bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
Authors: Noshay Jaclyn M , Marand Alexandre P , Anderson Sarah N , Zhou Peng , Mejia Guerra Maria Katherine , Lu Zefu , O’Connor Christine H , Crisp Peter A , Hirsch Candice N , Schmitz Robert J , Springer Nathan M 
Published: January 2021

Abstract
Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.
Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks
Authors: Kasimatis Katja R , Abraham Abin , Ralph Peter L , Kern Andrew D , Capra John A , Phillips Patrick C 
Published: January 2021

Abstract
Sex and sexual differentiation are pervasive across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest that sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very large to produce and maintain reported levels of between-sex allelic differentiation. We address this contradiction between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n = 487,999) along with a second large, independent cohort (BioVU, n = 93,864). We performed association tests between genetically ascertained sex and autosomal loci. Although we found dozens of genome-wide significant associations, none replicated across cohorts. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect clear evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.
Protein quality control degron-containing substrates are differentially targeted in the cytoplasm and nucleus by ubiquitin ligases
Authors: Hickey Christopher M , Breckel Carolyn , Zhang Mengwen , Theune William C , Hochstrasser Mark 
Published: January 2021

Abstract
Intracellular proteolysis by the ubiquitin–proteasome system regulates numerous processes and contributes to protein quality control (PQC) in all eukaryotes. Covalent attachment of ubiquitin to other proteins is specified by the many ubiquitin ligases (E3s) expressed in cells. Here we determine the E3s in Saccharomyces cerevisiae that function in degradation of proteins bearing various PQC degradation signals (degrons). The E3 Ubr1 can function redundantly with several E3s, including nuclear-localized San1, endoplasmic reticulum/nuclear membrane-embedded Doa10, and chromatin-associated Slx5/Slx8. Notably, multiple degrons are targeted by more ubiquitylation pathways if directed to the nucleus. Degrons initially assigned as exclusive substrates of Doa10 were targeted by Doa10, San1, and Ubr1 when directed to the nucleus. By contrast, very short hydrophobic degrons—typical targets of San1—are shown here to be targeted by Ubr1 and/or San1, but not Doa10. Thus, distinct types of PQC substrates are differentially recognized by the ubiquitin system in a compartment-specific manner. In human cells, a representative short hydrophobic degron appended to the C-terminus of GFP-reduced protein levels compared with GFP alone, consistent with a recent study that found numerous natural hydrophobic C-termini of human proteins can act as degrons. We also report results of bioinformatic analyses of potential human C-terminal degrons, which reveal that most peptide substrates of Cullin-RING ligases (CRLs) are of low hydrophobicity, consistent with previous data showing CRLs target degrons with specific sequences. These studies expand our understanding of PQC in yeast and human cells, including the distinct but overlapping PQC E3 substrate specificity of the cytoplasm and nucleus.
Health and Subjective Views on Aging: Longitudinal Findings From the ActiFE Ulm Study
Authors: Schönstein Anton , Dallmeier Dhayana , Denkinger Michael , Rothenbacher Dietrich , Klenk Jochen , Bahrmann Anke , Wahl Hans-Werner 
Published: January 2021

Abstract

Objectives
Previous research supports that subjective views on aging (VoA), such as older subjective age (SA) and negative attitudes toward own aging (ATOA), go along with negative outcomes. A differentiated treatment of health and disease as antecedents of VoA is largely lacking. Therefore, our objective was to estimate the relationship between generally framed physical, affective, and cognitive health as well as specific diseases and VoA, operationalized both as SA and ATOA.

Methods
Data were drawn from the ActiFE Ulm study for which a representative sample of community-dwelling older people (65–90 years) was recruited at baseline. Follow-ups were conducted 7.7 years (median) after recruitment (N = 526). Health- and disease-related data at baseline, based on established assessment procedures for epidemiological studies, were regressed on VoA (1-item SA indicator, 5-item ATOA scale) measures at follow-up.

Results
Reported severity of affective health problems such as depression was the strongest general risk factor for both older SA and negative ATOA. Also, some but not all major diseases considered were associated with VoA. Notably, back pain predicted negative ATOA, while cancer was associated with older SA. Rheumatism was linked with more negative ATOA along with higher SA. Throughout analyses, explained variance in ATOA was considerably higher than in SA.

Discussion
Affective health problems, such as depression, should be regarded as a major correlate of subjective aging views. Interestingly, diseases do not have to be life-threatening to be associated with older SA or negative ATOA.
The Formal Shift Operator on the Yangian Double
Authors: Wendlandt Curtis 
Published: January 2021

Abstract
Let ${\mathfrak{g}}$ be a symmetrizable Kac–Moody algebra with associated Yangian $Y_\hbar{\mathfrak{g}}$ and Yangian double $\textrm{D}Y_\hbar{\mathfrak{g}}$. An elementary result of fundamental importance to the theory of Yangians is that, for each $c\in{\mathbb{C}}$, there is an automorphism $\tau _c$ of $Y_\hbar{\mathfrak{g}}$ corresponding to the translation $t\mapsto t+c$ of the complex plane. Replacing $c$ by a formal parameter $z$ yields the so-called formal shift homomorphism $\tau _z$ from $Y_\hbar{\mathfrak{g}}$ to the polynomial algebra $Y_\hbar{\mathfrak{g}}[z]$. We prove that $\tau _z$ uniquely extends to an algebra homomorphism $\Phi _z$ from the Yangian double $\textrm{D}Y_\hbar{\mathfrak{g}}$ into the $\hbar $-adic closure of the algebra of Laurent series in $z^{-1}$ with coefficients in the Yangian $Y_\hbar{\mathfrak{g}}$. This induces, via evaluation at any point $c\in{\mathbb{C}}^\times $, a homomorphism from $\textrm{D}Y_\hbar{\mathfrak{g}}$ into the completion of the Yangian with respect to its grading. We show that each such homomorphism gives rise to an isomorphism between completions of $\textrm{D}Y_\hbar{\mathfrak{g}}$ and $Y_\hbar{\mathfrak{g}}$ and, as a corollary, we find that the Yangian $Y_\hbar{\mathfrak{g}}$ can be realized as a degeneration of the Yangian double $\textrm{D}Y_\hbar{\mathfrak{g}}$. Using these results, we obtain a Poincaré–Birkhoff–Witt theorem for $\textrm{D}Y_\hbar{\mathfrak{g}}$ applicable when ${\mathfrak{g}}$ is of finite type or of simply laced affine type.
Sufi Reformism and the Politics of Enchantment in Nasser’s Egypt (1954–1970)
Authors: Zárate Arthur Shiwa 
Published: January 2021

AbstractAlthough theories of disenchantment have been both utilized and critiqued by scholars of Islam, they have not received sufficient critical scrutiny within historical studies on Islamic reformism, a novel religiosity associated with modernity’s emergence in Muslim societies. Indeed, histories of Islamic reformism often portray this novel religiosity as an exclusive force of disenchantment, which is unhelpful for understanding the views of Muslims with reformist commitments and attachments to Sufi practices that invest supernatural powers into bodies and objects. Through an analysis of the Sufi Islamic reformist project of the ʿAshira Muhammadiyya organization in Egypt during the Nasser years (1954–1970), this article highlights how the history of Islamic reformism resonates with and diverges from disenchantment theories. Specifically, it foregrounds the way this Sufi reformism not only framed its objectives in terms of progress, science, and socialism but also presumed a reformist Sufi subject constituted through encounters with unseen supernatural agents.
Regulation of lysosomal positioning via TMEM55B phosphorylation
Authors: Araki Makoto , Kontani Kenji 
Published: January 2021

AbstractLysosomes are dynamic organelles that are transported along microtubules bidirectionally via kinesin and dynein motor proteins. Lysosomal positioning, which is determined by the balance of the bidirectional lysosomal movement, changes under various conditions and affects lysosomal functions such as autophagy and antigen presentation. A recent study by Takemasu et al. (Phosphorylation of TMEM55B by Erk/MAPK regulates lysosomal positioning. J. Biochem. 2019; 166:175–185) has shown that phosphorylation of the transmembrane protein TMEM55B is involved in the retrograde lysosomal trafficking towards the perinuclear region. They found that TMEM55B is phosphorylated upon stimulation with various ligands and that Erk/MAPK mediates the TMEM55B phosphorylation. They have also revealed that a phosphorylation mimic mutant of TMEM55B enhances perinuclear lysosomal clustering compared to the wild-type TMEM55B. These findings suggest that TMEM55B phosphorylation by Erk/MAPK is responsible for regulating lysosomal positioning in response to external stimuli.
Thioredoxin pathway in Anabaena sp. PCC 7120: activity of NADPH-thioredoxin reductase C
Authors: Deschoenmaeker Frédéric , Mihara Shoko , Niwa Tatsuya , Taguchi Hideki , Wakabayashi Ken-Ichi , Toyoshima Masakazu , Shimizu Hiroshi , Hisabori Toru 
Published: January 2021

Abstract
To understand the physiological role of NADPH-thioredoxin reductase C (NTRC) in cyanobacteria, we investigated an NTRC-deficient mutant strain of Anabaena sp., PCC 7120, cultivated under different regimes of nitrogen supplementation and light exposure. The deletion of ntrC did not induce a change in the cell structure and metabolic pathways. However, time-dependent changes in the abundance of specific proteins and metabolites were observed. A decrease in chlorophyll a was correlated with a decrease in chlorophyll a biosynthesis enzymes and photosystem I subunits. The deletion of ntrC led to a deregulation of nitrogen metabolism, including the NtcA accumulation and heterocyst-specific proteins while nitrate ions were available in the culture medium. Interestingly, this deletion resulted in a redox imbalance, indicated by higher peroxide levels, higher catalase activity and the induction of chaperones such as MsrA. Surprisingly, the antioxidant protein 2-CysPrx was downregulated. The deficiency in ntrC also resulted in the accumulation of metabolites such as 6-phosphogluconate, ADP and ATP. Higher levels of NADP+ and NADPH partly correlated with higher G6PDH activity. Rather than impacting protein expression levels, NTRC appears to be involved in the direct regulation of enzymes, especially during the dark-to-light transition period.
First Report of Insecticide Resistance to Organophosphates and Pyrethroids in the Small Hive Beetle (Coleoptera: Nitidulidae) and Development of a Resistance Monitoring Technique
Authors: Kanga Lambert H B , Marechal Walker , Legaspi Jesusa C , Haseeb Muhammad 
Published: January 2021

Abstract
The small hive beetle, Aethina tumida Murray (Coleoptera: Nitidulidae), is a serious threat to the honey bee industry, which relies on chemicals for the control of major honey bee pests. We developed a glass vial bioassay for resistance monitoring of adult A. tumida populations in honey bee colonies. We also determined concentrations that could be used to discriminate between susceptible and resistant strains. These include the pyrethroids cypermethrin (25.0 μg per vial) and fluvalinate (25.0 μg per vial) and the organophosphates malathion (10.0 μg per vial), chlorpyrifos (2.5 μg per vial), and coumaphos (25.0 μg per vial). Here, we report that resistance to fluvalinate and coumaphos was widespread in A. tumida populations in Florida in 2019. Aethina tumida populations were still susceptible to cypermethrin, malathion, and chlorpyrifos. The levels of resistance differed between pyrethroid and organophosphate insecticides. Over the last 10 yr, A. tumida populations have developed 43.7-fold resistance to coumaphos and 5.4-fold to fluvalinate. The levels of insecticide resistance were not similar within insecticides in the same class, which suggest that this type of resistance is manageable. Our results demonstrate the usefulness of glass vial bioassays to detect resistance in adult A. tumida and provide the foundation for a resistance management strategy. To the best of our knowledge, this is the first report of insecticide resistance in small hive beetle populations and suggests an urgent need for alternative control strategies for these serious pests of honey bee colonies.
Ameliorative effects of garlic oil on FNDC5 and irisin sensitivity in liver of streptozotocin-induced diabetic rats
Authors: Eser Nadire , Yoldas Atila , Turk Ahmet , Kalaycı Yigin Aysel , Yalcin Alper , Cicek Mustafa 
Published: January 2021

Abstract

Objectives
This study was aimed to investigate the effects of garlic oil (GO), an important natural constituent used in alleviating diabetes and its complications, on the expression levels of irisin and related genes.

Methods
Thirty-two rats were divided into four groups: Control, Diabetes-Control, Diabetes+GO 100 mg/kg/day and Control+GO 100 mg/kg/day for 45 days. The measurements included: changes in liver Peroxisome proliferator-activated receptor-gamma-coactivator (PGC)-1α, Fibronectin Type-III-Domain-Containing5 (FNDC5), irisin expression, mRNA expression of p38 and TNF-α (Tumour necrosis factor-α), total-antioxidant-status (L-TAS; S-TAS), total-oxidant-status (L-TOS; S-TOS) in liver and serum, respectively.

Key findings
There was a significant reduction in serum levels of irisin and S-TAS and expression of PGC-1α and FNDC5 in liver in Diabetes-control compared to Control-group, while a significant increase in serum levels of fasting blood glucose (FBG) and TOS, also p38 and TNF-α expressions in liver. In Diabetes+GO group, there was a significant increase in serum irisin and S-TAS, also expression of PGC-1α and FNDC5 in liver, while serum FBG, S-TOS levels, and mRNA expression of p38 and TNF-α in liver were decreased compared to Diabetes-control group (P &lt; 0.05).

Conclusions
GO alleviated the diabetic liver injury by decreasing Oxidative-Stress parameters and regulation PGC-lα, FNDC5, irisin and P38, keeping the balance of TAS/TOS and TNF-α.
Dual-modality emergency management of a rare cause of an aorto-oesophageal fistula: a case report
Authors: Vasanthan Rishi , Tabbakh Yasmin , Doran Sophie , Baker Daryll , Hague Julian , Qureshi Yassar , Dawas Khaled , Mohammadi Borzoueh 
Published: January 2021

Abstract
Aorto-oesophageal fistula (AOF) is a life-threatening condition that usually presents with upper gastro-intestinal haemorrhage. This case report details the emergency presentation and management of a 51-year-old male who presented with hematemesis secondary to an impacted denture (ingested two years previously) in the oesophagus that had led to an AOF. This necessitated urgent thoracic endovascular aortic repair followed by thoracotomy, oesophagotomy, T-tube insertion and oesophagostomy. This is the first documentation in the literature of the dual-modality management for this rare cause of AOF and demonstrates the multidisciplinary approach to successful management of this complex yet rare presentation.
Overproduction of ascorbic acid impairs pollen fertility in tomato
Authors: Deslous Paul , Bournonville Céline , Decros Guillaume , Okabe Yoshihiro , Mauxion Jean-Philippe , Jorly Joana , Gadin Stéphanie , Brès Cécile , Mori Kentaro , Ferrand Carine , Prigent Sylvain , Ariizumi Tohru , Ezura Hiroshi , Hernould Michel , Rothan Christophe , Pétriacq Pierre , Gibon Yves , Baldet Pierre 
Published: January 2021

AbstractAscorbate is a major antioxidant buffer in plants. Several approaches have been used to increase the ascorbate content of fruits and vegetables. Here, we combined forward genetics with mapping-by-sequencing approaches using an ethyl methanesulfonate (EMS)-mutagenized Micro-Tom population to identify putative regulators underlying a high-ascorbate phenotype in tomato fruits. Among the ascorbate-enriched mutants, the family with the highest fruit ascorbate level (P17C5, up to 5-fold wild-type level) had strongly impaired flower development and produced seedless fruit. Genetic characterization was performed by outcrossing P17C5 with cv. M82. We identified the mutation responsible for the ascorbate-enriched trait in a cis-acting upstream open reading frame (uORF) involved in the downstream regulation of GDP-l-galactose phosphorylase (GGP). Using a specific CRISPR strategy, we generated uORF-GGP1 mutants and confirmed the ascorbate-enriched phenotype. We further investigated the impact of the ascorbate-enriched trait in tomato plants by phenotyping the original P17C5 EMS mutant, the population of outcrossed P17C5 × M82 plants, and the CRISPR-mutated line. These studies revealed that high ascorbate content is linked to impaired floral organ architecture, particularly anther and pollen development, leading to male sterility. RNA-seq analysis suggested that uORF-GGP1 acts as a regulator of ascorbate synthesis that maintains redox homeostasis to allow appropriate plant development.
Finitism, imperative programs and primitive recursion
Authors: Leivant Daniel 
Published: January 2021

Abstract
Following the Crisis of Foundations Hilbert proposed to consider a finitistic form of arithmetic as mathematics’ safe core. This approach to finitism has often admitted primitive recursive function definitions as obviously finitistic, but some have advocated the inclusion of additional variants of recurrence, while others argued that, to the contrary, primitive recursion exceeds finitism. In a landmark essay, William Tait contested the finitistic nature of these extensions, due to their impredicativity, and advocated identifying finitism with primitive recursive arithmetic, a stance often referred to as Tait’s Thesis. However, a problem with Tait’s argument is that the recurrence schema has itself impredicative and non-finitistic facets, starting with an explicit reference to the functions being defined, which are after all infinite objects. It is therefore desirable to buttress Tait’s Thesis on grounds that avoid altogether any trace of concrete infinities or impredicativity. We propose here to do just that, building on the generic framework of [ 13].
We provide further evidence for Tait’s Thesis by outlining a proof of a purely finitistic version of Parsons’ theorem, whose intuitive gist is that finitistic reasoning is equivalent to finitistic computing.
Banal bordering: Everyday encounters between migrants and security officers
Authors: Innes Alexandria J 
Published: January 2021

Abstract
The encounter between a migrant and the state is almost always fraught. The power of the state to approve or deny immigration status produces a power imbalance whereby the migrant is subject to the whim of the state. This research extracts encounters between migrants, police, immigration officers, and interpreters in the UK to conceptualise how the minutia of these encounters, and the standardised practices they involve, might impact the ability of migrants to express themselves and exercise their own voice in interactions. Adopting a reflexive ethnographic methodology, and using data gathered with police workers as a pilot case, I consider how the varied objectives of agencies and actors in the migration sector intersect with migrant experiences in practice. Ultimately, implications for migrant security lie in the recognition that migrant voice can be obscured as a result of mundane and everyday procedures. Banal bordering processes can go unnoticed and unaddressed by policy makers, but are often loaded with meaning for migrants subject to them. The vulnerability of migrants and the unbalanced nature of encounters between migrants and the state highlights how state power manifests at an everyday level, suggesting that insecurity is not unique to migrants without documents, but is present in all encounters between migrants and the state. Nevertheless, the professionals who are interacting with migrants are often in a position whereby they have the experiential expertise to offer workable, though limited, solutions, although they do not always have access to the channels or the resources necessary to implement them.