bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development
in planta
Authors: Atsumi Go , Naramoto Satoshi , Nishihara Masahiro , Nakatsuka Takashi , Tomita Reiko , Matsushita Yosuke , Hoshi Nobue , Shirakawa Asuka , Kobayashi Kappei , Fukuda Hiroo , Sekine Ken-Taro 
Published: September 2023

ABSTRACT

Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (
KOBU
), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in
Nicotiana benthamiana
. Transgenic gentian expressing
KOBU
exhibited tumorous symptoms, confirming the gall-forming activity of
KOBU
. Surprisingly,
KOBU
expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal
N. benthamiana
and gentian leaves. Transcriptome analysis with
Arabidopsis thaliana
expressing
KOBU
revealed that
KOBU
activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that
KOBU
is a novel pleiotropic virulence factor that stimulates vascular and leaf development.

IMPORTANCE

While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in
Nicotiana benthamiana
. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.
Evolutionary conservation of an ancient retroviral
gagpol
gene in Artiodactyla
Authors: Simpson J'Zaria , Kozak Christine A. , Boso Guney 
Published: September 2023

ABSTRACT

The genomes of mammals contain fingerprints of past infections by ancient retroviruses that invaded the germline of their ancestors. Most of these endogenous retroviruses (ERVs) contain only remnants of the original retrovirus; however, on rare occasions, ERV genes can be co-opted for a beneficial host function. While most studies of co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation, there are examples of co-opted
gag
genes including one we recently discovered in simian primates. Here, we searched for other intact
gag
genes in non-primate mammalian lineages. We began by examining the genomes of extant camel species, which represent a basal lineage in the order Artiodactyla. This identified a
gagpol
gene with a large open reading frame (ORF) (>3,500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed
ARTgagpol
, contains recognizable matrix, capsid, nucleocapsid, and reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups
ARTgagpol
with gammaretroviruses. Transcriptomic analysis shows
ARTgagpol
expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived
gagpol
gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses.

IMPORTANCE

Retroviruses are unique among viruses that infect animals as they integrate their reverse-transcribed double-stranded DNA into host chromosomes. When this happens in a germline cell, such as sperm, egg, or their precursors, the integrated retroviral copies can be passed on to the next generation as endogenous retroviruses (ERVs). On rare occasions, the genes of these ERVs can be domesticated by the host. In this study we used computational similarity searches to identify an ancient ERV with an intact viral
gagpol
gene in the genomes of camels that is also found in the same genomic location in other even-toed ungulates suggesting that it is at least 64 million years old. Broad tissue expression and predicted preservation of the reverse transcriptase fold of this protein suggest that it may be domesticated for a host function. This is the oldest known intact
gagpol
gene of an ancient retrovirus in mammals.
Astrovirus replication is dependent on induction of double-membrane vesicles through a PI3K-dependent, LC3-independent pathway
Authors: Bub Theresa , Hargest Virginia , Tan Shaoyuan , Smith Maria , Vazquez-Pagan Ana , Flerlage Tim , Brigleb Pamela , Meliopoulos Victoria , Lindenbach Brett , Ramanathan Harish N. , Cortez Valerie , Crawford Jeremy Chase , Schultz-Cherry Stacey 
Published: September 2023

ABSTRACT
Human astrovirus is a positive-sense, single-stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive-strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double-membrane vesicles (DMVs). Here, we show that astrovirus infection leads to an increase in DMV formation through a replication-dependent mechanism that requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Both chemical and genetic inhibition of the PI3K complex lead to significant reduction in DMVs, as well as viral replication. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients.

IMPORTANCE
These studies provide critical new evidence that astrovirus replication requires formation of double-membrane vesicles, which utilize class III phosphatidylinositol 3-kinase (PI3K), but not LC3 conjugation autophagy machinery, for biogenesis. These results are consistent with replication mechanisms for other positive-sense RNA viruses suggesting that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive-sense RNA virus infections.
Bioluminescent monitoring of recombinant lactic acid bacteria and their products
Authors: Choi In Young , Oh Jee-Hwan , Wang Zhiying , van Pijkeren Jan-Peter 
Published: September 2023

ABSTRACT

Biotherapeutic strategies to promote health, including the application of engineered microbes to deliver therapeutic molecules, hold strong promise. However, without precision tools to detect therapeutic microbes and their products, we are hampered in our ability to monitor and fine-tune therapeutic delivery. Here, we adapted a bioluminescent peptide tagging system for use in lactic acid bacteria, a group of organisms whose members are commonly exploited as delivery vehicles of therapeutics and vaccines. As a proof of concept, we developed various
Limosilactobacillus reuteri
strains that each produced a recombinant therapeutic protein with an 11 amino acid tag, which is essential to yield a luminescent signal. Luminescent-based quantification of recombinant protein was more sensitive than commercially available immunoassays. In addition, we demonstrated that the bioluminescent peptide tagging system allows
in situ
recombinant protein detection in a continuous-culture parallel bioreactor system. This presents an exciting opportunity to determine recombinant protein production dynamics in response to different stimuli. Finally, following oral administration of recombinant microbes, luminescence in intestinal and fecal samples allowed for rapid detection of microbes with equal sensitivity to conventional plate count. Because we demonstrated the functionality of this bioluminescent peptide tagging system in 12 species encompassing nine genera
,
our approach will create previously unexplored opportunities in lactic acid bacteria research.

IMPORTANCE

Lactic acid bacteria constitute a genetically diverse group of microorganisms with significant roles in the food industry, biotechnology, agriculture, and medicine. A core understanding of bacterial physiology in diverse environments is crucial to select and develop bacteria for industrial and medical applications. However, there is a lack of versatile tools to track (recombinant) protein production in lactic acid bacteria. In this study, we adapted a peptide-based bioluminescent tagging system that is functional across multiple genera and species. This system enables tracking of tagged proteins both
in vitro
and
in situ
, while it also can be used to enumerate recombinant bacteria from the mouse gastrointestinal tract with accuracy comparable to that of conventional plate counts. Our work expands the lactic acid bacteria genetic toolbox and will facilitate researchers in industry and academia with opportunities to monitor microbes and proteins under different physiologically relevant conditions.
Characterization of a monoclonal antibody specific to California serogroup orthobunyaviruses and development as a chimeric immunoglobulin M-positive control in human diagnostics
Authors: Powers Jordan A. , Boroughs Karen L. , Mikula Sierra , Goodman Christin H. , Davis Emily H. , Thrasher Elisa M. , Hughes Holly R. , Biggerstaff Brad J. , Calvert Amanda E. 
Published: September 2023

ABSTRACT
California serogroup viruses (CSGVs) of medical importance in the United States include La Crosse virus, Jamestown Canyon virus (JCV), California encephalitis virus, and snowshoe hare virus. Current diagnosis of CSGVs relies heavily on serologic techniques for detecting immunoglobulin M (IgM), an indication of a recent CSGV infection. However, human-positive control sera reactive to viruses in the serogroup are scarce because detection of recent infections is rare. Here, we describe the development of new murine monoclonal antibodies (MAbs) reactive to CSGVs and the engineering of a human-murine chimeric antibody by combining the variable regions of the broadly CSGV cross-reactive murine MAb, 3-3B6/2-3B2 and the constant region of the human IgM. MAb 3-3B6/2-3B2 recognizes a tertiary epitope on the Gn/Gc heterodimer, and epitopes important in JCV neutralization were mapped to the Gc glycoprotein. This engineered human IgM constitutively expressed in a HEK-293 stable cell line can replace human-positive control sera in diagnostic serological techniques such as IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA). Compared to the parent murine MAbs, the human-chimeric IgM antibody had identical serological activity to CSGVs in ELISA and demonstrated equivalent reactivity compared to human immune sera in the MAC-ELISA.

Importance
Orthobunyaviruses in the California serogroup cause severe neurological disease in children and adults. While these viruses are known to circulate widely in North America, their occurrence is rare. Serological testing for CSGVs is hindered by the limited availability and volumes of human-positive specimens needed as controls in serologic assays. Here, we described the development of a murine monoclonal antibody cross-reactive to CSGVs engineered to contain the variable regions of the murine antibody on the backbone of human IgM. The chimeric IgM produced from the stably expressing HEK293 cell line was evaluated for use as a surrogate human-positive control in a serologic diagnostic test.
Income mortality paradox by immigrants’ duration of residence in Sweden: a population register-based study
Authors: Miething Alexander , Juárez Sol P 
Published: September 2023

BackgroundStudies have shown that, compared with the general native population, immigrants display weaker or absent income gradients in mortality. The aim of this study is to examine the extent to which the income gradient is modified by immigrants’ duration of residence in Sweden.MethodsSwedish register data from 2004 to 2016 were used to study the association between individual income and all-cause mortality among foreign-born and Swedish-born individuals at ages 25–64 years. Based on relative indices of inequality (RIIs) and slope indices of inequality (SIIs) derived from Poisson regressions, we measured relative and absolute mortality differentials between the least and most advantaged income ranks. The analyses were stratified by sex, immigrants’ European or non-European origin, and immigrants’ duration of residence in Sweden.ResultsThe relative income inequality in mortality among immigrant men was less than half (RII: 2.32; 95% CI: 2.15 to 2.50) than that of Swedish-born men (RII: 6.25; 95% CI: 6.06 to 6.44). The corresponding RII among immigrant women was 1.23 (95% CI: 1.13 to 1.34) compared with an RII of 2.75 (95% CI: 2.65 to 2.86) among Swedish-born women. Inequalities in mortality were lowest among immigrants who resided for less than 10 years in Sweden, and most pronounced among immigrants who resided for more than 20 years in the country. Corresponding analyses of absolute income inequalities in mortality based on the SII were largely consistent with the observed relative inequalities in mortality.ConclusionsIncome inequalities in mortality among immigrants differ by duration of residence in Sweden, suggesting that health inequalities develop in the receiving context.
Development and validation of frailty and malnutrition knowledge assessment scale for community-dwelling older adults
Authors: Sun Xuemei , Gao Yinyan , Chen Yancong , Qin Lang , Lin Yali , Song Jinlu , Zhang Zixuan , Wang Huan , Feng Hui , Tan Hongzhuan , Chen Qiong , Peng Linlin , Dai Wenjie , Wu Irene X.Y. 
Published: September 2023

There is a lack of reliable tools to assess the knowledge of frailty and malnutrition in community-dwelling older adults. To develop and validate reliable frailty and malnutrition knowledge assessment scales for this population, two scales were developed and validated through five phases. Phase 1: the item pools were constructed through a literature review and research panel based on the symptom interpretation model. Phase 2: the expert consultation was performed to select the items. Phase 3: a pilot survey was conducted to assess the clarity of the items and further revise the scales. Phase 4: 242 older adults were surveyed to finalize the items. Phase 5: 241 older adults were surveyed to test the psychometric properties. The two scales each comprise 3 dimensions (symptoms, risk factors, and management strategies) and 11 items. They had good construct validity, with all indicators of correlation analysis and confirmatory factor analysis meeting their specific criteria. The reliability of the frailty and malnutrition knowledge assessment scales was good, with composite reliability coefficients all >0.60, Cronbach's alpha being 0.81 and 0.83, and the Spearman–Brown coefficient being 0.74 and 0.80, respectively. Their acceptability was good, with both having a completion rate of 92.18% and an average completion time of 3 min. The two scales are reliable tools to assess the knowledge of frailty and malnutrition among community-dwelling older adults, especially for large-scale surveys. They can help identify knowledge gaps in older adults and provide a basis for developing targeted educational interventions.
The evolution of the primordial curvature perturbation in the ultraslow-roll inflation
Authors: Zhao Hao-Ran , Liu Yi-Chen , Zhao Ji-Xiang , Li Nan 
Published: September 2023

AbstractA plateau on the background inflaton potential can lead inflation into the ultraslow-roll (USR) stage, during which the primordial curvature perturbation $${{{\mathscr {R}}}}$$
R
can still remarkably evolve outside the horizon. In this paper, the evolution of the Fourier mode $${{{\mathscr {R}}}}_k$$

R
k

and the resulting power spectrum $${{\mathscr {P}}}_{{{\mathscr {R}}}}(k)$$

P
R

(
k
)

are systematically investigated. It is found that, when a scale crosses the horizon well before or after the USR stage, $${{{\mathscr {R}}}}_k$$

R
k

only revolves around the origin in the complex plane. In contrast, if a scale crosses the horizon around the start of the USR stage, the argument of $${{{\mathscr {R}}}}_k$$

R
k

will be nearly frozen and $${{{\mathscr {R}}}}_k$$

R
k

will have a subsequent linear evolution accordingly, in which it may stop rather near or extremely far away from the origin, naturally explaining the entire growing stage of $${{\mathscr {P}}}_{{{\mathscr {R}}}}(k)$$

P
R

(
k
)

on small scales from the minimum to the peak. Moreover, there is a sharp dip in $${{\mathscr {P}}}_{{{\mathscr {R}}}}(k)$$

P
R

(
k
)

, but the lowest point cannot reach 0 exactly. Our work provides a whole picture for $${{{\mathscr {R}}}}_k$$

R
k

and $${{\mathscr {P}}}_{{{\mathscr {R}}}}(k)$$

P
R

(
k
)

in the USR inflation and will help our understanding of the relevant primordial black hole and gravitational wave physics.
Geodesic completeness of effective null geodesics in regular space-times with non-linear electrodynamics
Authors: Guerrero Merce , Olmo Gonzalo J. , Rubiera-Garcia Diego 
Published: September 2023

AbstractWe study the completeness of light trajectories in certain spherically symmetric regular geometries found in Palatini theories of gravity threaded by non-linear (electromagnetic) fields, which makes their propagation to happen along geodesics of an effective metric. Two types of geodesic restoration mechanisms are employed: by pushing the focal point to infinite affine distance, thus unreachable in finite time by any sets of geodesics, or by the presence of a defocusing surface associated to the development of a wormhole throat. We discuss several examples of such geometries to conclude the completeness of all such effective paths. Our results are of interest both for the finding of singularity-free solutions and for the analysis of their optical appearances e.g. in shadow observations.
Lomonosov Ridge Composite Tectono-Sedimentary Element, Arctic Ocean
Authors: Abdelmalak Mansour M. , Minakov Alexander , Faleide Jan Inge , Drachev Sergey S. 
Published: September 2023

Abstract
The Lomonosov Ridge (LR) is a sliver of continental crust, a microcontinent that stretches across the Arctic Ocean and separates the Mesozoic Amerasia Basin from the Cenozoic Eurasia Basin. The LR is thought to have been separated from the northern Barents Sea–Kara Sea passive continental margin by continental rifting at about 56–53 Ma and the subsequent formation of the oceanic crust in the Eurasia Basin. Following the nomenclature of this volume, the sedimentary succession of the LR and nearby area forms a composite tectono-sedimentary element containing an assemblage of the following main tectono-sedimentary elements (TSEs): (1) an undefined group of pre-rift TSEs mostly composed of Mesozoic and poorly known Paleozoic successions; (2) the Cretaceous–Paleocene synrift TSE; and (3) the Eocene–Holocene post-rift TSE. The age of the LR's folded and metamorphosed basement can be inferred based on correlations to basement units of the northern Eurasian passive continental margin, which may include a variety of geological structures formed during Timanian, Caledonian, late Paleozoic and Mesozoic orogenic events. The pre-rift TSE includes the oldest and most poorly known offshore sedimentary succession in the Arctic region. The lithostratigraphic units of these basins were mainly characterized from a handful samples collected at the seafloor and by correlation with better known stratigraphy of the conjugate continental margin. The synrift TSE of Cretaceous–Paleocene age has been defined based on seismic data and samples of sedimentary rocks recovered during the Arctic Coring Expedition (ACEX), as well as from seismic facies correlation between the LR and the Podvodnikov–Makarov, Laptev and East Siberian Sea basins. The post-rift Cenozoic sedimentary record was documented by the ACEX well in the central part of the LR.
Making Progress Through Disagreement: Meeting Residents Where They
Are on Climate Change
Authors: Elszasz Hayley 
Published: September 2023

Abstract
While Americans do not agree about climate change, what to do to overcome this disagreement is a topic of debate. Climate communications researchers warn that messaging must overcome the challenges of communicating scientific information to lay audiences, the uncertainty of scientific predictions, and the massive scale of climate change to be effective at mobilizing a population. Such work focuses on “top-down” communication of what the scientific reality of climate change requires of citizens: how to get them in line with what needs to happen to prevent catastrophic change. In this article, I document how nongovernmental organizations (NGOs) and community-based climate organizations (CBOs) make progress on climate action by dialoguing with their constituents and building on preexisting community connections. I argue that, instead of focusing on achieving climate consensus, these organizations rely on narratives around the local experience of environmental disruption to mobilize communities.
Are Underserved Populations Left Out of National Flood Mitigation Efforts and Facing Greater Impact? A Method to Assess Racial Inequality at the Census Tract Level
Authors: Kruczkiewicz Andrew , Hultquist Carolynne , Dutta Maya , Iyer Ryan 
Published: September 2023

Abstract
Development policies have systematically relegated certain populations to undesirable locations including areas at risk of flooding. Over time many properties will no longer be inhabitable and others will see damage from significant flooding. Current U.S. federal policy funds flood risk mitigation measures, such as property acquisition, relocation, and retrofitting; however, depending on various factors at the subcounty level, these actions can in some contexts provide disproportionate benefit to higher income, mostly White areas, failing to appropriately benefit underserved and exposed populations. Here, we present an exploratory method, building off existing research on programmatic-wide and event-specific analysis to explore patterns allowing state- and county-level decision-makers to identify inequalities in federal funding, potentially supporting reprioritization. This work evaluates the National Flood Insurance Program (NFIP) claims data from 1975 to 2019 and Federal Emergency Management Agency (FEMA) mitigation efforts from 1989 to 2018 to explore the distribution of mitigation measures related to tract to county racial disproportionalities (for example, majority non-White census tracts in majority White counties). We find that for majority non-White census tracts in majority White counties, there are disproportionately fewer NFIP claims. This supports previous work, which shows lower levels of assistance in flood recovery, resilience, and preparedness in these areas.