bluuebunny/crossref_metadata_2025_split huggingface dataset:
The alphavirus determinants of intercellular long extension formation
Authors: Martin Caroline K. , Wan Judy J. , Yin Peiqi , Morrison Thomas E. , Messer William B. , Rivera-Amill Vanessa , Lai Jonathan R. , Grau Nina , Rey Félix A. , Couderc Thérèse , Lecuit Marc , Kielian Margaret 
Published: December 2024

ABSTRACT

The alphavirus chikungunya virus (CHIKV) is a serious human pathogen that can cause large-scale epidemics characterized by fever and joint pain and often resulting in chronic arthritis. Infection by alphaviruses including CHIKV and the closely related Semliki Forest virus (SFV) can induce the formation of filopodia-like intercellular long extensions (ILEs). ILEs emanate from an infected cell, stably attach to a neighboring cell, and mediate cell-to-cell viral transmission that is resistant to neutralizing antibodies. However, our mechanistic understanding of ILE formation is limited, and the potential contribution of ILEs to CHIKV virulence or human CHIKV infection is unknown. Here, we used well-characterized virus mutants and monoclonal antibodies with known epitopes to dissect the virus requirements for ILE formation. Our results showed that both the viral E2 and E1 envelope proteins were required for ILE formation, while viral proteins 6K and transframe, and cytoplasmic nucleocapsid formation were dispensable. A subset of CHIKV monoclonal antibodies reduced ILE formation by masking specific regions particularly on the E2 A domain. Studies of the viral proteins from different CHIKV strains showed that ILE formation is conserved across the four major CHIKV lineages. Sera from convalescent human CHIKV patients inhibited ILE formation in cell culture, providing the first evidence for ILE inhibitory antibody production during human CHIKV infections.

IMPORTANCE
Chikungunya virus (CHIKV) infections can cause severe fever and long-lasting joint pain in humans. CHIKV is disseminated by mosquitoes and is now found world-wide, including in the Americas, Asia, and Africa. In cultured cells, CHIKV can induce the formation of long intercellular extensions that can transmit virus to another cell. However, our understanding of the formation of extensions and their importance in human CHIKV infection is limited. We here identified viral protein requirements for extension formation. We demonstrated that specific monoclonal antibodies against the virus envelope proteins or sera from human CHIKV patients can inhibit extension formation. Our data highlight the importance of evaluation of extension formation in the context of human CHIKV infection.
African swine fever virus biotype identification tool
Authors: Dinhobl Mark , Spinard Edward , Birtlery Hillary , Tesler Nicolas , Masembe Charles , Ribeca Paolo , Borca Manuel V. , Gladue Douglas P. 
Published: December 2024

ABSTRACT

African swine fever virus biotyping is a recently described classification technique that is based on an isolate’s encoded proteome. In short, proteomes are compared and grouped based on unsupervised machine learning. This tool analyzes African swine fever virus (ASFV) genomes and will report their closest matches along with their ASFV biotypes. Here, we describe a standalone implementation that can be freely downloaded and used.
Draft genome sequence of
Levilactobacillus brevis
CHEE98
Authors: Kim Ryeong-Hui , Lee DoKyung , Jung Da-Ryung , Sliti Amani , Shin Jae-Ho 
Published: December 2024

ABSTRACT

The draft genome sequence of
Levilactobacillus brevis
CHEE98, isolated from cheese, is presented here. The whole-genome assembly is 2.7 Mbp in size, with a GC content of 45.67%, and includes 2,731 predicted protein-coding genes.
Discovery of reproductive tissue-associated bacteria and the modes of microbiota acquisition in male honey bees (drones)
Authors: Burks Alexis , Gallagher Patrick , Raymann Kasie 
Published: December 2024

ABSTRACT

Honey bees are the third most economically important agricultural animal in the world due to their role as pollinators. Honey bee pollination services and all hive duties are performed by female workers, while the male drones have one job to mate and share their genetics with a virgin queen from another colony. Thus, drone fitness is directly tied to queen success and colony survival, yet they have been severely understudied compared to their female counterparts. In other insects, microbes discovered in the gut and reproductive organs have been shown to be important for reproductive success and/or overall host health. To our knowledge, the existence of microbes in drone reproductive tissues has never been investigated. Moreover, our understanding of the gut microbiota of drones is severely limited, especially when compared to honey bee workers. Here, we sampled conventional drones from healthy colonies and used 16S amplicon sequencing to identify and characterize bacteria in the reproductive organs of immature and mature drones. After identifying bacteria in drone reproductive tissues, we performed a controlled experiment in which newly emerged drones were exposed to different rearing conditions in order to determine when and how they acquire their reproductive and gut microbiota. Overall, we discovered a set of core bacteria in the reproductive and gut tissues of conventionally reared drones and revealed that social interactions are important for the proper development of the drone microbiota. Determining if these bacteria play a role in drone fecundity and health should be a goal of future research efforts.

IMPORTANCE
Over the last decade, annual honey bee colony loss has increased, resulting in a critical need to determine what factors contribute to honey bee and colony health. Gut microbes have been shown to play important roles in the health of the nonreproductive female honey bee workers, which make up 90% or more of a honey bee colony. However, we currently know very little about the impact of microbes on the health of male honey bees (drones), who only make up a small portion of the colony population but play a very key role in the success of future colonies by mating with virgin queens. Here, we discovered microbes within the reproductive organs of drones and illustrated that social interactions with worker bees are necessary for the proper development of the gut and reproductive tissue microbial communities in drones. Further studies are needed to determine if microbes play an important role in honey bee reproductive health and fitness.
Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment
Authors: Lustermans Jamie J. M. , Sereika Mantas , Burdorf Laurine D. W. , Albertsen Mads , Schramm Andreas , Marshall Ian P. G. 
Published: December 2024

ABSTRACT

Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

IMPORTANCE
Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor “shortcut” to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.
Detection of CRISPR‒Cas and type I R–M systems in
Klebsiella pneumoniae
of human and animal origins and their relationship to antibiotic resistance and virulence
Authors: Li Xue , Wang Ling , Lin Jinghuan , Gu Yingjuan , Liu Zhihua , Hu Jing 
Published: December 2024

ABSTRACT

The clustered regularly interspaced short palindromic repeats (CRISPR)‒CRISPR-associated protein (Cas) and restriction‒modiﬁcation (R–M) systems are important immune systems in bacteria. Information about the distributions of these two systems in
Klebsiella pneumoniae
from different hosts and their mutual effect on antibiotic resistance and virulence is still limited. In this study, the whole genomes of 520 strains of
K. pneumoniae
from GenBank, including 325 from humans and 195 from animals, were collected for CRISPR‒Cas systems and type I R-M systems, virulence genes, antibiotic resistance genes, and multilocus sequence typing detection. The results showed that host origin had no obvious influence on the distributions of the two systems (CRISPR‒Cas systems in 29.8% and 24.1%, type I R-M systems in 9.8% and 11.8% of human-origin and animal-origin strains, respectively) in
K. pneumoniae
. Identical spacer sequences from different hosts demonstrated there was a risk of human–animal transmission. All virulence genes (yersiniabactin, colibactin, aerobactin, salmochelin,
rmpADC
, and
rmpA2
) detection rates were higher when only the CRISPR‒Cas systems were present but were all reduced when coexisting with type I R-M systems. However, a lower prevalence of most antibiotic-resistance genes was found when the CRISPR‒Cas systems were alone, and when type I R-M systems were coexisting, some of the antibiotic resistance gene incidence rates were even lower (quinolones, macrolides, tetracyclines and carbapenems), and some of them were higher instead (aminoglycosides, clindamycins, rifampicin-associated, sulfonamides, methotrexates, beta-lactamases and ultrabroad-spectrum beta-lactamases). The synergistic and opposed effects of the two systems on virulence and antibiotic-resistance genes need further study.

IMPORTANCE

K. pneumoniae
is an important opportunistic pathogen responsible for both human and animal infections, and the emergence of hypervirulent and multidrug-resistant
K. pneumoniae
has made it difficult to control this pathogen worldwide. Here, we find that CRISPR‒Cas and restriction–modification systems, which function as adaptive and innate immune systems in bacteria, have synergistic and opposed effects on virulence and antibiotic resistance genes in
K. pneumoniae
. Moreover, this study provides insights into the distributions of the two systems in
K. pneumoniae
from different hosts, and there is no significant difference in the prevalence of the two systems among
K. pneumoniae
spp. In addition, this study also characterizes the CRISPR arrays of
K. pneumoniae
from different hosts, suggesting that the strains sharing the same spacer sequences have the potential to spread between humans and animals.
Diagnosing gastrointestinal infections based on cycle threshold cut-offs of PCR
Authors: Karam Rania , Kechker Peter , Ken-Dror Shifra , Peretz Avi , Azrad Maya 
Published: December 2024

ABSTRACT

This study compared the performance of molecular vs stool culture assays for gastrointestinal infection (GII) detection, with focus on defining cycle threshold (Ct) cut-off values for positive culture results. A total of 6,000 records of patients with suspected GII between October 2022 and February 2023 and registered at Clalit HealthCare Services in Haifa, Israel, were reviewed. Stool samples were collected from all patients with suspected GII. PCR was performed with the Seegene Allplex GI-Bacteria (I) assay kit. PCR-positive samples were cultured on bacteria-specific agar media. Out of 356 PCR-positive samples, 196 (55.1%) were culture-positive. Significant differences were noted between the mean Ct of culture-positive vs culture-negative samples for
Shigella
spp. (
P
< 0.0001),
E. coli
O157 (
P
= 0.0001), and
Campylobacter
spp. (
P
= 0.004).
Shigella
had the lowest Ct cutoff (27.14). Negative culture results for PCR-positive samples may result from low bacterial load. At the same time, false-positive PCR results may exist. Thus, PCR result should be considered along with clinical presentation and with Ct value consideration.

IMPORTANCE
GII diagnostic procedures have shifted from traditional- to molecular-based assays, which may increase missdiagnosis due to the high PCR sensitivity and false positives. This study suggests to consider a Ct threshold for each pathogen in order to reduce inaccurate diagnosis. Alternatively, culture should be performed for PCR-positive samples.
Emergence and clonal dissemination of KPC-2- and NDM-1-coharboring
Citrobacter freundii
in China with an IncR plasmid
Authors: Zhou Juanjuan , Zhen Minghui , Gao Kaijie , Xu Lu , Zhang Dongyu , Yang Junmei 
Published: December 2024

ABSTRACT

The rise of carbapenem-resistant
Enterobacteriaceae
coharboring KPC-2 and NDM-1 poses a significant public health threat. KPC-2-NDM-1-
Citrobacter freundii
is rarely reported in clinical settings. In this study, we report the largest cohort of eight KPC-2-NDM-1-
C. freundii
isolated from children with urinary tract infections. Comprehensive characterization, including antimicrobial susceptibility testing, plasmid conjugation, whole-genome sequencing, and comparative genomics, was conducted for these clinical strains. Antimicrobial susceptibility testing indicated that all strains were resistant to meropenem [minimal inhibitory concentration (MICs) ≥ 8 µg/mL] and imipenem (MICs > 8 µg/mL). Genotyping and comparative genomics analyses identified the eight KPC-2-NDM-1-
C. freundii
belonging to ST523, exhibiting a close relationship characterized by 45 single nucleotide polymorphisms. Whole-genome sequencing and plasmid analysis confirmed the presence of
bla
KPC-2
and
bla
NDM-1
on an IncR plasmid named pC275-2 with 46,050 bp. The
bla
NDM-1
was integrated within the
bla
NDM-1
related region, which includes ΔIS
Aba125
,
bla
NDM-1
,
ble-MBL
,
trpF
,
dsbD
, and IS
CR1
, while the
bla
KPC-2
gene was located on a novel non-Tn
4401
genetic element. The
bla
KPC-2
genetic architectures containing
bla
KPC-2
differed from classical structures, underscoring the ongoing evolution of these genetic elements.

IMPORTANCE

Our study described the largest cohort to date of eight ST523 KPC-2-NDM-1-
C. freundii
isolated from children with urinary tract infections. The cooccurrence of KPC-2, a serine
β
-lactamases, and NDM-1, a metallo-β-lactamase on an IncR plasmid pC275-2 from a clinical carbapenem-resistant
C
.
freundii
. The conserved insertion structure mediated the
bla
NDM-1
, and the propagation of
bla
KPC-2
gene with a new genetic background using IncR plasmid in clinical settings promotes the emergence of superbugs necessitating vigilant monitoring. Our research detected that ST523 KPC-2- NDM-1-
C. freundii
were disseminated in a children’s hospital. The potential spread of an IncR plasmid within the hospital raises concerns about the pandemic potential of this clone that produces two carbapenemases: KPC-2 and NDM-1. Further investigations will be necessary to control and prevent the spread of KPC-2-NDM-1-
C. freundii
s.
Random files for fission fragment evaporation in TALYS: a total Monte Carlo approach
Authors: Karlsson P. , Al-Adili A. , Göök A. , Gao Z. , Pomp S. , Sjöstrand H. , Solders A. , Koning A. 
Published: December 2024

Abstract
In this study, we have applied the Total Monte Carlo (TMC) methodology in the simulation of the de-excitation process of primary fission fragments (FF) within the TALYS code. Our objective was to develop a method for assessing fission model deficiencies and parameter sensitivities. The input fission fragment data used by TALYS were systematically varied. This was done using the GEF code to generate 10,000 random files by randomizing the 94 model parameters of GEF that influence both fission yields and their energy distributions. The GEF parameters were varied randomly within 3% of the default value, assuming a normal probability distribution. As a result of this parameter variation, significant changes could be identified for several observables, including the multiplicities of

$$\gamma $$

γ

rays and prompt neutrons, as well as their spectra. Additionally, we investigate the impact of angular momentum distribution on the de-excitation data of both GEF and TALYS. Finally, we present an attempt to construct a best parameter file benchmarked against evaluated nuclear data files.
Thermalization and non-monotonic entanglement growth in an exactly solvable model
Authors: Paranjape Shruti , Sorokhaibam Nilakash 
Published: December 2024

Abstract
We study quantum quenches and subsequent non-equilibrium dynamics of free Dirac fermions in 1 + 1 spacetime dimensions using time dependent mass. The final state is a normalized boundary state which is called generalized Calabrese-Cardy (gCC) state and the system thermalizes to a generalized Gibb’s Ensemble(GGE). We can also tune the initial states so that the final states are exact Calabrese-Cardy (CC) state and special gCC states. The system in the CC state thermalizes to a Gibb’s ensemble. We derive closed-form analytic expressions for the growth of entanglement entropy of subsystems consisting of arbitrary number of disjoint intervals in CC state. We show that the entanglement entropy of a single interval grows monotonically before saturation. In case of certain gCC states, for particular charges, the entanglement entropy of a single interval grows non-monotonically when the effective chemical potential is increased beyond a critical value. We argue that the non-monotonic growth of entanglement entropy is a boundary effect which arises due to increase in long range correlation and decrease in short range correlation at early times.
A power law solution for FLRW universe with observational constraints
Authors: Sharma Lokesh Kumar , Parekh Suresh , Maurya Sanjay , Singh Kuldeep , Ray Saibal , Mehta Kalyani C. K. , Trivedi Vaibhav 
Published: December 2024

This work analyzes a power law solution under [Formula: see text] gravity for an isotropic and homogeneous universe. To construct [Formula: see text] gravity model, we consider the functional form of [Formula: see text] as the sum of two independent functions of the Ricci scalar R and the trace of the energy–momentum tensor T, i.e. [Formula: see text], with [Formula: see text] being a positive constant where we study the cosmological model under the following two cases: (i) [Formula: see text] and (ii) [Formula: see text]. In the framework of [Formula: see text] gravity with homogeneous and isotropic spacetime, the constructed model yields several features on application of the scale factor [Formula: see text]. We employed the Markov Chain Monte Carlo (MCMC) approach to get model parameters [Formula: see text], [Formula: see text] and [Formula: see text] over a redshift range of [Formula: see text]. The model parameter’s restricted values are listed below: [Formula: see text] km [Formula: see text][Formula: see text]Mpc[Formula: see text], [Formula: see text][Formula: see text]km[Formula: see text] Mpc[Formula: see text], [Formula: see text][Formula: see text]km[Formula: see text]s[Formula: see text] Mpc[Formula: see text], [Formula: see text][Formula: see text]km[Formula: see text]s[Formula: see text][Formula: see text]Mpc[Formula: see text], [Formula: see text][Formula: see text]km[Formula: see text]s[Formula: see text][Formula: see text]Mpc[Formula: see text]. The model was constrained using the Hubble parameter ([Formula: see text]) dataset, Baryon Acoustic Oscillations (BAO) dataset, Pantheon dataset, joint [Formula: see text] + Pantheon dataset and collective [Formula: see text] + BAO + Pantheon dataset. The results from the Planck collaboration group are consistent with these calculated Ho observed values. In order to study and analyze the model, we first look at how the energy circumstances affected our power law assumption. The validity of the model has also been evaluated using the [Formula: see text] diagnostic and the jerk parameter, which are state finding diagnostic tools. We find that the model under investigation agrees with the observed fingerprints within a certain range of constraints.
Ultra-Long and Rapid Operating Sodium Metal Batteries Enabled By Multifunctional Polarizable Interface Stabilizer
Authors: Ryu Won-Hee , Jun Seo-Young 
Published: December 2024

Sodium metal batteries (SMBs) have been considered as one of the most favorable and economic candidates for next generation batteries to overcome low enenrgy density limitation of sodium ion batteries (SIBs) due to high theoretical specific capacity (1166 mAh g-1), low electrochemical redox potential (-2.71 V vs. SHE). However, ‘moss-like’ dendrite growth that occurs during continuous charging and discharging processes not only threatens the safety of batteries, but also poses several problems to be solved, such as electrolyte consumption, hugh volume expansion, dead Na formation, and low coulombic efficiency. The dendrite problem in the SMBs is similr to that of lithium-metal batteries (LMBs), yet the degree of the issue is further severe than LMBs. Surface stabilization of sodium metal anode should be achieved to realize SMB technologies.
The introduction of functional electrolyte additives is an effective and economical way to overcome these problems and improve the cyclability of SMBs. Based on the similarity between electroplating and sodium deposition reaction, utilization of surface leveler additive in the electrolyte could allow a substantial impact to stabilize sodium metal surface during repeated deposition and stripping process.
In this presentation, we confirmed the surface flattening effect of molecular dipole electrolyte additives at the anode through the Na-Na symmetric cell test. Sodium metal deposition and stripping behavior has been successfully controlled by introducing surface leveler additives for realization of SMBs. Even under rapid charging and discharging situations, additive containing Na-Na symmetric cells showed stable performance for over 2000 hours, which is 5 times longer than the pristine cell without the additive. We confirmed that controlling intrinsic properties of surface leveler additive can effectively further improve cycle performance of SMBs.
[1] S.-Y. Jun, K. Shin, C. Y. Son, J. Park, H.-S. Kim, J.-Y. Hwang, W.-H. Ryu, Advanced Energy Materials, 2024, 2304504
[2] S.-Y. Jun, K. Shin, Y. Lim, S. Kim, H. Kim, C. Y. Son, W.-H. Ryu, Small Structures, 2024, 5, 2300578
[3] S.-Y. Jun, K. Shin, J.-S. Lee, S. Kim, J. Chun, W.-H. Ryu, Advanced Science, 2023, 10, 2301426
[4] J.-S. Lee, K. Shin, S.-Y. Jun, S. Kim, W.-H. Ryu, Chemical Engineering Journal, 2023, 458, 141383

Figure 1