bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural decoding, the Atlantis machine, and zombies
Authors: Cao Rosa , Warren Jared 
Published: October 2023

AbstractNeural decoding studies seem to show that the “private” experiences of others are more accessible than philosophers have traditionally believed. While these studies have many limitations, they do demonstrate that by capturing patterns in brain activity, we can discover a great deal about what a subject is experiencing. We present a thought experiment about a super‐decoder — the Atlantis machine — and argue that given plausible assumptions, an Atlantis machine could one day be built. On the basis of this argument, we then argue for the rejection of robust notions of consciousness, which have generated numerous puzzles, including puzzles about the possibility of philosophical zombies. In light of the Atlantis machine, it can be seen that robust notions of consciousness do not earn their explanatory or descriptive keep. More modest concepts of consciousness are sufficient to account for all phenomena — in both senses of the term. This kind of antirobustness about consciousness is a deflationary approach to conscious experience that differs in important ways from illusionist approaches.
Wicked policy problems and COVID‐19 in small island developing states: The cases of Mauritius and Seychelles
Authors: Kasseeah Harshana , Opp Susan 
Published: October 2023

AbstractThe COVID‐19 pandemic represented one of the most significant wicked policy problems in modern history. Global policy efforts to combat the pandemic reflect a diverse set of approaches, with varying underlying goals and values driving the policy choices. This article studies the pandemic response of two small island developing states, Mauritius and Seychelles, to better understand the policy landscape in this understudied African region. Evidence from these two island nations provides important insights into the opportunities and constraints faced by island developing states. Using in‐depth qualitative interviews with policy actors and reviews of official policy documents, this article studies the policy landscape of these two small island developing states. Findings from this research offer insights for scholars and practitioners interested in the intersection of wicked problems and policy.Related ArticlesOnyango, Gedion, and Japheth Otieno Ondiek. 2022. “Open Innovation during the COVID‐19 Pandemic Policy Responses in South Africa and Kenya.” Politics & Policy 50(5): 1008–31. https://doi.org/10.1111/polp.12490.Vince, Joanna. 2023. “A Creeping Crisis When an Urgent Crisis Arises: The Reprioritization of Plastic Pollution Issues during COVID‐19.” Politics & Policy 51(1): 26–40. https://doi.org/10.1111/polp.12512.Kinyondo, Abel, and Riccardo Pelizzo. 2013. “Strengthening Legislatures: Some Lessons from the Pacific Region.” Politics & Policy 41(3): 420–46. https://doi.org/10.1111/polp.12020.
Immoral, infectious, or both? How disgust sensitivity predicts judgments of violations against COVID‐19 mitigation actions
Authors: Schwarz Sascha , Klümper Lisa , Jansen Markus Thomas , Agthe Maria 
Published: October 2023

AbstractViolations against mitigation actions to prevent the spreading of the SARS‐CoV‐2 virus causing COVID‐19, such as not wearing a mask or not practicing social distancing, were seen as immoral and could also increase the likelihood of spreading the virus. In two studies (N1 = 318, N2 = 293), we found that moral and pathogen disgust sensitivity differentially predicted perceptions of such COVID‐19 violations against mitigation actions, framed as a moral, pathogen, or on a good‐bad dimension, albeit in a less specific way than initially hypothesized (e.g., regarding the pathogenic framed violations, not only pathogen but also moral disgust was associated with higher perceptions of infectiousness). These results suggest that individual differences, especially in pathogen disgust (and, more inconsistently, moral disgust), are important when evaluating violations against mitigation actions. Further research on the role of moral disgust is needed.
Correlation of multiplicative functions over Fq[x]$\mathbb {F}_q[x]$: A pretentious approach
Authors: Darbar Pranendu , Mukhopadhyay Anirban 
Published: October 2023

AbstractLet denote the set of monic polynomials of degree n over a finite field of q elements. For multiplicative functions , using the recently developed “pretentious method,” we establish a “local‐global” principle for correlation functions of the form
where are fixed polynomials. These results were then applied to find limiting distributions of sums of additive functions. We also study correlations with Dirichlet characters and Hayes characters. As a consequence, we give a new proof of a function field analog of Kátai's conjecture that states that if the average of the first divided difference of a completely multiplicative function whose values lie on the unit circle is zero, then it must be a Hayes character. We further extend this result to pairs and triplets of completely multiplicative functions.
An Electro-Chemo-Mechanical Theory With Flexoelectricity: Application to Ionic Conductivity of Soft Solid Electrolytes
Authors: Mathew Anand , Kulkarni Yashashree 
Published: October 2023

Abstract
Flexible batteries are gaining momentum in several fields, including wearable medical devices and biomedical sensors, flexible displays, and smartwatches. These energy storage devices are subjected to electro-chemo-mechanical effects. Here, we present a theoretical framework that couples diffusion and electromechanical theory with flexoelectricity. As an example, we investigate the effect of flexoelectricity on the ionic conductivity in soft materials. Our analytical results for a thin film made of a soft material reveal that the ionic conductivity is significantly higher at the nanoscale and decreases exponentially to approach the bulk value with increasing film thickness. Furthermore, we find that flexoelectricity reduces the ionic conductivity dramatically at film thickness smaller than the length scale associated with flexoelectricity. This behavior is attributed to the opposite directions of polarization induced by flexoelectricity and the flow of ions driven by the chemical potential. These findings shed light on the interplay between flexoelectricity and diffusion which would be paramount in designing miniaturized energy storage devices.
A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC
Authors: de Hoog Sybren , Walsh Thomas J. , Ahmed Sarah A. , Alastruey-Izquierdo Ana , Alexander Barbara D. , Arendrup Maiken Cavling , Babady Esther , Bai Feng-Yan , Balada-Llasat Joan-Miquel , Borman Andrew , Chowdhary Anuradha , Clark Andrew , Colgrove Robert C. , Cornely Oliver A. , Dingle Tanis C. , Dufresne Philippe J. , Fuller Jeff , Gangneux Jean-Pierre , Gibas Connie , Glasgow Heather , Gräser Yvonne , Guillot Jacques , Groll Andreas H. , Haase Gerhard , Hanson Kimberly , Harrington Amanda , Hawksworth David L. , Hayden Randall T. , Hoenigl Martin , Hubka Vit , Johnson Kristie , Kus Julianne V. , Li Ruoyu , Meis Jacques F. , Lackner Michaela , Lanternier Fanny , Leal Jr. Sixto M. , Lee Francesca , Lockhart Shawn R. , Luethy Paul , Martin Isabella , Kwon-Chung Kyung J. , Meyer Wieland , Nguyen M. Hong , Ostrosky-Zeichner Luis , Palavecino Elizabeth , Pancholi Preeti , Pappas Peter G. , Procop Gary W. , Redhead Scott A. , Rhoads Daniel D. , Riedel Stefan , Stevens Bryan , Sullivan Kaede Ota , Vergidis Paschalis , Roilides Emmanuel , Seyedmousavi Amir , Tao Lili , Vicente Vania A. , Vitale Roxana G. , Wang Qi-Ming , Wengenack Nancy L. , Westblade Lars , Wiederhold Nathan , White Lewis , Wojewoda Christina M. , Zhang Sean X. 
Published: October 2023

ABSTRACT
The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.
Alphavirus-based replicons demonstrate different interactions with host cells and can be optimized to increase protein expression
Authors: Dominguez Francisco , Palchevska Oksana , Frolova Elena I. , Frolov Ilya 
Published: October 2023

ABSTRACT
Alphaviruses have been used as vectors for the expression of heterologous genetic information for a few decades. Their genomes contain two open reading frames. One of these encodes viral nonstructural proteins (nsPs), which mediate the replication of viral genome (G RNA) and synthesis of subgenomic (SG) RNA. Viral structural proteins encoded by SG RNA are dispensable for G RNA replication and transcription of the SG RNA. Their genes can be replaced by heterologous genetic materials. Such defective viral genomes, replicons, can efficiently express the encoded heterologous genes of interest. Within recent years, alphavirus replicons, also termed self-amplifying RNAs (saRNAs), attracted additional attention as a tool to increase the expression level of mRNA vaccines. The results of this study demonstrate that replicons derived from both New World and Old World alphaviruses can efficiently express heterologous genetic information. However, the levels of expression are cell-specific and are strongly determined by the origin of the replicons. Moreover, replication of alphavirus replicons mimics many aspects of alphavirus infections in terms of virus-host interactions and induction of the innate immune response. They also express viral nsPs that may induce vector immunity. These characteristics need to be carefully examined before the wide application of saRNAs. On the other hand, the data show that alphavirus replicons are very flexible expression systems. The efficiencies of protein expression and interactions with host cells can be manipulated by introducing mutations into nsPs and other modifications in replicon genomes.

IMPORTANCE
Alphavirus replicons are being developed as self-amplifying RNAs aimed at improving the efficacy of mRNA vaccines. These replicons are convenient for genetic manipulations and can express heterologous genetic information more efficiently and for a longer time than standard mRNAs. However, replicons mimic many aspects of viral replication in terms of induction of innate immune response, modification of cellular transcription and translation, and expression of nonstructural viral genes. Moreover, all replicons used in this study demonstrated expression of heterologous genes in cell- and replicon’s origin-specific modes. Thus, many aspects of the interactions between replicons and the host remain insufficiently investigated, and further studies are needed to understand the biology of the replicons and their applicability for designing a new generation of mRNA vaccines. On the other hand, our data show that replicons are very flexible expression systems, and additional modifications may have strong positive impacts on protein expression.
Duck Tembusu virus NS3 protein induces apoptosis by activating the PERK/PKR pathway and mitochondrial pathway
Authors: Pan Yuhong , Cai Wenjun , Cheng Anchun , Wang Mingshu , Huang Juan , Chen Shun , Yang Qiao , Wu Ying , Sun Di , Mao Sai , Zhu Dekang , Liu Mafeng , Zhao Xinxin , Zhang Shaqiu , Gao Qun , Ou Xumin , Tian Bin , Yin Zhongqiong , Jia Renyong 
Published: October 2023

ABSTRACT
Duck Tembusu virus (DTMUV) infection causes severe infectious diseases in poultry and can induce apoptosis in host cells. In this study, the mechanisms underlying DTMUV-induced apoptosis were investigated. First, DTMUV infection can activate the endoplasmic reticulum stress (ERS), and administration of the ERS inhibitor 4-phenylbutyric acid can protect cells from DTMUV-induced apoptosis, indicating that ERS is involved in DTMUV-induced apoptosis. Interestingly, suppression of either apoptosis or ERS led to impaired DTMUV proliferation. Then, we found that DTMUV activated three branches of unfolded protein response signaling [RNA-activated protein kinase-like endoplasmic reticulum kinase (PERK), inositol-requiring enzyme 1, and activating transcription factor 6] in duck embryo fibroblasts. Further study revealed that activation of PERK-eukaryotic initiation factor 2α up-regulated CCAAT/enhancer-binding protein homologous protein and DNA damage-inducible protein 34, which subsequently promoted apoptosis. Moreover, we found that among the DTMUV viral proteins, the nonstructural protein 3 (NS3) is the main inducer of apoptosis. On the one hand, the PERK/PKR pathway is involved in the NS3-mediated mitochondrial apoptosis pathway. On the other hand, NS3 interacts with voltage-dependent anion channel 2 (VDAC2) and inhibits the anti-apoptotic protein VDAC2 to induce apoptosis, which is accompanied by the depolarization of mitochondrial membrane potential and accumulation of intracellular reactive oxygen species. This study provides a theoretical basis for revealing the pathogenic mechanism of DTMUV infection and lays a foundation for finding antiviral targets.

IMPORTANCE

Duck Tembusu virus (DTMUV) is an emerging pathogenic flavivirus that replicates well in mosquito, bird, and mammalian cells. An
in vivo
study revealed that BALB/c mice and Kunming mice were susceptible to DTMUV after intracerebral inoculation. Moreover, there are no reports about DTMUV-related human disease, but antibodies against DTMUV and viral RNA were detected in the serum samples of duck industry workers. This information implies that DTMUV has expanded its host range and poses a threat to mammalian health. Thus, understanding the pathogenic mechanism of DTMUV is crucial for identifying potential antiviral targets. In this study, we discovered that NS3 can induce the mitochondria-mediated apoptotic pathway through the PERK/PKR pathway; it can also interact with voltage-dependent anion channel 2 to induce apoptosis. Our findings provide a theoretical basis for understanding the pathogenic mechanism of DTMUV infection and identifying potential antiviral targets and may also serve as a reference for exploring the pathogenesis of other flaviviruses.
Adaptation to bile and anaerobicity limits
Vibrio cholerae
phage adsorption
Authors: Netter Zoe , Dunham Drew T. , Seed Kimberley D. 
Published: October 2023

ABSTRACT

Bacteriophages (viruses of bacteria) play a pivotal role in shaping both the evolution and dynamics of bacterial populations. Bacteria employ arsenals of genetically encoded phage defense systems, but can alternatively achieve protection by changing the availability of cellular resources that phages rely on for propagation. These physiological changes are often adaptive responses to unique environmental signals. The facultative pathogen
Vibrio cholerae
adapts to both aquatic and intestinal environments with niche-specific physiological changes that ensure its evolutionary success in such disparate settings. In both niches,
V. cholerae
is susceptible to predation by lytic phages like ICP1. However, both phages and susceptible bacterial hosts coexist in nature, indicating that environmental cues may modulate
V. cholerae
cell state to protect against phage infection. This work explores one such modification in response to the intestine-specific signals of bile and anaerobicity. We found that
V. cholerae
grown in these conditions reduces O1-antigen decoration on its outer membrane lipopolysaccharide. Because the O1-antigen is an essential moiety for ICP1 phage infection, we investigated the effect of partial O1-antigen depletion as a mechanism of phage defense and observed that O1-depletion limits phage adsorption. We identified mechanistic contributions to O1-depletion, including the essentiality of a weak acid tolerance system for O1 production at low pH and alterations in transcriptional profiles indicating limitations in resources for O1-biosynthesis. This analysis illustrates a complex interplay between signals relevant to the intestinal environment and bacterial physiology that provides
V. cholerae
with protection from phage predation.

IMPORTANCE

Vibrio cholerae
is the bacterial pathogen responsible for cholera, a diarrheal disease that impacts people in areas without access to potable water. In regions that lack such infrastructure, cholera represents a large proportion of disease outbreaks. Bacteriophages (phages, viruses that infect bacteria) have recently been examined as potential therapeutic and prophylactic agents to treat and prevent bacterial disease outbreaks like cholera due to their specificity and stability. This work examines the interaction between
V. cholerae
and vibriophages in consideration for a cholera prophylaxis regimen (M. Yen, L. S. Cairns, and A. Camilli, Nat Commun 8:14187, 2017,
https://doi.org/10.1038/ncomms14187
) in the context of stimuli found in the intestinal environment. We discover that common signals in the intestinal environment induce cell surface modifications in
V. cholerae
that also restrict some phages from binding and initiating infection. These findings could impact considerations for the design of phage-based treatments, as phage infection appears to be limited by bacterial adaptations to the intestinal environment.
Genome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by
Klebsiella pneumoniae
Authors: Cheung Bettina H. , Alisoltani Arghavan , Kochan Travis J. , Lebrun-Corbin Marine , Nozick Sophia H. , Axline Christopher M. R. , Bachta Kelly E. R. , Ozer Egon A. , Hauser Alan R. 
Published: October 2023

ABSTRACT

Gastrointestinal (GI) colonization by
Klebsiella pneumoniae
is a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. Thus, we aimed to study strain-specific requirements for
K. pneumoniae
GI colonization by applying transposon insertion sequencing to three classical clinical strains: a carbapenem-resistant strain, an extended-spectrum beta-lactamase-producing strain, and a non-epidemic antibiotic-susceptible strain. The transposon insertion libraries were screened in a murine model of GI colonization. At 3 days post-inoculation, 27 genes were required by all three strains for colonization. Isogenic deletion mutants for three genes/operons (
acrA
,
carAB
, and
tatABCD
) confirmed colonization defects in each of the three strains. Additionally, deletion of
acrA
reduced bile tolerance
in vitro
, while complementation restored both bile tolerance
in vitro
and colonization ability
in vivo
. Transposon insertion sequencing suggested that some genes were more important for the colonization of one strain than the others. For example, deletion of the sucrose porin-encoding gene
scrY
resulted in a colonization defect in the carbapenemase-producing strain but not in the extended-spectrum beta-lactamase producer or the antibiotic-susceptible strain. These findings demonstrate that classical
K. pneumoniae
strains use both shared and strain-specific strategies to colonize the mouse GI tract.

IMPORTANCE

Klebsiella pneumoniae
is a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistant
K. pneumoniae
has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization in patients with
K. pneumoniae
has been linked to subsequent infection, making it a key process to control in the prevention of multidrug-resistant infections. However, the bacterial factors which contribute to
K. pneumoniae
colonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain dependent. This study identifies the enteric colonization factors of three classical strains using transposon mutant screens to define a core colonization program for
K. pneumoniae
as well as detecting strain-to-strain differences in colonization strategies.
Contrasting roles of MERS-CoV and SARS-CoV-2 internal proteins in pathogenesis in mice
Authors: Wong Lok-Yin Roy , Odle Abby , Luhmann Emma , Wu Douglas C. , Wang Yiquan , Teo Qi Wen , Ptak Celeste , Sariol Alan , Lowery Shea , Mack Matthias , Meyerholz David K. , Wu Nicholas C. , Radoshevich Lilliana , Perlman Stanley 
Published: October 2023

ABSTRACT

Betacoronaviruses encode an internal (I) gene via an alternative reading frame within the nucleocapsid gene, called ORF8b for
M
iddle-
E
ast
r
espiratory
s
yndrome
c
oronavirus (MERS-CoV) and ORF9b for
s
evere
a
cute
r
espiratory
s
yndrome
c
oronavirus (SARS-CoV) and SARS-CoV-2. Previous reports suggested that proteins 8b and 9b are involved in evading multiple innate immune signaling pathways. However, their roles in mediating pathogenesis in infected animals have not been determined. In this study, we abrogated the expression of protein 8b in MERS-CoV and protein 9b in SARS-CoV-2. Using mouse models of MERS-CoV and SARS-CoV-2 infection, we found that MERS-CoV lacking protein 8b expression was more virulent, while SARS-CoV-2 lacking protein 9b expression was attenuated compared with the respective wild-type viruses. Upon further analysis, we detected increased levels of type I interferon and enhanced infiltration of immune cells to the lungs of mice infected with MERS-CoV lacking protein 8b expression. These data suggest that the I protein of MERS-CoV plays a role in limiting pathogenesis while that of SARS-CoV-2 enhances disease severity.

IMPORTANCE

The function of betacoronavirus internal protein has been relatively understudied. The earliest report on the internal protein of mouse hepatitis virus suggested that the internal protein is a structural protein without significant functions in virus replication and virulence. However, the internal proteins of
s
evere
a
cute
r
espiratory
s
yndrome
c
oronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus, and SARS-CoV-2 have been shown to evade immune responses. Despite the reported functions of the internal protein in these highly pathogenic human coronaviruses, its role in mediating pathogenesis in experimentally infected animals has not been characterized. Our data indicated that despite the similar genomic location and expression strategy of these internal proteins, their effects on virulence are vastly different and virus specific, highlighting the complexity between host-virus interaction and disease outcome.