bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs
Authors: Gonzalez Sara T , Alberto Filipe , Molano Gary 
Published: March 2023

AbstractGiant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.
The human RAP1 and GFAPɛ proteins increase γ-secretase activity in a yeast model system
Authors: Swanson Mark J , Lewis Kelsey N , Carpenter Robert , Whetzel Alexis , Bae Nancy S 
Published: March 2023

Abstract
Alzheimer's disease (AD) is an age-related disorder that results in progressive cognitive impairment and memory loss. Deposition of amyloid β (Aβ) peptides in senile plaques is a hallmark of AD. γ-secretase produces Aβ peptides, mostly as the soluble Aβ40 with fewer insoluble Aβ42 peptides. Rare, early-onset AD (EOAD) occurs in individuals under 60 years of age. Most EOAD cases are due to unknown genetic causes, but a subset is due to mutations in the genes encoding the amyloid precursor protein that is processed into Aβ peptides or the presenilins (PS1 and PS2) that process APP. PS1 interacts with the epsilon isoform of glial fibrillary acidic protein (GFAPɛ), a protein found in the subventricular zone of the brain. We have found that GFAPɛ interacts with the telomere protection factor RAP1 (TERF2IP). RAP1 can also interact with PS1 alone or with GFAPɛ in vitro. Our data show that the nuclear protein RAP1 has an extratelomeric role in the cytoplasm through its interactions with GFAPɛ and PS1. GFAPɛ coprecipitated with RAP1 from human cell extracts. RAP1, GFAPɛ, and PS1 all colocalized in human SH-SY5Y cells. Using a genetic model of the γ-secretase complex in Saccharomyces cerevisiae, RAP1 increased γ-secretase activity, and this was potentiated by GFAPɛ. Our studies are the first to connect RAP1 with an age-related disorder.
Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors
Authors: Wang Yan , Chang Ying , Ortañez Jericho , Peña Jesús F , Carter-House Derreck , Reynolds Nicole K , Smith Matthew E , Benny Gerald , Mondo Stephen J , Salamov Asaf , Lipzen Anna , Pangilinan Jasmyn , Guo Jie , LaButti Kurt , Andreopolous William , Tritt Andrew , Keymanesh Keykhosrow , Yan Mi , Barry Kerrie , Grigoriev Igor V , Spatafora Joseph W , Stajich Jason E 
Published: March 2023

AbstractFungi have evolved over millions of years and their species diversity is predicted to be the second largest on the earth. Fungi have cross-kingdom interactions with many organisms that have mutually shaped their evolutionary trajectories. Zygomycete fungi hold a pivotal position in the fungal tree of life and provide important perspectives on the early evolution of fungi from aquatic to terrestrial environments. Phylogenomic analyses have found that zygomycete fungi diversified into two separate clades, the Mucoromycota which are frequently associated with plants and Zoopagomycota that are commonly animal-associated fungi. Genetic elements that contributed to the fitness and divergence of these lineages may have been shaped by the varied interactions these fungi have had with plants, animals, bacteria, and other microbes. To investigate this, we performed comparative genomic analyses of the two clades of zygomycetes in the context of Kingdom Fungi, benefiting from our generation of a new collection of zygomycete genomes, including nine produced for this study. We identified lineage-specific genomic content that may contribute to the disparate biology observed in these zygomycetes. Our findings include the discovery of undescribed diversity in CotH, a Mucormycosis pathogenicity factor, which was found in a broad set of zygomycetes. Reconciliation analysis identified multiple duplication events and an expansion of CotH copies throughout the Mucoromycotina, Mortierellomycotina, Neocallimastigomycota, and Basidiobolus lineages. A kingdom-level phylogenomic analysis also identified new evolutionary relationships within the subphyla of Mucoromycota and Zoopagomycota, including supporting the sister-clade relationship between Glomeromycotina and Mortierellomycotina and the placement of Basidiobolus as sister to other Zoopagomycota lineages.
Long noncoding RNA CR46040 is essential for injury-stimulated regeneration of intestinal stem cells in Drosophila
Authors: Xu Qi , Liu Jun , Du Xiao , Xue Di , Li Dong , Bi Xiaolin 
Published: March 2023

Abstract
Long noncoding RNAs (lncRNAs) play important regulatory roles in stem cell self-renewal, pluripotency maintenance, and differentiation. Till now, there is very limited knowledge about how lncRNAs regulate intestinal stem cells (ISCs), and lncRNAs mediating ISC regeneration in Drosophila have yet been characterized. Here, we identify a lncRNA, CR46040, that is essential for the injury-induced ISC regeneration in Drosophila. Loss of CR46040 greatly impairs ISC proliferation in response to tissue damage caused by dextran sulfate sodium (DSS) treatment. We demonstrate that CR46040 is a genuine lncRNA that has two isoforms transcribed from the same transcription start site and works in trans to regulate intestinal stem cells. Mechanistically, CR46040 knock-out flies failed to fully activate JNK, JAK/STAT, and HIPPO signaling pathways after tissue damage, which are required for ISC proliferation after intestinal injury. Moreover, CR46040 knock-out flies are highly susceptible to DSS treatment and enteropathogenic bacteria Erwinia carotovora ssp. carotovora 15 (Ecc15) infection. Our findings characterize, for the first time, a lncRNA that mediates damage-induced ISC proliferation in Drosophila and provide new insights into the functional links among the long noncoding RNAs, ISC proliferation, and tissue homeostasis.
The case for supermajority requirements in referendums
Authors: Qvortrup Matt , Trueblood Leah 
Published: March 2023

Abstract
Referendums appear to be the most majoritarian of democratic processes. The simplicity and equality they offer through voting look like the essence of majoritarianism. Indeed, this simplicity and equality are often argued to be central to referendums’ appeal. This article argues that this appearance of majoritarianism is misleading. Paradoxically, without supermajority requirements, binding referendums on constitutional issues cannot offer the simplicity and equality majoritarianism requires. This article identifies three different types of majority requirements and where and when these requirements are used worldwide. It then demonstrates why, at least for binding referendums on constitutional questions, special majority requirements are necessary to maintain the principles of majoritarianism. It shows that there is always a case for turnout thresholds in referendums and further special majority requirements depending on the context. Finally, the article argues that the case for special majority requirements can be context-dependent without collapsing into indeterminacy.
The myth of populist constitutionalism in Hungary and Poland: Populist or authoritarian constitutionalism?
Authors: Szente Zoltán 
Published: March 2023

Abstract
The article seeks to answer the question whether the analytical framework of “populist constitutionalism” adequately describes and explains the constitutional changes that the Hungarian and Polish populist governments have implemented, respectively, since 2010 and 2015. After presenting the similarities and differences between the Hungarian and Polish constitutional developments, the article discusses the conceptual attempts of populist constitutionalism, identifying the primary and secondary characteristics that the literature attributes to this phenomenon. The main point of the article is that these criteria only partially characterize the recent constitutional changes in these two countries, and that the features that do really prevail are more indicative of an unmarked authoritarian transition than of a new, specific version of constitutionalism. It describes the different reasons for the misapplication of constitutional populism to these two countries. Finally, it explains how counterproductive the misconception of populist constitutionalism is for understanding the recent constitutional development in Hungary and Poland.
Exponential state estimate of positive systems with time-varying delays: a Lyapunov–Razumikhin approach
Authors: Ngoc Nguyen Tran 
Published: March 2023

AbstractIn this paper, for the first time, a linear Lyapunov–Razumikhin function is introduced to find an $\alpha$-exponential state estimate for positive systems with time delays. A new set of conditions for the existence of exponential state boundedness of positive systems with bounded time-varying delays is established. Two procedures are then proposed to find the factor vector of $\alpha$-exponential state estimate, in which some techniques of optimization are applied to find the smallest possible factor vector. Numerical experiments are presented to demonstrate the effectiveness of the linear Lyapunov–Razumikhin function as well as of the optimization techniques.
A hybrid high-order scheme for the stationary, incompressible magnetohydrodynamics equations
Authors: Droniou Jérôme , Yemm Liam 
Published: March 2023

Abstract
We propose and analyse a hybrid high-order scheme for the stationary incompressible magnetohydrodynamics equations. The scheme has an arbitrary order of accuracy and is applicable on generic polyhedral meshes. For sources that are small enough, we prove error estimates in energy norm for the velocity and magnetic field, and $L^2$-norm for the pressure; these estimates are fully robust with respect to small faces, and of optimal order with respect to the mesh size. Using compactness techniques, we also prove that the scheme converges to a solution of the continuous problem, irrespective of the source being small or large. Finally, we illustrate our theoretical results through 3D numerical tests on tetrahedral and Voronoi mesh families.
Newton Polygons of Sums on Curves II: Variation in p-adic Families
Authors: Kramer-Miller Joe , Upton James 
Published: March 2023

Abstract
In this article, we study the behavior of Newton polygons along $\mathbb{Z}_p$-towers of curves. Fix an ordinary curve $X$ over a finite field $\mathbb{F}_q$ of characteristic $p$. By a $\mathbb{Z}_p$-tower $X_\infty /X$, we mean a tower of covers $ \dots \to X_2 \to X_1 \to X$ with $\textrm{Gal}(X_n/X) \cong \mathbb{Z}/p^n\mathbb{Z}$. We show that if the ramification along the tower is sufficiently moderate, then the slopes of the Newton polygon of $X_n$ are equidistributed in the interval $[0,1]$ as $n$ tends to $\infty $. Under a stronger congruence assumption on the ramification invariants, we completely determine the slopes of the Newton polygon of each curve. This is the first result towards “regularity” in Newton polygon behavior for $\mathbb{Z}_p$-towers over higher genus curves. We also obtain similar results for $\mathbb{Z}_p$-towers twisted by a generic tame character.
The Kobayashi–Hitchin Correspondence of Generalized Holomorphic Vector Bundles Over Generalized Kähler Manifolds of Symplectic Type
Authors: Goto Ryushi 
Published: March 2023

Abstract
In this paper, we establish the Kobayashi–Hitchin correspondence, that is, the equivalence of the existence of an Einstein–Hermitian metric and $\psi $-polystability of a generalized holomorphic vector bundle over a compact generalized Kähler manifold of symplectic type. Poisson modules provide intriguing generalized holomorphic vector bundles, and we obtain $\psi $-stable Poisson modules over complex surfaces that are not stable in the ordinary sense.
Biotypes of Central Nervous System Complications in People With Human Immunodeficiency Virus: Virology, Immunology, and Neuropathology
Authors: Joseph Sarah B , Gianella Sara , Burdo Tricia H , Cinque Paola , Gisslen Magnus , Letendre Scott , Nath Avindra , Morgello Susan , Ndhlovu Lishomwa C , Spudich Serena 
Published: March 2023

AbstractDespite viral suppression with antiretroviral therapy (ART), people with human immunodeficiency virus (HIV) continue to experience central nervous system (CNS) complications, primarily in the form of mild cognitive impairment and mental health disorders (eg, depression, anxiety, other neuropsychiatric problems). The multifactorial pathogenesis and heterogeneity of mechanisms likely underlying CNS complications must be addressed in the development of preventive interventions and effective treatments. The biotyping approach has previously been useful to define phenotypes of other CNS diseases based on underlying mechanisms and could be translated to the field of neuroHIV. The purpose of the Biotype Workshop series, and the Virology, Immunology and Neuropathology Working Group in particular, is to capitalize on current and new technologies and guide future research efforts using the wealth of available immunological, virologic, and neuropathological data collected from people with HIV on and off ART.
Neither promoting nor projecting democracy: Indonesia’s middlepowermanship in the Bali democracy forum under Joko Widodo
Authors: Rosyidin Mohamad , Kusumawardhana Indra 
Published: March 2023

AbstractDespite the pragmatic character of Indonesian President Joko Widodo’s foreign policy and the regression of the country’s democracy index, Indonesia remains eager for the continuation of Bali Democracy Forum (BDF). This article aims to solve this apparent contradiction using the concept of middle power diplomacy. This article argues that, in contrast to his predecessor, Widodo does not perceive BDF as an instrument to promote or project democracy abroad. Rather, Widodo considers the BDF to accentuate Indonesia’s leadership role in multilateral fora. This ‘middlepowermanship’ challenges the elite-based approach in explaining Indonesia’s foreign policy, which puts a strong emphasis on Jokowi’s personal character traits. The continuation of the BDF under Widodo reflects Indonesia’s default thinking of its status as a middle power.
Staphylococcus coagulanspossesses many virulence factors ofStaph. aureusandStaph. pseudintermedius
Authors: Murugesan Ananda Chitra , Ramachandran Maya , Varughese Hridya Susan , Kumaragurubaran Karthik 
Published: March 2023

AbstractAimsTo understand the Staphylococcus coagulans prevalence in causing skin infections in dogs and detection of various virulence genes in Staph. coagulans isolates.Methods and ResultsStaph. coagulans was isolated from pus swabs collected from dogs with skin infection and identified by detecting thermonuclease, coagulase, and urease genes. The presence of methicillin-resistant gene (mecA) was performed by PCR. Antimicrobial susceptibility test was carried out by disc diffusion method. In total, 38 Staph. coagulans clinical isolates and 42 Staph. coagulans genomes available in NCBI database were screened for 19 virulence genes by PCR and in silico prediction, respectively. A prevalence of 13.8% (38/275) of Staph. coagulans dog skin infection was observed and 15.8% (6/38) of Staph. coagulans isolates carried mecA gene. Many Staph. coagulans isolates were susceptible to all tested antimicrobials. Twenty nine per cent isolates were resistant to ciprofloxacin. Genes encoding leukotoxins, DNase, exfoliative toxin, superantigen-like exotoxin, immunoglobulin-binding proteins, fibrinogen-binding proteins, autolysin, and rod shape-determining protein were detected in almost all the Staph. coagulans clinical isolates and genomes from NCBI database, whereas anti-adhesin plasma-sensitive protein genes were present in relatively lesser number of Staph. coagulans clinical isolates and genomes from NCBI database.ConclusionsStaph. coagulans possesses many virulence factors that are present in other coagulase-positive staphylococci, such as Staph. aureus and Staph. pseudintermedius. The presence of two bi-component leukotoxin genes in tandem with other virulence factor genes in a single pathogenic island in the Staph. coagulans genomes explained their eminence in the virulence of Staph. coagulans causing infections. Staph. coagulans was classified as a separate species in the year 2020 and primarily causes skin infections in dogs. Identification of this species is not included in any of the automated bacterial identification systems. Hence, many veterinary laboratories do not have a strategy to identify this bacterium. This study will help in the identification of Staph. coagulans in veterinary laboratories by PCR apart from detecting various virulence factors present in this pathogen. The existence of many virulence factors and prevalence in different animals in varied geographical locations suggest that Staph. coagulans is an important coagulase-positive staphylococcal pathogen in animals.
Probiotic lactobacilli mediate their immunoregulatory functions in intestinal cells via modulation of H3 histone acetylation
Authors: Kumari Ankita , Bhawal Shalaka , Kapila Suman , Kapila Rajeev 
Published: March 2023

AbstractAimsProbiotics are known to maintain intestinal homeostasis through the regulation of the immune response of the host. Hence, the role of histone modifications as epigenetic agents on immune modulations by potential probiotic bacteria has been investigated.Methods and ResultsHuman colonic epithelial cells (Caco-2) pre-treated with class I histone deacetylase (HDAC) specific inhibitor, MS-275, were incubated either with potential probiotic bacteria (Limosilactobacillus fermentum MTCC 5898 and Lacticaseibacillus rhamnosus MTCC 5897) or Escherichia coli (ATCC 14948) as an inflammatory agent. Initially, transcriptional expression of potential immune-related genes (IL-6, IL-8, and hBD-2) was analyzed using RT-qPCR, and later H3 histone acetylation (H3Ac) at the promoter region of these genes was confirmed with a chromatin immunoprecipitation (ChIP) assay respectively. Potential probiotic L. fermentum (MTCC 5898) significantly suppressed (P &lt; 0.05) the inhibitor-mediated elevated expression of immune-related genes while another strain L. rhamnosus (MTCC 5897), did not influence these gene expression results. In contrast, as an inflammatory agent, E. coli (ATCC 14948) synergistically augmented the expression of immune-related genes. Later, ChIP analysis confirmed the occurrence of H3 acetylation at these genes’ promoter regions, which was directly related to the transcriptional activity of host epithelial cells stimulated by L. fermentum and E. coli, respectively. But in the case of L. rhamnosus, MTCC 5897, acetylation did not follow the transcription pattern and potentiated H3Ac on the promoter regions of these genes.ConclusionsPotential probiotics used in the study were found to regulate the immune response of host cells through histone acetylation in a strain-specific manner.Significance and Impact of StudyOccurrence of probiotic-mediated regulation of immune genes by H3 acetylation in a strain-specific manner.
Isolation, identification, and evaluation of the biocontrol potential of aBacillus velezensisstrain against tobacco root rot caused byFusarium oxysporum
Authors: Li X J , Yao C X , Qiu R , Bai J K , Liu C , Chen Y G , Li S J 
Published: March 2023

AbstractAimsTobacco (Nicotiana tabacum) is an economically important crop. Root rot caused by Fusarium oxysporum has become a damaging disease in N. tabacum crops grown in Henan province of China. Therefore, the objectives of this study were to screen bacterial isolates against F. oxysporum from rhizosphere soils of tobacco growing areas and to evaluate their antifungal activities, biocontrol effects, and effects on plant growth.Methods and resultsNineteen strains with antifungal inhibition effects of &gt;60% against F. oxysporum were obtained using the method of flat confrontation; the strain Ba-0321 was the strongest, with an antifungal effect of 75%. Moreover, this strain had broad spectrum antimicrobial activity to eight additional tobacco pathogens. The strain was identified as Bacillus velezensis by morphology and the 16S rDNA sequence. The B. velezensis strain Ba-0321 had strong UV resistance as well as tolerance to high temperatures and low nutrition. The bacteria inhibited spore germination and mycelial growth of F. oxysporum under in vitro co-culture conditions. In vivo assays demonstrated that the Ba-0321 strain significantly reduced the pathogenicity of F. oxysporum, resulting in a control effect on tobacco root rot of 81.00%. Simultaneously, the bacteria significantly promoted root development and the growth of tobacco plants.ConclusionOur results confirmed that the B. velezensis strain Ba-0321 has a strong antifungal effect and stress resistance that enable it to be used as a biological control agent for tobacco root rot caused by F. oxysporum.Significance and impact of the studyTobacco root rot caused by F. oxysporum has become a damaging disease in China. The B. velezensis strain Ba-0321 has promising application value for controlling tobacco root rot diseases, and it could provide a new biocontrol agent against root rot caused by F. oxysporum in other plant species.
Distinct microbiome profiles in convergent wisdom tooth impactions
Authors: Campbell Paul M , Toedtling Verena , Humphreys Gavin J , Knight Christopher G , Devlin Hugh , McBain Andrew J 
Published: March 2023

AbstractAimsLong-term retention of impacted third molars (wisdom teeth) is associated with plaque stagnation and the development of caries on the adjacent surface of the neighboring second molar. While caries and tooth loss are common outcomes of impaction, there is currently insufficient evidence to support the pre-emptive removal of asymptomatic wisdom teeth. Emerging evidence suggests that convergently growing impactions are associated with caries. We have therefore investigated the composition of dental plaque on the distal surface of the mandibular second molar at various impaction angles.Methods and ResultsWe have compared the microbiome of these surfaces at four impaction angulations using short-read sequencing of the bacterial 16S rRNA gene: two convergent (horizontal and mesial) and two divergent (distal and vertical) angulations, and in cases where the wisdom tooth is missing. Horizontal angulations exhibited lower microbial diversity than mesial impactions. Amplicon Sequence Variants (ASVs) associated with Veillonella were significantly more abundant at impactions with angulations toward the midline. Using machine learning, a random forest classifier trained to distinguish microbiome profiles was used to predict the native angulations for a subset of samples, with samples from the two convergent impactions estimated with the greatest accuracy.ConclusionsDifferences in microbial diversity were apparent between caries-associated convergent (horizontal and mesial) impacted wisdom teeth, as well as greater abundances of Veillonella ASVs at horizontal impactions.