bluuebunny/crossref_metadata_2025 huggingface dataset:
Linking electoral realignment to welfare politics: an assessment of partisan effects on active labour market policy in post-industrial democracies
Authors: Hieda Takeshi
Published: June 2021

This article examines the political determinants of the variations in active labour market policies across advanced democracies. Specifically, it investigates the conditions under which a welfare state accommodates rather than disregards the interests of labour market outsiders. Relying on the literature on post-industrial electoral realignment, this article argues that ideological orientations not only in socio-economic but also in sociocultural dimensions dictate the policy preferences of political parties for labour market programmes. This study then hypothesizes that libertarian governments are more likely than authoritarian governments to support human capital formation of labour market outsiders. An analysis of cabinet-based periodization data of 21 advanced industrialized countries from 1985 to 2017 shows that left- and right-libertarian governments favour public spending on active labour market programmes, thereby supporting this study’s hypothesis. Furthermore, it also reveals that while left-libertarian governments increase expenditures for direct job creation schemes, right-libertarian ones do so for employment assistance and training programmes.
The role of perovskite oxides in solar energy conversion
Authors: Patrick Chris
Published: June 2021

The use of inorganic perovskite oxides promotes solar-driven water splitting, a source of renewable energy.
Diagnosis analysis of rectal function through using ensemble empirical mode decomposition–deep belief networks algorithm
Authors: Zan Peng , Hong Rui , Yang Banghua , Zhang Guofu , Shao Yong , Ding Qiao , Zhao Yutong , Zhong Hua
Published: June 2021

The rectal motility function can reflect a person’s rectal health status. To diagnose the rectal motility function after artificial anal sphincter implantation, this paper proposes a rectal function diagnosis model based on ensemble empirical mode decomposition–deep belief networks (EEMD–DBNs). Because of the rectal pressure signals that are unstable and subjected to noise interferences, an EEMD framework based on EMD, which can reduce the effect of signal modal mixing, is proposed. EMD and EEMD were used to decompose the analog signal, respectively, and it was found that EEMD can significantly reduce the effect of mode aliasing. During the rectal pressure signal decomposition experiment, by analyzing the intrinsic mode functions generated by the signals from normal people and diseased patients, the rectal signals at these two different conditions can be well distinguished. Additionally, the DBN was introduced to perform deep learning to extract the multi-dimensional features of rectal signals and then output the classification results via using the top-level classifier, which can overcome the difficulties in extracting the rectal signal features. The results showed that, following the principle of balancing the diagnosis accuracy and model running speed, the best diagnosis performance was achieved when three restricted Boltzmann machines and five layers of DBN model were set, with the diagnosis rate of 85%. The diagnostic model used in this study can distinguish the signals between normal and abnormal rectal functions with accurate performance, thus providing the technical support for the recovery of the rectal motility function of artificial anal sphincter implanters.
Embedded heating, ventilation, and air-conditioning control systems: From traditional technologies toward radar advanced sensing
Authors: Cardillo Emanuele , Li Changzhi , Caddemi Alina
Published: June 2021

This paper comprehensively reviews the state of the art of Heating, Ventilation, and Air-Conditioning (HVAC) control sensing. The topic has broad impacts on society, by affecting energy consumption, Earth’s climate, and the environmental health. Great effort was taken by researchers to study and test new technologies and methodologies for improving HVAC energy efficiency, but this large amount of works is often fragmentary, and a complete and recent review paper does not yet exist. This paper aims at filling this gap by clarifying the key points of HVAC sensing, the main technologies, and their pros and cons. The advancement in this sector is fueled by the premium performance of the embedded systems exploited as sensors and their beneficial features. The state of the art of the available solutions has been summarized with the purpose of fueling and better organizing the research effort on this hot topic. Particular attention has been paid to investigate not only the performance and reliability of the current systems but also the advanced features that can be provided by the newly evolved and complex technologies, e.g., the radar technology that has been identified as the emerging one in this field.
Strict deformations of quantum field theory in de Sitter spacetime
Authors: Fröb M. B. , Much A.
Published: June 2021

We propose a new deformed Rieffel product for functions in de Sitter spacetimes and study the resulting deformation of quantum field theory in de Sitter using warped convolutions. This deformation is obtained by embedding de Sitter in a higher-dimensional Minkowski spacetime, deforming there using the action of translations and subsequently projecting back to de Sitter. We determine the two-point function of a deformed free scalar quantum field, which differs from the undeformed one, in contrast to the results in deformed Minkowski spacetime where they coincide. Nevertheless, we show that in the limit where the de Sitter spacetime becomes flat, we recover the well-known non-commutative Minkowski spacetime.
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

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

Background and Aims

Domesticated 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.

Methods

Seedling 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 Results

Seminal 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.

Conclusions

Seminal 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

Urbanization 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

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

Motivation

DNA 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.

Results

We 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 implementation

We 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 information

Supplementary 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

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

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

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.
The next phase in the development of 13C isotopically non-stationary metabolic flux analysis
Authors: Wieloch Thomas
Published: June 2021

This viewpoint devises recommendations for future studies utilizing 13C isotopically non-stationary metabolic flux analysis to characterize plant metabolism. Most importantly, it highlights the necessity for model validation.
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

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

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

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

The 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

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.
Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons
Authors: Ichihara Kazuya , Matsumoto Akinobu , Nishida Hiroshi , Kito Yuki , Shimizu Hideyuki , Shichino Yuichi , Iwasaki Shintaro , Imami Koshi , Ishihama Yasushi , Nakayama Keiichi I
Published: June 2021

Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here, we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are most probably dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity
Authors: Bader Samuel B , Ma Tiffany S , Simpson Charlotte J , Liang Jiachen , Maezono Sakura Eri B , Olcina Monica M , Buffa Francesca M , Hammond Ester M
Published: June 2021

Tumor heterogeneity includes variable and fluctuating oxygen concentrations, which result in the accumulation of hypoxic regions in most solid tumors. Tumor hypoxia leads to increased therapy resistance and has been linked to genomic instability. Here, we tested the hypothesis that exposure to levels of hypoxia that cause replication stress could increase APOBEC activity and the accumulation of APOBEC-mediated mutations. APOBEC-dependent mutational signatures have been well-characterized, although the physiological conditions which underpin them have not been described. We demonstrate that fluctuating/cyclic hypoxic conditions which lead to replication catastrophe induce the expression and activity of APOBEC3B. In contrast, stable/chronic hypoxic conditions which induce replication stress in the absence of DNA damage are not sufficient to induce APOBEC3B. Most importantly, the number of APOBEC-mediated mutations in patient tumors correlated with a hypoxia signature. Together, our data support the conclusion that hypoxia-induced replication catastrophe drives genomic instability in tumors, specifically through increasing the activity of APOBEC3B.
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms
Authors: Figueiredo Rebeca Queiroz , Raschka Tamara , Kodamullil Alpha Tom , Hofmann-Apitius Martin , Mubeen Sarah , Domingo-Fernández Daniel
Published: June 2021

We attempt to address a key question in the joint analysis of transcriptomic data: can we correlate the patterns we observe in transcriptomic datasets to known interactions and pathway knowledge to broaden our understanding of disease pathophysiology? We present a systematic approach that sheds light on the patterns observed in hundreds of transcriptomic datasets from over sixty indications by using pathways and molecular interactions as a template. Our analysis employs transcriptomic datasets to construct dozens of disease specific co-expression networks, alongside a human protein-protein interactome network. Leveraging the interoperability between these two network templates, we explore patterns both common and particular to these diseases on three different levels. Firstly, at the node-level, we identify most and least common proteins across diseases and evaluate their consistency against the interactome as a proxy for their prevalence in the scientific literature. Secondly, we overlay both network templates to analyze common correlations and interactions across diseases at the edge-level. Thirdly, we explore the similarity between patterns observed at the disease-level and pathway knowledge to identify signatures associated with specific diseases and indication areas. Finally, we present a case scenario in schizophrenia, where we show how our approach can be used to investigate disease pathophysiology.
Organic molecules encapsulated in single-walled carbon nanotubes
Authors: Cadena Ana , Botka Bea , Kamarás Katalin
Published: June 2021

Hybrid materials based on carbon nanotubes continue to attract considerable interest due to the broad variety of both the cages outside and the encapsulated species inside. This review focuses on organic molecules as guests in single-walled carbon nanotube hosts. The majority of results presented here has been attained in recent years by various methods of optical spectroscopy, complemented by transmission electron microscopy. These spectroscopic methods yield information on electronic structure, as well as dynamic processes as structural transformations and chemical reactions.
Spaces of Peace
Authors: Björkdahl Annika , Kappler Stefanie
Published: June 2021

This chapter shows that war-making and peace-making “take place” and that sometimes the legacy of conflict obscures manifestations of peacebuilding. The analysis of a “bridge that divides” in the city of Mitrovica in northern Kosovo and a “wall that unites” in Belfast, Northern Ireland, casts light on the benefits that a spatial reading of peace can provide to understand the ways in which spatial infrastructures are lived by the people who use them. The process of space-making (the generation of meanings from a material location) will help explain the agency that emerges by the creators, users, and inhabitants of (post)conflict spaces.
Divine Revelation and Digital Religion
Authors: Sheldon Zachary , Campbell Heidi A.
Published: June 2021

This chapter considers the relationship between divine revelation and digital religion by exploring how revelation of divine or religious truth is presented and negotiated on the internet and within digital culture. Revelation is a fundamental component of religious practice and experience and has long been studied in its relation to mediation. Digital culture offers unique resources that allow individuals to receive, engage, and share in divine revelation in digital contexts. The multiplicity of digital contexts and their blended ties to offline practices in worship practices have become known as digital religion (Campbell 2013), which can be likened to a bridge which connects and extends religious practice online into offline religious spaces and contexts. This chapter will consider how revelation is understood and enacted in different spaces of digital religion by providing an overview of Digital Religion Studies and looking at Campbell and DeLashmutt’s (2014) research on multi-site churches to offer insights into how churches structure and negotiate their digital worship practices to assist people in engaging with divine revelation. In particular, we emphasize questions of presence and authority that churches ought to consider in regard to how their use of digital technology may impact views on divine revelation in digital contexts.
The Becoming of Change in 3D: Dialectics, Darwin, and Dewey
Authors: Farjoun Moshe
Published: June 2021

Dialectical development through a conflict process of affirmation, negation, and synthesis, provides a template, both for modelling organizational change, and for constructing new, synthetic conceptual models of change. This chapter highlights two other important means by which dialectics can stimulate new change models: as a relational process philosophy, and as an evolutionary theory. A selective review of the history of ideas about change, from Greek philosophy to Hegelian and Marxian dialectics, to Darwin, to pragmatism, underscores how relational process principles link several, not commonly connected, “becoming” literatures, and how these principles can stimulate key conceptual innovations. The contrast of dialectics with Darwin’s evolutionary theory uncovers several, non-obvious affinities: in underlying principles, change patterns, and mechanisms. The capacity of dialectics—as a philosophy and as an evolutionary theory—to inspire new ideas, is illustrated by a reading of Dewey’s work anew, and through other examples pertinent to contemporary phenomena.
Affirmation and Safety: An Intersectional Analysis of Trans and Nonbinary Youths in Quebec
Authors: Pullen Sansfaçon Annie , Gelly Morgane A , Ens Manning Kimberly
Published: June 2021

This article presents the results of a combined grounded theory and community-based participatory action research project with 54 trans and nonbinary youths (TNBY) residing in the province of Quebec, Canada. The project includes two important sensitizing concepts: intersectionality and recognition. In the research, intersectionality was defined as an approach that explores how people navigate manifold identities (class, race, disability, and so on) in the context of structural oppression. Authors applied an intersectional lens to the recruitment of research participants through an iterative, community-based process, and to the analysis of the oppressive structures that negatively influence the well-being of TNBY and the specific factors that enable TNBY to thrive. Drawing on Honneth’s concept of recognition, authors argue for a contextualized, dynamic, and relational understanding of how well-being is produced. Specifically, they show two presenting needs: one for affirmation and one for safety, access to which springs from resources of privilege that emerge in the environment in which young people are embedded and from which they self-advocate. Understanding the dynamic relationship between these two needs and how they shift according to context is an important component of applying an intersectional approach to supporting TNBY in social work settings.
The Effect of Auricular Acupressure for Chronic Low Back Pain in Elders
Authors: Kim Soo Kyoung , Park Hyojung
Published: June 2021

Chronic low back pain (CLBP) is a major problem throughout the world and getting worse because of population increase and aging. The cost of treatment increases as the population of people with CLBP increases. This study aimed to examine the effect of auricular acupressure (AA) on pain and disability in elders with chronic low back pain. The randomized, single-blinded, and placebo-controlled study was conducted on 51 elders with CLBP in South Korea from June 2019 to August 2019. The experimental group (n = 26) received AA on low back pain-related points, whereas the placebo control group (n = 25) received AA on points unrelated to low back pain. Participants received 6 weeks of AA in weekly cycles. Collected data were analyzed using IBM SPSS Statistics, version 25. Statistically significant differences between the 2 groups emerged in the visual analog scale (P < .001), pain threshold (P < .001), and Oswestry Disability Index (P < .001). This study showed that 6 weeks of AA improved CLBP and pain-related disability. Therefore, AA can be used as a noninvasive and self-managed alternative intervention for CLBP in older adults.
Implementation of the MATRIX Staffing Grid Improves Nurse Satisfaction With Rehabilitation Unit Staffing
Authors: Riley Yahaddy , Stitt Jacqueline , Hill Cynthia M. , Stutzman Sonja E. , Venkatachalam Aardhra M. , Aguilera Veronica , Ifejika Nneka L.
Published: June 2021

BACKGROUND: Information on nurse satisfaction and unit acuity is scarce in the literature. The purpose of this study is to evaluate the effect of the MATRIX Staffing Grid (MSG) on nurse assignment satisfaction in a 20-bed inpatient rehabilitation facility. METHODS: Prospective systematic implementation study of the MSG occurred in 5 phases: development, baseline, run-in, implementation, and sustainability. Pretest/posttest nursing satisfaction data were analyzed using Wilcoxon-Mann-Whitney tests. RESULTS: Analysis of 128 satisfaction surveys demonstrated that the median total satisfaction score increased by 35% after MSG implementation (P < .05), with no change in patient satisfaction or adverse event rates. CONCLUSION: A systematic approach to implementation of the MSG evidence-based practice significantly improved nursing satisfaction with patient assignment in a way that addressed specific needs. The MSG has now been adopted into practice at our institution. The MSG may be feasible for implementation in inpatient rehabilitation units to improve staffing satisfaction.
Oropharyngoesophageal Scintigraphy in a Case of Complex Swallowing Disorders After a Major Oral Surgery
Authors: Maccora Daria , Parrilla Claudio , Lanni Valerio , Galli Jacopo , Longobardi Ylenia , Valenza Venanzio
Published: June 2021

A 75-year-old woman had an occasional finding of a left tonsil mass for dysphagia, which resulted a high-grade squamous carcinoma. Therefore, the patient was sent to have a left pharyngectomy. After the pharyngectomy, the patient reported persistent swallowing disorders and nasal reflux. Consequently, she had an oropharyngoesophageal scintigraphy, demonstrating irregular oral and pharyngeal swallowing phases and confirming reflux episodes into the rhinopharynx and into the oropharynx. In line with these findings, the patient was send to rehabilitation; the abnormal functional mechanisms, previously identified by the scintigraphy, allowed to guide the speech therapy, with a progressive clinical improvement.
Antimicrobial resistance profiles and genetic basis of resistance among non-fastidious Gram-negative bacteria recovered from ready-to-eat foods in Kibera informal housing in Nairobi, Kenya
Authors: Maina John , Ndung’u Perpetual , Muigai Anne , Kiiru John
Published: June 2021

Objective. This cross-sectional study conducted in Kibera, Kenya, sought to gain insights on relative microbial contamination levels of popular unprocessed food types, determine antimicrobial resistance (AMR) burden and the carriage of integrons that are essential elements for spreading antimicrobial resistance genes (ARG). Foods analysed consisted of cooked vegetables (kale, cabbage, and nightshades), boiled cereal foods (beans, rice, and Githeri, which is a mixture of beans and maize), meat, Omena fish (fried silver cyprinids), and Ugali (a product of simmered maize flour in boiled water).

Results. The analysis detected contamination levels exceeding 2×104 c.f.u. ml−1 in 106 (38 %) of the 281 ready-to-eat foods analysed. The majority of food types had microbial contaminations of between 4.0×104 and 2.3×106 c.f.u. ml−1. Kale was the most contaminated with a mean of 2.3×106 c.f.u. ml−1, while Omena was the least contaminated with 4.0×104 c.f.u. ml−1. Foods sold close to open sewage and refuse sites were more contaminated than those sold in relatively ‘cleaner’ settings (P <0.0001, O.R 0.1162, C.I 0.1162–0.120). A total of 405 bacterial isolates were recovered and included;

Klebsiella

spp 116 (29 %),

Escherichia coli

104 (26 %),

Enterobacter agglomerans

88 (22 %),

Proteus mirabilis

30 (7 %),

Salmonella

spp 28 (7 %),

Citrobacter freundii

27 (7 %) and

Serratia marcescens

12 (3 %). Imipenem (IPM, 100 %) was the most effective antimicrobial agent, followed by cefepime (98 %). Ampicillin (AMP, 33 %), trimethoprim (TMP, 27 %), and sulfamethoxazole (SMX, 23 %) on the other hand, were the least effective antimicrobials. The analysis also found ten isolates (2 %) that had co-resistance to third-generation cephalosporins, fluoroquinolone (CIP), quinolones (NAL) and aminoglycosides (GEN); hereby we refer to this phenotype as the βFQA. The prevalence of multidrug-resistant (MDR) strains was 23 % (93), while that of extended-spectrum β-lactamases (ESBL) producing strains was 4 % (17). The bla
TEM was the most prevalent (55 %) β-lactamase (bla) gene among the screened 93 MDR-strains. Carriage of class one integrons (intI1) was more common (23 %) than intl2 (3 %) among these MDR-strains. Bacterial diversity analysis using the GTG5-PCR found no significant clusters for analysed

E. coli

and K. pneumoniae, suggesting recovered isolates were genetically diverse and not due to non-clonal expansion. The findings of this study are an indication that contaminated foods can be a reservoir for enteric pathogens and a source of AMR strains.