bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway
Authors: Aksenova Vasilisa , Smith Alexandra , Lee Hangnoh , Bhat Prasanna , Esnault Caroline , Chen Shane , Iben James , Kaufhold Ross , Yau Ka Chun , Echeverria Carlos , Fontoura Beatriz , Arnaoutov Alexei , Dasso Mary 
Published: September 2020

AbstractNuclear pore complexes (NPCs) are important for cellular functions beyond nucleocytoplasmic trafficking, including genome organization and gene expression. This multi-faceted nature and the slow turnover of NPC components complicates investigations of how individual nucleoporins act in these diverse processes. To address this question, we apply an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins NUP153, NUP50 and TPR. Acute depletion of TPR causes rapid and pronounced changes in transcriptomic profiles. These changes are dissimilar to shifts observed after loss of NUP153 or NUP50, but closely related to changes caused by depletion of mRNA export receptor NXF1 or the GANP subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex. Moreover, TPR depletion disrupts association of TREX-2 subunits (GANP, PCID2, ENY2) to NPCs and results in abnormal RNA transcription and export. Our findings demonstrate a unique and pivotal role of TPR in gene expression through TREX-2- and/or NXF1-dependent mRNA turnover.
Hyperacetylated chromatin domains mark cell type-specific genes and suggest distinct modes of enhancer function
Authors: Fox Sierra , Myers Jacquelyn A. , Davidson Christina , Getman Michael , Kingsley Paul D. , Frankiewicz Nicholas , Bulger Michael 
Published: September 2020

AbstractStratification of enhancers by signal strength in ChIP-seq assays has resulted in the establishment of super-enhancers as a widespread and useful tool for identifying cell type-specific, highly expressed genes and associated pathways. We examine a distinct method of stratification that focuses on peak breadth, termed hyperacetylated chromatin domains (HCDs), which classifies broad regions exhibiting histone modifications associated with gene activation. We find that this analysis serves to identify genes that are both more highly expressed and more closely aligned to cell identity than super-enhancer analysis does using multiple data sets. Moreover, genetic manipulations of selected gene loci suggest that some enhancers located within HCDs work at least in part via a distinct mechanism involving the modulation of histone modifications across domains and that this activity can be imported into a heterologous gene locus. In addition, such genetic dissection reveals that the super-enhancer concept can obscure important functions of constituent elements.
Seafloor evidence for pre-shield volcanism above the Tristan da Cunha mantle plume
Authors: Geissler Wolfram H. , Wintersteller Paul , Maia Marcia , Strack Tonke , Kammann Janina , Eagles Graeme , Jegen Marion , Schloemer Antje , Jokat Wilfried 
Published: September 2020

AbstractTristan da Cunha is assumed to be the youngest subaerial expression of the Walvis Ridge hot spot. Based on new hydroacoustic data, we propose that the most recent hot spot volcanic activity occurs west of the island. We surveyed relatively young intraplate volcanic fields and scattered, probably monogenetic, submarine volcanoes with multibeam echosounders and sub-bottom profilers. Structural and zonal GIS analysis of bathymetric and backscatter results, based on habitat mapping algorithms to discriminate seafloor features, revealed numerous previously-unknown volcanic structures. South of Tristan da Cunha, we discovered two large seamounts. One of them, Isolde Seamount, is most likely the source of a 2004 submarine eruption known from a pumice stranding event and seismological analysis. An oceanic core complex, identified at the intersection of the Tristan da Cunha Transform and Fracture Zone System with the Mid-Atlantic Ridge, might indicate reduced magma supply and, therefore, weak plume-ridge interaction at present times.
Efficient rational modification of non-ribosomal peptides by adenylation domain substitution
Authors: Calcott Mark J. , Owen Jeremy G. , Ackerley David F. 
Published: September 2020

AbstractNon-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module governs the incorporation of a specific monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains. This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains. For over 20 years, it has been considered that C domains play key roles in proof-reading the substrate; a presumption that has greatly complicated rational NRPS redesign. Here we present evidence from both directed and natural evolution studies that any substrate-specifying role for C domains is likely to be the exception rather than the rule, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate modified pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating modified dipeptide products at yields that are inconsistent with the prevailing dogma.
Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility
Authors: Gouma Sigrid , Kim Kangchon , Weirick Madison E. , Gumina Megan E. , Branche Angela , Topham David J. , Martin Emily T. , Monto Arnold S. , Cobey Sarah , Hensley Scott E. 
Published: September 2020

AbstractInfluenza virus exposures in childhood can establish long-lived memory B cell responses that can be recalled later in life. Here, we complete a large serological survey to elucidate the specificity of antibodies against contemporary H3N2 viruses in differently aged individuals who were likely primed with different H3N2 strains in childhood. We find that most humans who were first infected in childhood with H3N2 viral strains from the 1960s and 1970s possess non-neutralizing antibodies against contemporary 3c2.A H3N2 viruses. We find that 3c2.A H3N2 virus infections boost non-neutralizing H3N2 antibodies in middle-aged individuals, potentially leaving many of them in a perpetual state of 3c2.A H3N2 viral susceptibility.
Prediction of hydrogenated group IV–V hexagonal binary monolayers
Authors: Mohebpour Mohammad Ali , Mozvashi Shobair Mohammadi , Vishkayi Sahar Izadi , Tagani Meysam Bagheri 
Published: September 2020

AbstractGroup IV and V monolayers are very crucial 2D materials for their high carrier mobilities, tunable band gaps, and optical linear dichroism. Very recently, a novel group IV–V binary compound, $${\hbox {Sn}}_2{\hbox {Bi}}$$

Sn
2

Bi

, has been synthesized on silicon substrate, and has shown very interesting electronic properties. Further investigations have revealed that the monolayer would be stable in freestanding form by hydrogenation. Inspired by this, by means of first-principles calculations, we systematically predict and investigate eight counterparts of $${\hbox {Sn}}_2{\hbox {Bi}}$$

Sn
2

Bi

, namely $${\hbox {Si}}_2{\hbox {P}}$$

Si
2

P

, $${\hbox {Si}}_2{\hbox {As}}$$

Si
2

As

, $${\hbox {Si}}_2{\hbox {Sb}}$$

Si
2

Sb

, $${\hbox {Si}}_2{\hbox {Bi}}$$

Si
2

Bi

, $${\hbox {Ge}}_2{\hbox {P}}$$

Ge
2

P

, $${\hbox {Ge}}_2{\hbox {As}}$$

Ge
2

As

, $${\hbox {Ge}}_2{\hbox {Sb}}$$

Ge
2

Sb

, and $${\hbox {Ge}}_2{\hbox {Bi}}$$

Ge
2

Bi

. The cohesive energies, phonon dispersions, and AIMD calculations show that, similar to $${\hbox {Sn}}_2{\hbox {Bi}}$$

Sn
2

Bi

, all of these freestanding monolayers are stable in hydrogenated form. These hydrogenated monolayers are semiconductors with wide band gaps, which are favorable for opto-electronic purposes. The $${\hbox {Si}}_2{\hbox {YH}}_2$$

Si
2

YH
2

and $${\hbox {Ge}}_2{\hbox {YH}}_2$$

Ge
2

YH
2

structures possess indirect and direct band gaps, respectively. They represent very interesting optical characteristics, such as good absorption in the visible region and linear dichroism, which are crucial for solar cell and beam-splitting devices, respectively. Finally, the $${\hbox {Si}}_2{\hbox {SbH}}_2$$

Si
2

SbH
2

and $${\hbox {Si}}_2{\hbox {BiH}}_2$$

Si
2

BiH
2

monolayers have suitable band gaps and band edge positions for photocatalytic water splitting. Summarily, our investigations offer very interesting and promising properties for this family of binary compounds. We hope that our predictions open ways to new experimental studies and fabrication of suitable 2D materials for next generation opto-electronic and photocatalytic devices.
Genetic variation regulates opioid-induced respiratory depression in mice
Authors: Bubier Jason A. , He Hao , Philip Vivek M. , Roy Tyler , Hernandez Christian Monroy , Bernat Rebecca , Donohue Kevin D. , O’Hara Bruce F. , Chesler Elissa J. 
Published: September 2020

AbstractIn the U.S., opioid prescription for treatment of pain nearly quadrupled from 1999 to 2014. The diversion and misuse of prescription opioids along with increased use of drugs like heroin and fentanyl, has led to an epidemic in addiction and overdose deaths. The most common cause of opioid overdose and death is opioid-induced respiratory depression (OIRD), a life-threatening depression in respiratory rate thought to be caused by stimulation of opioid receptors in the inspiratory-generating regions of the brain. Studies in mice have revealed that variation in opiate lethality is associated with strain differences, suggesting that sensitivity to OIRD is genetically determined. We first tested the hypothesis that genetic variation in inbred strains of mice influences the innate variability in opioid-induced responses in respiratory depression, recovery time and survival time. Using the founders of the advanced, high-diversity mouse population, the Diversity Outbred (DO), we found substantial sex and genetic effects on respiratory sensitivity and opiate lethality. We used DO mice treated with morphine to map quantitative trait loci for respiratory depression, recovery time and survival time. Trait mapping and integrative functional genomic analysis in GeneWeaver has allowed us to implicateGalnt11, anN-acetylgalactosaminyltransferase, as a gene that regulates OIRD.
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
Authors: Vaga Stefania , Lee Sunjae , Ji Boyang , Andreasson Anna , Talley Nicholas J. , Agréus Lars , Bidkhori Gholamreza , Kovatcheva-Datchary Petia , Park Junseok , Lee Doheon , Proctor Gordon , Ehrlich Stanislav Dusko , Nielsen Jens , Engstrand Lars , Shoaie Saeed 
Published: September 2020

AbstractGut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities’ compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.
Anterior pituitary gland T1 signal intensity is influenced by time delay after injection of gadodiamide
Authors: Mallio Carlo A. , Messina Laura , Parillo Marco , Lo Vullo Gianguido , Beomonte Zobel Bruno , Parizel Paul M. , Quattrocchi Carlo C. 
Published: September 2020

AbstractTo test the hypothesis of washout from the anterior pituitary (AP) gland after serial injections of gadodiamide. We included 59 patients with history of at least 5 injections of gadodiamide. Values of mean signal intensity of the AP and of the central pons were measured on unenhanced sagittal T1-weighted images. AP-to-pons signal intensity ratios were calculated dividing the values of the AP by those of the pons. The measurements were performed using MR images acquired at four different time points including baseline (prior to any gadodiamide injection), minimum post-injection time delay, maximum post-injection time delay, and last available MR scans. Normalized ratios (i.e. ratios divided total volume of injected gadodiamide) were also calculated. To assess the difference between ratios, non-parametric Wilcoxon signed-rank test was applied. The correlations were tested with non-parametric Spearman correlation coefficient. A p-value < 0.05 was considered as statistically significant. A statistically significant increase of AP signal intensity was found by comparing the baseline scans with both the minimum time delay (p = 0.003) and maximum time delay scans (p = 0.005). We found significant higher normalized ratios for minimum post-injection time delay with respect to maximum post-injection time delay (p < 0.001). The normalized ratios demonstrated a statistically significant negative correlation with the post-injection time delay (r = − 0.31; p = 0.006). The findings of this study suggest that washout phenomena of retained/deposited gadolinium from the AP are influenced by the total injected volume and post-injection time delay.
Bleb plication: a minimally invasive repair method for a leaking ischemic bleb after trabeculectomy
Authors: Sugimoto Koichiro , Murata Hiroshi , Yamashita Takehiro , Asaoka Ryo 
Published: September 2020

AbstractBleb leakage is a serious complication of glaucoma filtering surgery. This study describes the method and the results of a new repair method for ischemic bleb leaks. The subjects were consecutive eleven eyes of 11 patients with bleb leakage who underwent the bleb plication surgery. The bleb plication surgery consisted of two steps: 1) bleb needle redirection to float the conjunctiva away from the sclera as extensively as possible around the ischemic conjunctiva; and 2) multiple “O-shaped” sutures were applied between the non-ischemic conjunctiva just outside the ischemic conjunctiva and corneal limbus. The ischemic conjunctiva was not removed, but undermined beneath the advanced non-ischemic conjunctiva. This bleb plication method was repeated until the leakage was sealed. All patients were followed up for at least 6 months after final bleb plication. After final bleb plication, no recurrence of bleb leakage was observed. Moreover, ischemic changes were no longer observed in the advanced non-ischemic conjunctiva. Pre-operative and final intraocular pressure was 3.2 ± 4.1 and 11.9 ± 2.8 mmHg, respectively. This new repair method of bleb plication was safe and effective in sealing the leakage. The conjunctiva is not excised, and hence it does not run out.
Information transfer via temporal convolution in nonlinear optics
Authors: Lassonde Philippe , Ibrahim Heide , Leblanc Adrien , Azaña José , Schmidt Bruno E. , Légaré François 
Published: September 2020

AbstractNonlinear parametric processes involving ultrashort pulses are typically carried out in time domain, which mathematically corresponds to a convolution of their frequency spectra. In contrast, this spectral convolution changes into a multiplication operation when performing the nonlinear interaction in frequency domain. Here, we extend the scope of frequency-domain nonlinear optics by demonstrating its ability to perform a temporal convolution. Through this approach, nonlinear optical operations that are inaccessible in time domain can be realised: specific optical information can be coherently advanced by picoseconds within a pulse sequence—a newly generated second harmonic pulse carries the amplitude and phase information of two input pulses. This central pulse is isolated when using an input field consisting of two cross-polarized input pulses in combination with type-II second harmonic generation. The effects of nonlinear temporal convolution can be viewed from the aspect of signal processing and pulse shaping, where the nonlinear interaction in the parametric crystal plays the role of a dynamic linear optical filter—in contrast to conventional static filters—with a shaping mask instantaneously adapting to the laser field.
Navigating the DNA encoded libraries chemical space
Authors: Martín Alfredo , Nicolaou Christos A. , Toledo Miguel A. 
Published: September 2020

AbstractDNA-encoded library (DEL) technology is a novel ligand identification strategy that allows the synthesis and screening of unprecedented chemical diversity more efficiently than conventional methods. However, no reports have been published to systematically study how to increase the diversity and improve the molecular property space that can be covered with DEL. This report describes the development and application of eDESIGNER, an algorithm that comprehensively generates all possible library designs, enumerates and profiles samples from each library and evaluates them to select the libraries to be synthesized. This tool utilizes suitable on-DNA chemistries and available building blocks to design and identify libraries with a pre-defined molecular weight distribution and maximal diversity compared with compound collections from other sources.
Energy relaxation pathways between light-matter states revealed by coherent two-dimensional spectroscopy
Authors: Mewes Lars , Wang Mao , Ingle Rebecca A. , Börjesson Karl , Chergui Majed 
Published: September 2020

AbstractCoupling matter excitations to electromagnetic modes inside nano-scale optical resonators leads to the formation of hybrid light-matter states, so-called polaritons, allowing the controlled manipulation of material properties. Here, we investigate the photo-induced dynamics of a prototypical strongly-coupled molecular exciton-microcavity system using broadband two-dimensional Fourier transform spectroscopy and unravel the mechanistic details of its ultrafast photo-induced dynamics. We find evidence for a direct energy relaxation pathway from the upper to the lower polariton state that initially bypasses the excitonic manifold of states, which is often assumed to act as an intermediate energy reservoir, under certain experimental conditions. This observation provides new insight into polariton photophysics and could potentially aid the development of applications that rely on controlling the energy relaxation mechanism, such as in solar energy harvesting, manipulating chemical reactivity, the creation of Bose–Einstein condensates and quantum computing.
Identification and seasonality of rhinovirus and respiratory syncytial virus in asthmatic children in tropical climate
Authors: Lopes Giselmo Pinheiro , Amorim Ítalo Patrick Souza , Melo Bruna de Oliveira de , Maramaldo Carlos Eduardo Campos , Bomfim Maria Rosa Quaresma , Lima Neto Lídio Gonçalves , Alves Matheus Silva , Silva Fabrício Brito , Soeiro-Pereira Paulo Vítor , Falcai Angela 
Published: September 2020

Abstract
Introduction: Asthma is a disease that has been associated with the presence of different genetic and socio-environmental factors.
Objective: To identify and evaluate the seasonality of respiratory syncytial virus (RSV) and human rhinovirus (RV) in asthmatic children and adolescents in tropical climate, as well as to assess the socioeconomic and environmental factors involved.
Methods: The study was conducted in a referral hospital, where a total of 151 children were recruited with a respiratory infection. The International Study of Asthma and Allergies in Childhood (ISAAC) protocol and a questionnaire were applied, and a skin prick test was performed. The nasal swab was collected to detect RV and RSV through molecular assay. National Meteorological Institute (INMET) database was the source of climatic information.
Results: The socio-environmental characterization of asthmatic children showed the family history of allergy, disturbed sleep at night, dry cough, allergic rhinitis, individuals sensitized to at least one mite. We identified RV in 75% of children with asthma and 66.7% of RSV in children with asthma. There was an association between the presence of RV and the dry season whereas the presence of the RSV was associated with the rainy season. Contributing to these results, a negative correlation was observed between the RSV and the wind speed and the maximum temperature (T. Max) and a positive correlation with precipitation.
Conclusions: The results suggest a high prevalence of RV and RSV in asthmatic children and the seasonality of these viruses were present in different climatic periods. This has significant implications for understanding short- and long-term clinical complications in asthmatic patients.
Preschool Speech Intelligibility and 8-Year Literacy: A Moderated Mediation Analysis
Authors: Jin Fufen , Schjølberg Synnve , Eadie Patricia , Nes Ragnhild Bang , Røysamb Espen 
Published: September 2020

Purpose
The aims of this study were (a) to examine the relationship between speech intelligibility at the age of 5 years and literacy skills at the age of 8 years, (b) to explore the possible mediating or moderating role of broader language skills at 5 years in the relationship of interest, and (c) to assess whether the potential risk factors (child gender; maternal education levels; and family history of speech, language, reading, and writing difficulties) influence the relationship between speech intelligibility and literacy in terms of moderated mediation effects.

Method
We used mother-reported questionnaire data on 16,184 children participating in the population-based, prospective Norwegian Mother, Father and Child Cohort Study as well as conducted linear regression analyses using the PROCESS macro in SPSS. In addition, logistic regression was conducted to make predictions about risk.

Results

The association between speech intelligibility at 5 years and literacy skills at 8 years was statistically significant (β = .168,
p
< .001). Children with speech problems at 5 years had a risk ratio of 2.38 (95% CI [2.10, 2.70]) and an odds ratio of 2.74 (95% CI [2.35, 3.19]), as compared to children without such problems. Broader language skills at 5 years partially mediated the relationship between speech intelligibility at 5 years and literacy at 8 years, and the effect of language skills appeared to be moderated by child gender, a family history of language difficulties, a family history of reading difficulties, and maternal education.

Conclusions
Severity of speech problems indexed by parent-reported speech intelligibility in preschool predicted school-age literacy problems. Broader language skills are a crucial mediating mechanism through which these problems are linked, and the mediated relationship is amplified by female gender, low maternal education, family history of language difficulties, and family history of reading difficulties. The findings call for increased use of a multiple-risk model when planning early interventions in children with unclear speech.