bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete holography‐based system for the identification of microparticles in water samples
Authors: Júnior Andouglas Gonçalves da Silva , Distante Cosimo , Gonçalves Luiz Marcos Garcia 
Published: December 2023

AbstractHere, we present a comprehensive holography‐based system designed for detecting microparticles through microscopic holographic projections of water samples. This system is designed for researchers who may be unfamiliar with holographic technology but are engaged in microparticle research, particularly in the field of water analysis. Additionally, our innovative system can be deployed for environmental monitoring as a component of an autonomous sailboat robot. Our system's primary application is for large‐scale classification of diverse microplastics that are prevalent in water bodies worldwide. This paper provides a step‐by‐step guide for constructing our system and outlines its entire processing pipeline, including hologram acquisition for image reconstruction.
Competition from informal firms and new‐to‐market product innovation: A competitive rivalry framework
Authors: Wang Kui , Wang Tao 
Published: December 2023

AbstractAlthough informal firms are rare in developed economies, they are prevalent in emerging economies and create significant competitive pressure for formal firms. Recent literature has focused on the effects of informal competition on product innovation, but the results have been inconsistent. This discordance motivated this study. Drawing on insights from competitive rivalry, this study investigates how informal competition affects formal firms’ product innovativeness (i.e., whether to develop new‐to‐market products or not). Using a sample of firms operating in Eastern Europe and Central Asia from the World Bank Enterprise Survey, we find that if formal firms encounter intense competitive pressure from informal firms, they are less inclined to develop new‐to‐market products. Furthermore, credit constraints strengthen the adverse effect of competitive pressure from informal firms on the development of new‐to‐market product innovation, but state legitimacy weakens this effect. This investigation provides insight into the barriers to innovation in emerging economies and adds to the existing literature by highlighting the need to consider the varied effects of informal competition on different types of product innovation.
Prediction of viscoelastic properties of peanut‐based 3D printable food ink
Authors: Kadival Amaresh , Mitra Jayeeta , Kaushal Manish , Machavaram Rajendra 
Published: December 2023

AbstractViscoelastic properties of 3D printable peanut‐based food ink were investigated using frequency sweep and relaxation test. The incorporation of xanthan gum (XG) improved the shear thinning behavior (n value ranging from 0.139 to 0.261) and lowered the η*, G′, and G′′ values, thus making food ink 3D printable. The addition of XG also caused a downward shift in the relaxation curve. This study evaluates the possibility of an artificial neural network (ANN) approach as a substitute for the Maxwell three‐element and Peleg model for predicting the viscoelastic behavior of food ink. The results revealed that all three models accurately predicted the decay forces. The inclusion of XG decreased the hardness and enhanced the cohesiveness, so enabling the 3D printing of food ink. The hardness was highly positively correlated with Maxwell model parameters Fe, F1, F2, F3, and Peleg constant k2 (0.57) and negatively correlated with k1 (−0.76).
Monetary policy, inflation and distributional impact: South Africa's case
Authors: Miyajima Ken 
Published: December 2023

AbstractThis paper presents further empirical support for the finding that the impact of inflation and that of policy instruments to manage inflation are not distributed equally across households of different income groups. In particular, the evidence using South African data suggests that monetary policy tightening, which seeks to maintain low and stable inflation, has a relatively modest effect on real consumption of poorer households, who tend to rely on government grants and spend larger shares of income on food stuff, while the reduction in real consumption of wealthier households is much larger. This may be due to the fact that low and stable inflation help maintain the value of government grants and cap food prices both in real terms, and higher interest rates reduce labour income, weaken asset price performance and increase debt service cost.
Twenty natural amino acid substitution screening at the last residue 121 of influenza A virus NS2 protein reveals the critical role of NS2 in promoting virus genome replication by coordinating with viral polymerase
Authors: Zhang Lei , Shao Yuekun , Wang Yingying , Yang Qiuxian , Guo Jiamei , Gao George F. , Deng Tao 
Published: December 2023

ABSTRACT

Both influenza A virus genome transcription (vRNA→mRNA) and replication (vRNA→cRNA→vRNA), catalyzed by the influenza RNA polymerase (FluPol), are dynamically regulated across the virus life cycle. It has been reported that the last amino acid I
121
of the viral NS2 protein plays a critical role in promoting viral genome replication in influenza mini-replicon systems. Here, we performed a 20 natural amino acid substitution screening at residue NS2-I
121
in the context of virus infection. We found that the hydrophobicity of the residue 121 is essential for virus survival. Interestingly, through serial passage of the rescued mutant viruses, we further identified adaptive mutations PA-K19E and PB1-S713N on FluPol which could effectively compensate for the replication-promoting defect caused by NS2-I
121
mutation in the both mini-replicon and virus infection systems. Structural analysis of different functional states of FluPol indicates that PA-K19E and PB1-S713N could stabilize the replicase conformation of FluPol. By using a cell-based NanoBiT complementary reporter assay, we further demonstrate that both wild-type NS2 and PA-K19E/PB1-S713N could enhance FluPol dimerization, which is necessary for genome replication. These results reveal the critical role NS2 plays in promoting viral genome replication by coordinating with FluPol.

IMPORTANCE

The intrinsic mechanisms of influenza RNA polymerase (FluPol) in catalyzing viral genome transcription and replication have been largely resolved. However, the mechanisms of how transcription and replication are dynamically regulated remain elusive. We recently reported that the last amino acid of the viral NS2 protein plays a critical role in promoting viral genome replication in an influenza mini-replicon system. Here, we conducted a 20 amino acid substitution screening at the last residue 121 in virus rescue and serial passage. Our results demonstrate that the replication-promoting function of NS2 is important for virus survival and efficient multiplication. We further show evidence that NS2 and NS2-I
121
adaptive mutations PA-K19E/PB1-S713N regulate virus genome replication by promoting FluPol dimerization. This work highlights the coordination between NS2 and FluPol in fulfilling efficient genome replication. It further advances our understanding of the regulation of viral RNA synthesis for influenza A virus.
EFHD2 cooperates with E3 ubiquitin ligase Smurf1 to facilitate virus infection by promoting the degradation of TRAF6 in teleost fish
Authors: Wang Pengfei , Li Ye , Sun Yuena , Xu Tianjun 
Published: December 2023

ABSTRACT

The ubiquitin-proteasome system is one of the most important protein stability regulation systems. It can precisely regulate host immune responses by targeting signaling proteins. TRAF6 is a crucial E3 ubiquitin ligase in host antiviral signaling pathway. Here, we discovered that EF-hand domain-containing protein D2 (EFHD2) collaborated with the E3 ubiquitin ligase Smurf1 to potentiate the degradation of TRAF6, hence facilitating RNA virus
Siniperca chuatsi
rhabdovirus infection. The mechanism analysis revealed that EFHD2 interacted with Smurf1 and enhanced its protein stability by impairing K48-linked polyubiquitination of Smurf1, thereby promoting Smurf1-catalyzed degradation of TRAF6. This study initially demonstrated a novel mechanism by which viruses utilize host EFHD2 to achieve immune escape and provided a new perspective on the exploration of mammalian innate immunity.

IMPORTANCE
Viruses induce host cells to activate several antiviral signaling pathways. TNF receptor-associated factor 6 (TRAF6) plays an essential role in these pathways. Numerous studies have been done on the mechanisms of TRAF6-mediated resistance to viral invasion. However, little is known about the strategies that viruses employ to antagonize TRAF6-mediated antiviral signaling pathway. Here, we discovered that EFHD2 functions as a host factor to promote viral replication. Mechanistically, EFHD2 potentiates Smurf1 to catalyze the ubiquitin-proteasomal degradation of TRAF6 by promoting the deubiquitination and stability of Smurf1, which in turn inhibits the production of proinflammatory cytokines and interferons. Our study also provides a new perspective on mammalian resistance to viral invasion.
Host factor MxA restricts Dabie bandavirus infection by targeting the viral NP protein to inhibit NP-RdRp interaction and ribonucleoprotein activity
Authors: Chang Meng , Min Yuan-Qin , Xu Zhao , Deng Fei , Wang Hualin , Ning Yun-Jia 
Published: December 2023

ABSTRACT
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with high case mortality rates, which is caused by Dabie bandavirus (DBV), a novel pathogen also termed as SFTS virus (SFTSV). Currently, no specific therapeutic drugs or vaccines are available for SFTS. Myxovirus resistance protein A (MxA) has been shown to inhibit multiple viral pathogens; however, the role of MxA in DBV infection is unknown. Here, we demonstrated that DBV stimulates MxA expression which, in turn, restricts DBV infection. Mechanistic target analysis revealed that MxA specifically interacts with the viral nucleocapsid protein (NP) in a manner independent of RNA. Minigenome reporter assay showed that in agreement with its targeting of NP, MxA inhibits DBV ribonucleoprotein (RNP) activity. In detail, MxA interacts with the NP N-terminal and disrupts the interaction of NP with the viral RNA-dependent RNA polymerase (RdRp) but not NP multimerization, the critical activities of NP for RNP formation and function. Furthermore, MxA N-terminal domain was identified as the functional domain inhibiting DBV infection, and, consistently, then was shown to interact with NP and obstruct the NP-RdRp interaction. Additionally, threonine 103 within the N-terminal domain is important for MxA inhibition to DBV, and its mutation (T103A) attenuates MxA binding to NP and obstruction of the NP-RdRp interaction. This study uncovers MxA inhibition of DBV with a series of functional and mechanistical analyses, providing insights into the virus−host interactions and probably helping inform the development of antiviral agents in the future.

IMPORTANCE
DBV/SFTSV is an emerging high-pathogenic virus. Since its first identification in China in 2009, cases of DBV infection have been reported in many other countries, posing a significant threat to public health. Uncovering the mechanisms of DBV-host interactions is necessary to understand the viral pathogenesis and host response and may advance the development of antiviral therapeutics. Here, we found that host factor MxA whose expression is induced by DBV restricts the virus infection. Mechanistically, MxA specifically interacts with the viral NP and blocks the NP-RdRp interaction, inhibiting the viral RNP activity. Further studies identified the key domain and amino acid residue required for MxA inhibition to DBV. Consistently, they were then shown to be important for MxA targeting of NP and obstruction of the NP-RdRp association. These findings unravel the restrictive role of MxA in DBV infection and the underlying mechanism, expanding our knowledge of the virus-host interactions.
Selective whole-genome sequencing of
Plasmodium
parasites directly from blood samples by nanopore adaptive sampling
Authors: De Meulenaere Katlijn , Cuypers Wim L. , Gauglitz Julia M. , Guetens Pieter , Rosanas-Urgell Anna , Laukens Kris , Cuypers Bart 
Published: December 2023

ABSTRACT

Whole-genome sequencing of
Plasmodium
is becoming an increasingly important tool for genomic surveillance of malaria. Due to the predominance of human DNA in a patient blood sample, time-consuming laboratory procedures are required to deplete human DNA or enrich
Plasmodium
DNA. Here, we investigated the potential of nanopore adaptive sampling to enrich
Plasmodium falciparum
reads while sequencing unenriched patient blood samples. To compare adaptive sampling versus regular sequencing on a MinION device, a dilution series consisting of 0%–84%
P
.
falciparum
DNA in human DNA was sequenced. Half of the flow cell channels were run in adaptive sampling mode, enriching for the
P. falciparum
reference genome, resulting in a three- to five-fold enrichment of
P. falciparum
bases in samples containing 0.1%–8.4%
P. falciparum
DNA. This finding was confirmed by sequencing three
P. falciparum
patient blood samples with common levels of parasitemia, that is, 0.1%, 0.2%, and 0.6% in adaptive mode. Their estimated enrichment was 5.8, 3.9, and 2.7, respectively, which was sufficient to cover at least 97% of the
P. falciparum
reference genome at a median depth of 5 (lowest parasitemia) or 355 (highest parasitemia). In all, 38 drug resistance loci were compared to Sanger sequencing results, showing high concordance, which suggests that the obtained sequencing data are of sufficient quality to address common clinical research questions for patients with parasitemias of 0.1% and higher. Overall, our results indicate that adaptive nanopore sequencing has the potential to replace more time-consuming
Plasmodium
enrichment protocols in the future.

IMPORTANCE

Malaria is caused by parasites of the genus
Plasmodium
, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich
Plasmodium
DNA. We used the Oxford Nanopore Technologies’ adaptive sampling feature to circumvent this problem and enrich
Plasmodium
reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches
Plasmodium
reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.
Crosstalk between glucagon-like peptide 1 and gut microbiota in metabolic diseases
Authors: Zeng Yuan , Wu Yifan , Zhang Qian , Xiao Xinhua 
Published: December 2023

ABSTRACT
Gut microbiota exert influence on gastrointestinal mucosal permeability, bile acid metabolism, short-chain fatty acid synthesis, dietary fiber fermentation, and farnesoid X receptor/Takeda G protein-coupled receptor 5 (TGR5) signal transduction. The incretin glucagon-like peptide 1 (GLP-1) is mainly produced by L cells in the gut and regulates postprandial blood glucose. Changes in gut microbiota composition and function have been observed in obesity and type 2 diabetes (T2D). Meanwhile, the function and rhythm of GLP-1 have also been affected in subjects with obesity or T2D. Therefore, it is necessary to discuss the link between the gut microbiome and GLP-1. In this review, we describe the interaction between GLP-1 and the gut microbiota in metabolic diseases. On the one hand, gut microbiota metabolites stimulate GLP-1 secretion, and gut microbiota affect GLP-1 function and rhythm. On the other hand, the mechanism of action of GLP-1 on gut microbiota involves the inflammatory response. Additionally, we discuss the effects and mechanism of various interventions, such as prebiotics, probiotics, antidiabetic drugs, and bariatric surgery, on the crosstalk between gut microbiota and GLP-1. Finally, we stress that gut microbiota can be used as a target for metabolic diseases, and the clinical application of GLP-1 receptor agonists should be individualized.
Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation
Authors: Chong Trisha N. , Panjalingam Mayura , Saurabh Saumya , Shapiro Lucy 
Published: December 2023

ABSTRACT

Cell differentiation is an essential biological process that is subject to strict temporal regulation.
Caulobacter crescentus
undergoes obligate differentiation from a swarmer cell to a stationary, replication-competent stalked cell with each cell cycle. We report that the switch from phosphatase to kinase activity of the histidine kinase PleC contributes to timing this differentiation event. PleC
P
er-
A
rnt-
S
im (PAS) domain interaction with the polar scaffold protein PodJ localizes PleC to the cell pole and inhibits
in vivo
kinase activity. Upon PodJ degradation, released PleC switches to its kinase form and phosphorylates the PleD diguanylate cyclase, initiating the signaling pathway responsible for differentiation. While PodJ inhibits PleC kinase activity, it does not impact PleC phosphatase activity on DivK, which is required for pili biogenesis and flagellar rotation. Thus, PleC PAS domains affect enzymatic function on diverse substrates by relying on context-dependent binding partners, thereby controlling the timing of
Caulobacter
cell differentiation.

IMPORTANCE

The process of cell differentiation is highly regulated in both prokaryotic and eukaryotic organisms. The aquatic bacterium,
Caulobacter crescentus
, undergoes programmed cell differentiation from a motile swarmer cell to a stationary stalked cell with each cell cycle. This critical event is regulated at multiple levels. Kinase activity of the bifunctional enzyme, PleC, is limited to a brief period when it initiates the molecular signaling cascade that results in cell differentiation. Conversely, PleC phosphatase activity is required for pili formation and flagellar rotation. We show that PleC is localized to the flagellar pole by the scaffold protein, PodJ, which is known to suppress PleC kinase activity
in vitro
. PleC mutants that are unable to bind PodJ have increased kinase activity
in vivo
, resulting in premature differentiation. We propose a model in which PodJ regulation of PleC’s enzymatic activity contributes to the robust timing of cell differentiation during the
Caulobacter
cell cycle.
Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen
Authors: Kang Zhiwei , Martinson Vincent G. , Wang Yin , Coon Kerri L. , Valzania Luca , Strand Michael R. 
Published: December 2023

ABSTRACT

Increased diversity in host-associated microbial communities often benefits animal health by provisioning nutrients and protecting against pathogens. In contrast, whether the diversity of environmental microbial communities can also benefit animal health is much less studied. In aquatic environments, water enables environmental microbes to more directly interact with pathogens and animals than in terrestrial environments, which also suggests the potential for community diversity to benefit animal health. In this study, we addressed this question by identifying a strain of
Chromobacterium haemolyticum
named Rain 0013 (
Ch_
R13) that is a virulent pathogen of mosquito larvae, which live in aquatic habitats. Comparative genomic and functional data suggested many
Chromobacterium
are both mosquitocidal and opportunistic pathogens of other animals due to conservation of virulence factors that include a broad-spectrum toxin (cyanide). However, we also identified a strongly negative correlation between diversity of the environmental microbiota and disease severity due to
Ch_
R13 needing to achieve a threshold density to kill mosquito larvae. Experiments using defined (gnotobiotic) microbial communities further suggested certain environmental community members reduced
Ch_
R13 densities more than others. Altogether, our results indicate
Ch_
R13 and other
Chromobacterium
have the potential to broadly cause disease but the environmental communities of microbes in aquatic habitats attenuate disease risk.

IMPORTANCE

The host-specific microbiotas of animals can both reduce and increase disease risks from pathogens. In contrast, how environmental microbial communities affect pathogens is largely unexplored. Aquatic habitats are of interest because water enables environmental microbes to readily interact with animal pathogens. Here, we focused on mosquitoes, which are important disease vectors as terrestrial adults but are strictly aquatic as larvae. We identified a pathogen of mosquito larvae from the field as a strain of
Chromobacterium haemolyticum
. Comparative genomic analyses and functional assays indicate this strain and other
Chromobacterium
are mosquitocidal but are also opportunistic pathogens of other animals. We also identify a critical role for diversity of the environmental microbiota in disease risk. Our study characterizes both the virulence mechanisms of a pathogen and the role of the environmental microbiota in disease risk to an aquatic animal of significant importance to human health.
Intraocular pressure reduction and progression of highly myopic glaucoma: a 12-year follow-up cohort study
Authors: Shin Young In , Kim Young Kook , Jeoung Jin Wook , Park Ki Ho 
Published: December 2023

AimsTo investigate any association between intraocular pressure (IOP) reduction amount and open-angle glaucoma (OAG) progression in highly myopic eyes and to determine the associated risk factors.MethodsOne hundred and thirty-one (131) eyes of 131 patients with highly myopic OAG, all of whom had received topical medications and been followed for 5 years or longer, were enrolled. Based on the IOP reduction percentage, patients were categorised into tertile groups, and subsequently, the upper-tertile and lower-tertile groups were compared for the cumulative probability of glaucoma progression. Kaplan-Meier survival analysis and log-rank testing were applied in the comparison, and multivariate analysis with Cox’s proportional hazard model, additionally, was performed to identify progression risk factors.ResultsThroughout the average 11.6±4.4 year follow-up on the 131 eyes (mean age, 41.2 years at initial visit; baseline IOP, 16.4 mm Hg), 72 eyes (55.0%) showed glaucoma progression. The upper-tertile group (IOP reduction percentage>23.7%) showed a high cumulative probability of non-progression relative to the lower-tertile group (IOP reduction percentage<11.0%; p=0.034), according to the Kaplan-Meier analysis. Presence of disc haemorrhage (DH; HR=2.189; p=0.032) was determined by the multivariate Cox’s proportional hazard model to be significantly associated with glaucoma progression. For progressors, the average rate of retinal nerve fibre layer thickness thinning was −0.88±0.74 µm/year, while the MD change was −0.42±0.36 dB/year.ConclusionsGlaucoma progression is associated with amount of IOP reduction by topical medications in highly myopic eyes, and DH occurrence is a glaucoma progression risk factor.