bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bryophyte rhizoid‐sphere microbiome responds to water deficit
Authors: Berdaguer Roland , van der Wielen Nicky , Lorenzo Zulema Carracedo , Testerink Christa , Karlova Rumyana 
Published: July 2024

AbstractThe roots of vascular plants are colonised by a multitude of microbes, which play an important role in plant health and stress resilience. Drought stress in particular is devastating for crop yield and causes major shifts in the rhizosphere microbial communities. However, the microbiome associated to the rhizoids (hereafter termed rhizoid‐sphere) of the nonvascular bryophytes remains largely unexplored. Here, we use amplicon sequencing to explore the rhizoid‐sphere microbiome of three bryophyte species under drought and well‐watered conditions. Comparing rhizoid‐sphere microbial communities associated with the two liverworts Marchantia polymorpha and Marchantia paleacea and the moss Physcomitrium patens showed characteristic differences in composition between host species and both conserved and unique changes under drought. At phylum level, these changes were similar to changes in the rhizosphere of angiosperms under drought. Furthermore, we observed strong differences in rhizoid‐sphere colonisation between bryophyte species for taxa known for nitrogen fixation and plant growth promotion. Interestingly, M. polymorpha prioritised the growth of belowground organs under osmotic stress, as is the case for angiosperms under drought. Taken together, our results show interesting parallels between bryophytes and angiosperms in the relation with their rhizo(id‐)sphere, suggesting evolutionary conservation among land plants in their response to drought stress.
Noonan syndrome‐like disorder: Case report and review of the literature
Authors: Mar Kristie , Lam Joseph M. 
Published: July 2024

AbstractOf patients with a Noonan syndrome phenotype, only about 1% are found to be related to pathological variants in CBL, also known as Noonan syndrome‐like disorder (NSLD). We present a case of a 4‐year‐old boy diagnosed with NSLD, presenting with multiple melanocytic nevi and superficial neurofibromas. A literature review identified common cutaneous findings of NSLD, for example, café‐au‐lait macules (22%), juvenile xanthogranuloma (16%), and thin hair (10%). As there are no documented cases of neurofibromas associated with NSLD, and only a single report of multiple melanocytic nevi, inclusion of these features in the phenotype may be warranted and mitigate the necessity for future biopsies in other children.
Pediatric dermatology eConsultation: Insights to reduce barriers to utilization and increase access to care
Authors: Crockett Jessica L. , Cordoro Kelly M. 
Published: July 2024

AbstractProvider‐to‐provider outpatient pediatric dermatology eConsultation services increase access to care, but barriers exist that may prevent eConsult implementation and survival. We deployed cross‐sectional surveys to referring pediatric primary care physicians and consulting pediatric dermatologists participating in our eConsult program to identify barriers to utilization and sustainability. Our data suggest that eConsultation increases access to care and offers iterative educational opportunities for primary care providers, which may ultimately reduce office referrals for common outpatient skin issues. Sustainability of eConsult services requires simple order templates, clear representative photos, concise submission reports, and provider reimbursement.
Elastography—The New Standard in the Assessment of Fibrosis After Pediatric Liver Transplantation?
Authors: Kehler Thomas , Grothues Dirk , Evert Katja , Wahlenmayer Janka , Knoppke Birgit , Melter Michael 
Published: July 2024

ABSTRACTBackgroundThe development of graft fibrosis after pediatric liver transplantation (PLT) remains a major concern as it can lead to graft failure and ultimately graft loss. Elastography is a non‐invasive method to assess liver fibrosis, but its role in the posttransplant setting is unclear. The aim of our study was to evaluate shear wave elastography (SWE) in the assessment of liver fibrosis after PLT, including split‐liver recipients.MethodsWe retrospectively analyzed data from PLT recipients who underwent surveillance liver biopsy and concurrent 2D‐SWE during the study period from April 2018 to July 2021. Spearman's correlation was used to compare histologic fibrosis stages with liver stiffness measurements (LSM) by 2D‐SWE. AUROC analysis was performed to evaluate the performance. One sample t‐test was used to compare results with reference values of healthy children.Results62 cases were included. 29% showed histologic fibrosis. LSM by 2D‐SWE were feasible in all children regardless of age or graft type. There was a significant correlation between LSM and fibrosis stage for all three scoring systems used (Ishak, p = 0.003; METAVIR, p = 0.005; LAF Score, p = 0.003). Patients with a history of biliary complications had increased liver stiffness (p = 0.015). The AUROC of 2D‐SWE for predicting significant liver graft fibrosis was 0.81. Liver stiffness after PLT without graft fibrosis was higher than in healthy subjects, but comparable to that in children with chronic liver disease without fibrosis.Conclusion2D‐SWE can reliably detect children with significant liver graft fibrosis, even in split‐liver recipients. This study demonstrates the value of a non‐invasive tool for fibrosis staging after PLT. 2D‐SWE has the potential to improve long‐term outcomes after PLT and to reduce the number of surveillance liver biopsies. But elastography is not a substitute for liver biopsy.
Risk science and politics: What is and should be the relationship?
Authors: Aven Terje 
Published: July 2024

AbstractRisk science is the most updated and justified knowledge—in the form of concepts, principles, approaches, methods, and models—for understanding, assessing, characterizing, communicating, and handling risk, with applications. It is also about the practice that gives us this knowledge. It is commonly stated that risk science is politically neutral. This perspective article discusses this assertion by scrutinizing the relationship between risk science and politics. In particular, it looks into the position of The Society for Risk Analysis (SRA) on this matter. Using some current risk problems as illustrating examples, including COVID‐19 and climate change risk, the article argues that defending the political neutrality aim is paramount, especially with today's increasingly divisive political landscape.
Oral health care for individuals with intellectual and developmental disabilities: A statewide model
Authors: Morgan John , Zavras Athanasios (Thanos) 
Published: July 2024

AbstractBackground and AimEffective strategies and practices can assist in forming future initiatives and policies to improve oral health for individuals with intellectual and developmental disabilities (IDD). This manuscript aims to describe the Tufts Dental Facilities (TDF), a university‐state collaboration providing sustained statewide access to comprehensive oral health care for individuals with IDD.Program DescriptionThe TDF program was established in 1976 as the result of a class action lawsuit to improve medical and dental care for individuals with IDD residing at state institutions in Massachusetts. TDF, A partnership, between Tufts University School of Dental Medicine (TUSDM) and the Commonwealth of Massachusetts, is a network of seven dental clinics strategically positioned across the state. These clinics are specifically designed to meet the oral health needs of individuals with IDD. TUSDM's oral health providers with expertise in special care dentistry deliver comprehensive oral health care for over 6500 individuals with IDD, incorporating supportive care services and access to general anesthesia. Additionally, the program provides training in special care dentistry for dental residents and pre‐doctoral dental students.ConclusionsLeveraging state and university resources, TDF provides a model of a sustainable, long‐term system for statewide access to oral health care for individuals with IDD.
Deep borehole discoveries beneath the Appalachian Basin: Broad Rodinian rift and Neoproterozoic tectonothermal event
Authors: Valentino David W. , Chiarenzelli Jeffrey R. , Jordan Teresa E. , Jacobi Robert D. , Gates Alexander E. 
Published: July 2024

AbstractBesides a few isolated rift basins along the Neoproterozoic eastern Laurentian margin, the Appalachian Palaeozoic strata rest unconformably on Mesoproterozoic crystalline basement, reflecting a ca. 550+ Ma hiatus. However, a nearly 3 km deep experimental geothermal borehole through the Appalachian basin at Cornell University, New York, unexpectedly encountered deformed Neoproterozoic greenschist facies phyllites and metavolcanics (Cayuta Formation) beneath the Cambrian non‐conformity. Magnetic modelling shows they are in the 5000 km2 fault‐bounded Ithaca basin, proposed to be associated with Iapetan rifting. The volcanism and metamorphism appear linked to ca. 600–650 Ma thermal events related or unrelated to extension, but requiring uplift and denudation of 5–10 km of rock prior to deposition of the Cambrian Potsdam Group. The Ithaca basin is >350 km inboard of the Laurentian Iapetus margin, indicating a broad Neoproterozoic rift zone for at least the NY and PA portion of eastern Laurentia.
A fuzzy rough approach to analyze the significance of semantic levels for building tags in OpenStreetMap
Authors: Ahmadian Somayeh , Pahlavani Parham 
Published: July 2024

AbstractIn the realm of volunteered geographic information (VGI), the existence of comparable tags, attributes, and values across diverse categories of geographic objects gives rise to major categorization challenges such as conceptual overlap and indiscernibility. Enhancing the semantic data retrieval of VGI relies on the semantic quality of descriptive content annotated for tagging geographic objects. The main focus of this study is analyzing the descriptive content of OpenStreetMap to assess the significance of semantic levels. The proposed methodology relies on fuzzy rough set calculations to determine the degrees of dependency and significance of semantic levels. Three indicators, namely, the significance of semantic levels, decreasing the heterogeneity of attributes, and replicability were defined and assessed for a subset of building‐related tags. Analyzing building‐related tags in OpenStreetMap unveiled the higher significance for simple object, similarity, purpose, and function levels. The value of decreasing the heterogeneity of attributes was calculated at 63%, and the average replicability indicator of important attributes was doubled. Based on the results, the significance of semantic levels was deemed fit to enhance semantic homogeneity and replicability.
Negative politeness and no worries in Australian English
Authors: Peters Pam , Burke Isabelle 
Published: July 2024

AbstractThis paper explores how a distinctive politeness token can establish itself in a variety of world English by virtue of its pragmatics. It examines the usage of no worries as a negative politeness thanking response in a large multigenerational corpus of informal dialogues by men and women recorded at the University of Western Australia (UWA). Data from this UWA corpus reflect the steady evolution of no worries, from its indexical association with Australian men's talk to be taken up by younger Australian women. Though rooted in laconic spoken exchanges, the data also show extended uses of no worries in quoted speech as well as narrative reconstructions of spoken encounters to highlight their outcomes. In its further linguistic evolution, it works as a stance adverbial in dramatized interior monologues. It thus acquires new functions in various discourse contexts where a modicum of negative politeness adds value to the narrative or argument.
Hybrid subconvexity bound for GL(3)×GL(2)L$GL(3)\times GL(2) \ L$‐functions: t$t$ and level aspect
Authors: Harun Mohd , Kumar Sumit , Singh Saurabh Kumar 
Published: July 2024

AbstractIn this article, we will get nontrivial estimates for the central values of degree six Rankin–Selberg ‐functions associated with a form and a form using the delta symbol approach in the hybrid level and ‐aspect.
Japanese encephalitis virus NS5 protein interacts with nucleolin to enhance the virus replication
Authors: Deb Arundhati , Nagpal Shilpi , Yadav Rajnesh Kumari , Thakur Harsh , Nair Deepak , Krishnan Vengadesan , Vrati Sudhanshu 
Published: July 2024

ABSTRACT

Japanese encephalitis virus (JEV) is an arthropod-borne, plus-strand flavivirus causing viral encephalitis in humans with a high case fatality rate. The JEV non-structural protein 5 (NS5) with the RNA-dependent RNA polymerase activity interacts with the viral and host proteins to constitute the replication complex. We have identified the multifunctional protein Nucleolin (NCL) as one of the several NS5-interacting host proteins. We demonstrate the interaction and colocalization of JEV NS5 with NCL in the virus-infected HeLa cells. The siRNA-mediated knockdown of NCL indicated that it was required for efficient viral replication. Importantly, JEV grew to higher titers in cells over-expressing exogenous NCL, demonstrating its pro-viral role. We demonstrated that NS5 interacted with the RRM and GAR domains of NCL. We show that the NCL-binding aptamer AS1411 containing the G-quadruplex (GQ) structure and the GQ ligand BRACO-19 caused significant inhibition of JEV replication. The antiviral effect of AS1411 and BRACO-19 could be overcome in HeLa cells by the overexpression of exogenous NCL. We demonstrated that the synthetic RNAs derived from the 3′-NCR of JEV genomic RNA containing the GQ sequence could bind NCL
in vitro
. The replication complex binding to the 3′-NCR is required for the viral RNA synthesis. It is likely that NCL present in the replication complex destabilizes the GQ structures in the genomic RNA, thus facilitating the movement of the replication complex resulting in efficient virus replication.

IMPORTANCE
Japanese encephalitis virus (JEV) is endemic in most parts of South-East Asia and the Western Pacific region, causing epidemics of encephalitis with a high case fatality rate. While a tissue culture-derived JEV vaccine is available, no antiviral therapy exists. The JEV NS5 protein has RNA-dependent RNA polymerase activity. Together with several host and viral proteins, it constitutes the replication complex necessary for virus replication. Understanding the interaction of NS5 with the host proteins could help design novel antivirals. We identified Nucleolin (NCL) as a crucial host protein interactor of JEV NS5 having a pro-viral role in virus replication. The NS5-interacting NCL binds to the G-quadruplex (GQ) structure sequence in the 3′-NCR of JEV RNA. This may smoothen the movement of the replication complex along the genomic RNA, thereby facilitating the virus replication. This study is the first report on how NCL, a host protein, helps in JEV replication through GQ-binding.
Cell-surface
d
-glucuronyl C5-epimerase binds to porcine deltacoronavirus spike protein facilitating viral entry
Authors: Xiao Wenwen , Chen Chaoqun , Xia Sijin , Li Zhuang , Ding Tong , Zhou Junwei , Fang Liurong , Fang Puxian , Xiao Shaobo 
Published: July 2024

ABSTRACT

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus with zoonotic potential. The coronavirus spike (S) glycoprotein, especially the S1 subunit, mediates viral entry by binding to cellular receptors. However, the functional receptor of PDCoV remains poorly understood. In this study, we used the soluble PDCoV S1 protein as bait to capture the S1-binding cellular transmembrane proteins in combined immunoprecipitation and mass spectrometry analyses. A single guide RNA screen identified
d
-glucuronyl C5-epimerase (GLCE), a heparan sulfate-modifying enzyme, as a proviral host factor for PDCoV infection. GLCE knockout significantly inhibited the attachment and internalization stages of PDCoV infection. We also demonstrated the interaction between GLCE and PDCoV S with coimmunoprecipitation in both an overexpression system and PDCoV-infected cells. GLCE could be localized to the cell membrane, and an anti-GLCE antibody suppressed PDCoV infection. Although GLCE expression alone did not render nonpermissive cells susceptible to PDCoV infection, GLCE promoted the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. In conclusion, our results demonstrate that GLCE is a novel cell-surface factor facilitating PDCoV entry and provide new insights into PDCoV infection.

IMPORTANCE

The identification of viral receptors is of great significance, potentially extending our understanding of viral infection and pathogenesis. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus with the potential for cross-species transmission. However, the receptors or coreceptors of PDCoV are still poorly understood. The present study confirms that
d
-glucuronyl C5-epimerase (GLCE) is a positive regulator of PDCoV infection, promoting viral attachment and internalization. The anti-GLCE antibody suppressed PDCoV infection. Mechanically, GLCE interacts with PDCoV S and promotes the binding of PDCoV S to porcine amino peptidase N (pAPN), acting synergistically with pAPN to enhance PDCoV infection. This work identifies GLCE as a novel cell-surface factor facilitating PDCoV entry and paves the way for further insights into the mechanisms of PDCoV infection.
Molecular insight into the neutralization mechanism of human-origin monoclonal antibody AH100 against Hantaan virus
Authors: Wang Feiran , Liu Tiezhu , Liao Liying , Chai Yan , Qi Jianxun , Gao Feng , Liang Mifang , Gao George Fu , Wu Yan 
Published: July 2024

ABSTRACT

Both Old World and New World hantaviruses are transmitted through rodents and can lead to hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome in humans without the availability of specific therapeutics. The square-shaped surface spikes of hantaviruses consist of four Gn-Gc heterodimers that are pivotal for viral entry into host cells and serve as targets for the immune system. Previously, a human-derived neutralizing monoclonal antibody, AH100, demonstrated specific neutralization against the Old World hantavirus, Hantaan virus. However, the precise mode binding of this neutralizing monoclonal antibody remains unclear. In the present study, we determined the structure of the Hantaan virus Gn-AH100 antigen-binding fragment complex and identified its epitope. Crystallography revealed that AH100 targeted the epitopes on domain A and b-ribbon and E3-like domain. Epitope mapping onto a model of the higher order (Gn-Gc)
4
spike revealed its localization between neighboring Gn protomers, distinguishing this epitope as a unique site compared to the previously reported monoclonal antibodies. This study provides crucial insights into the structural basis of hantavirus neutralizing antibody epitopes, thereby facilitating the development of therapeutic antibodies.

IMPORTANCE
Hantaan virus (HTNV) poses a significant threat to humans by causing hemorrhagic fever with renal syndrome with high mortality rates. In the absence of FDA-approved drugs or vaccines, it is urgent to develop specific therapeutics. Here, we elucidated the epitope of a human-derived neutralizing antibody, AH100, by determining the HTNV glycoprotein Gn-AH100 antigen-binding fragment (Fab) complex structure. Our findings revealed that the epitopes situated on the domain A and b-ribbon and E3-like domain of the HTNV Gn head. By modeling the complex structure in the viral lattice, we propose that AH100 neutralizes the virus by impeding conformational changes of Gn protomer, which is crucial for viral entry. Additionally, sequence analysis of all reported natural isolates indicated the absence of mutations in epitope residues, suggesting the potential neutralization ability of AH100 in diverse isolates. Therefore, our results provide novel insights into the epitope and the molecular basis of AH100 neutralization.
Conserved cysteine residues in Kaposi’s sarcoma herpesvirus ORF34 are necessary for viral production and viral pre-initiation complex formation
Authors: Watanabe Tadashi , McGraw Aidan , Narayan Kedhar , Tibebe Hasset , Kuriyama Kazushi , Nishimura Mayu , Izumi Taisuke , Fujimuro Masahiro , Ohno Shinji 
Published: July 2024

ABSTRACT

Kaposi’s sarcoma herpesvirus (KSHV) ORF34 plays a significant role as a component of the viral pre-initiation complex (vPIC), which is indispensable for late gene expression across beta- and gammaherpesviruses. Although the key role of ORF34 within the vPIC and its function as a hub protein have been recognized, further clarification regarding its specific contribution to vPIC functionality and interactions with other components is required. This study employed a deep learning algorithm-assisted structural model of ORF34, revealing highly conserved amino acid residues across human beta- and gammaherpesviruses localized in structured domains. Thus, we engineered ORF34 alanine-scanning mutants by substituting conserved residues with alanine. These mutants were evaluated for their ability to interact with other vPIC factors and restore viral production in cells harboring the ORF34-deficient KSHV-BAC. Our experimental results highlight the crucial role of the four cysteine residues conserved in ORF34: a tetrahedral arrangement consisting of a pair of C-X
n
-C consensus motifs. This suggests the potential incorporation of metal cations in interacting with ORF24 and ORF66 vPIC components, facilitating late gene transcription, and promoting overall virus production by capturing metal cations. In summary, our findings underline the essential role of conserved cysteines in KSHV ORF34 for effective vPIC assembly and viral replication, thereby enhancing our understanding of the complex interplay between the vPIC components.

IMPORTANCE
The initiation of late gene transcription is universally conserved across the beta- and gammaherpesvirus families. This process employs a viral pre-initiation complex (vPIC), which is analogous to a cellular PIC. Although KSHV ORF34 is a critical factor for viral replication and is a component of the vPIC, the specifics of vPIC formation and the essential domains crucial for its function remain unclear. Structural predictions suggest that the four conserved cysteines (C170, C175, C256, and C259) form a tetrahedron that coordinates the metal cation. We investigated the role of these conserved amino acids in interactions with other vPIC components, late gene expression, and virus production to demonstrate for the first time that these cysteines are pivotal for such functions. This discovery not only deepens our comprehensive understanding of ORF34 and vPIC dynamics but also lays the groundwork for more detailed studies on herpesvirus replication mechanisms in future research.