the COVID-19 context
Authors: Edelman Alexandra , Marten Robert , Montenegro Hernán , Sheikh Kabir , Barkley Shannon , Ghaffar Abdul , Dalil Suraya , Topp Stephanie M 
Published: June 2021

Abstract
Since the Alma Ata Declaration of 1978, countries have varied in their progress towards establishing and sustaining comprehensive primary health care (PHC) and realizing its associated vision of ‘Health for All’. International health emergencies such as the coronavirus-19 (COVID-19) pandemic underscore the importance of PHC in underpinning health equity, including via access to routine essential services and emergency responsiveness. This review synthesizes the current state of knowledge about PHC impacts, implementation enablers and barriers, and knowledge gaps across the three main PHC components as conceptualized in the 2018 Astana Framework. A scoping review design was adopted to summarize evidence from a diverse body of literature with a modification to accommodate four discrete phases of searching, screening and eligibility assessment: a database search in PubMed for PHC-related literature reviews and multi-country analyses (Phase 1); a website search for key global PHC synthesis reports (Phase 2); targeted searches for peer-reviewed literature relating to specific components of PHC (Phase 3) and searches for emerging insights relating to PHC in the COVID-19 context (Phase 4). Evidence from 96 included papers were analysed across deductive themes corresponding to the three main components of PHC. Findings affirm that investments in PHC improve equity and access, healthcare performance, accountability of health systems and health outcomes. Key enablers of PHC implementation include equity-informed financing models, health system and governance frameworks that differentiate multi-sectoral PHC from more discrete service-focussed primary care, and governance mechanisms that strengthen linkages between policymakers, civil society, non-governmental organizations, community-based organizations and private sector entities. Although knowledge about, and experience in, PHC implementation continues to grow, critical knowledge gaps are evident, particularly relating to country-level, context-specific governance, financing, workforce, accountability and service coordination mechanisms. An agenda to guide future country-specific PHC research is outlined.
Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015–19
Authors: Biedrzycka M , Urbanowicz P , Guzek A , Brisse S , Gniadkowski M , Izdebski R 
Published: June 2021

Abstract

Objectives
To assess the spread of New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae ST147 organisms in Poland since an introduction from Tunisia in March 2015, including their phylogenetic position in the global population of the high-risk clone.

Methods
Out of 8925 unique NDM-positive K. pneumoniae isolates identified in Poland from April 2015 till December 2019, 126 isolates, including the Tunisian imports, were related by PFGE and blaNDM gene-carrying Tn125 transposon derivatives. Forty-seven representative isolates were sequenced by Illumina MiSeq. The phylogeny, resistome, virulome and plasmid replicons were analysed and compared with the international ST147 strains. Plasmids of six isolates were studied by the MinION sequencing.

Results
A high homogeneity of the 47 isolates was observed, with minor variations in their resistomes and plasmid replicon profiles. However, the detailed SNP comparison discerned a strict outbreak cluster of 40 isolates. All of the organisms were grouped within the ST147 phylogenetic international lineage, and four NDM-1 producers from Tunisia, Egypt and France were the closest relatives of the Polish isolates. Yersiniabactin genes (YbST280 type) were located within the ICEKpn12-like element in most of the outbreak isolates, characterized by O2v1 and KL64 antigen loci. The blaNDM-1 genes were located in double-replicon IncFIIK2+IncFIBK plasmids.

Conclusions
The continuous spread of K. pneumoniae ST147 NDM-1 in Poland since 2015, largely in the Warsaw area, is demonstrated by this genomic analysis. The isolates showed a high degree of homogeneity, and close relatedness to organisms spreading in the Mediterranean region.
Neutron star mergers as the astrophysical site of the r-process in the Milky Way and its satellite galaxies
Authors: Wanajo Shinya , Hirai Yutaka , Prantzos Nikos 
Published: June 2021

ABSTRACT
Recent progress of nucleosynthesis work as well as the discovery of a kilonova associated with the gravitational-wave source GW170817 indicates that neutron star mergers (NSM) can be a site of the r-process. Several studies of galactic chemical evolution, however, have pointed out inconsistencies between this idea and the observed stellar abundance signatures in the Milky Way: (a) the presence of Eu at low (halo) metallicity and (b) the descending trend of Eu/Fe at high (disc) metallicity. In this study, we explore the galactic chemical evolution of the Milky Way’s halo, disc, and satellite dwarf galaxies. Particular attention is payed to the forms of delay-time distributions for both type Ia supernovae (SN Ia) and NSMs. The Galactic halo is modelled as an ensemble of independently evolving building-block galaxies with different masses. The single building blocks as well as the disc and satellite dwarfs are treated as well-mixed one-zone systems. Our results indicate that the aforementioned inconsistencies can be resolved and thus NSMs can be the unique r-process site in the Milky Way, provided that the delay-time distributions satisfy the following conditions: (i) a long delay (∼1 Gyr) for the appearance of the first SN Ia (or a slow early increase of its number) and (ii) an additional early component providing ${\gtrsim}50{{\ \rm per\ cent}}$ of all NSMs with a delay of ∼0.1 Gyr. In our model, r-process-enhanced and r-process-deficient stars in the halo appear to have originated from ultrafaint dwarf-sized and massive building blocks, respectively. Our results also imply that the natal kicks of binary neutron stars have a little impact on the evolution of Eu in the disc.
Testing the flux-based statistical prediction of the three-body problem
Authors: Manwadkar Viraj , Kol Barak , Trani Alessandro A , Leigh Nathan W C 
Published: June 2021

Abstract
We present an extensive comparison between the statistical properties of non-hierarchical three-body systems and the corresponding three-body theoretical predictions. We perform and analyse 1 million realizations for each different initial condition considering equal and unequal mass three-body systems to provide high accuracy statistics. We measure 4 quantities characterizing the statistical distribution of ergodic disintegrations: escape probability of each body, the characteristic exponent for escapes by a narrow margin, predicted absorptivity as a function of binary energy and binary angular momentum, and, finally, the lifetime distribution. The escape probabilities are shown to be in agreement down to the 1 per cent level with the emissivity-blind, flux-based theoretical prediction. This represents a leap in accuracy compared to previous three-body statistical theories. The characteristic exponent at the threshold for marginally unbound escapes is an emissivity-independent flux-based prediction, and the measured values are found to agree well with the prediction. We interpret both tests as strong evidence for the flux-based three-body statistical formalism. The predicted absorptivity and lifetime distributions are measured to enable future tests of statistical theories.
Long-term X-ray observations of seyfert 1 galaxy ark 120: on the origin of soft-excess
Authors: Nandi Prantik , Chatterjee Arka , Chakrabarti Sandip K , Dutta Broja G 
Published: June 2021

ABSTRACT
We present the long-term X-ray spectral and temporal analysis of a ‘bare-type AGN’ Ark 120. We consider the observations from XMM–Newton, Suzaku, Swift, and NuSTAR from 2003 to 2018. The spectral properties of this source are studied using various phenomenological and physical models present in the literature. We report (a) the variations of several physical parameters, such as the temperature and the optical depth of the electron cloud, the size of the Compton cloud, and the accretion properties for the last 15 yr. The spectral variations are explained from the changes in the accretion dynamics; (b) the X-ray time delay between 0.2–2 and 3–10 keV light-curves exhibited zero-delay in 2003, positive delay of 4.71 ± 2.1 ks in 2013, and negative delay of 2.90 ± 1.26 ks in 2014. The delays are explained considering Comptonization, reflection, and light-crossing time; (c) the long-term intrinsic luminosities, obtained using nthcomp, of the soft-excess and the primary continuum show a correlation with a Pearson correlation coefficient of 0.90. This indicates that the soft-excess and the primary continuum originate from the same physical process. From a physical model fitting, we infer that the soft excess for Ark 120 could be due to a small number of scatterings in the Compton cloud. Using Monte Carlo simulations, we show that indeed the spectra corresponding to fewer scatterings could provide a steeper soft-excess power law in the 0.2–3 keV range. Simulated luminosities are found to be in agreement with the observed values.
Evolution of plant telomerase RNAs: farther to the past, deeper to the roots
Authors: Fajkus Petr , Kilar Agata , Nelson Andrew D L , Holá Marcela , Peška Vratislav , Goffová Ivana , Fojtová Miloslava , Zachová Dagmar , Fulnečková Jana , Fajkus Jiří 
Published: June 2021

AbstractThe enormous sequence heterogeneity of telomerase RNA (TR) subunits has thus far complicated their characterization in a wider phylogenetic range. Our recent finding that land plant TRs are, similarly to known ciliate TRs, transcribed by RNA polymerase III and under the control of the type-3 promoter, allowed us to design a novel strategy to characterize TRs in early diverging Viridiplantae taxa, as well as in ciliates and other Diaphoretickes lineages. Starting with the characterization of the upstream sequence element of the type 3 promoter that is conserved in a number of small nuclear RNAs, and the expected minimum TR template region as search features, we identified candidate TRs in selected Diaphoretickes genomes. Homologous TRs were then used to build covariance models to identify TRs in more distant species. Transcripts of the identified TRs were confirmed by transcriptomic data, RT-PCR and Northern hybridization. A templating role for one of our candidates was validated in Physcomitrium patens. Analysis of secondary structure demonstrated a deep conservation of motifs (pseudoknot and template boundary element) observed in all published TRs. These results elucidate the evolution of the earliest eukaryotic TRs, linking the common origin of TRs across Diaphoretickes, and underlying evolutionary transitions in telomere repeats.
Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency
Authors: Qin Weihua , Ugur Enes , Mulholland Christopher B , Bultmann Sebastian , Solovei Irina , Modic Miha , Smets Martha , Wierer Michael , Forné Ignasi , Imhof Axel , Cardoso M Cristina , Leonhardt Heinrich 
Published: June 2021

Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.