bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lithium-Ion Battery Health State Estimation Based on Feature Reconstruction and Optimized Least Squares Support Vector Machine
Authors: Wu Tiezhou , Kang Jian , Zhu Junchao , Tu Te 
Published: June 2024

Abstract
The state of health (SOH) of a battery is the main indicator of battery life. In order to improve the SOH estimation accuracy, a model framework for lithium-ion battery health state estimation with feature reconstruction and improved least squares support vector machine is proposed. First, the indirect health features (HF) are obtained by processing multiple health features extracted from the charging and discharging phases through principal component analysis to remove the information redundancy among multiple features. Subsequently, multiple smooth component subsequences of different frequencies are obtained by using variational modal decomposition to efficiently capture the overall downtrend and regeneration fluctuations of the data. Then, use the sparrow search algorithm to optimize the least squares support vector machine to build an estimation model, predict and superimpose the reconstructed fusion features of multiple feature subsequences. Finally, use the mapping relationship between the reconstructed HF and the SOH for the estimation. The NASA battery dataset and the University of Maryland battery dataset (CACLE) are used to perform validation tests on multiple batteries with different cycle intervals. The results show that the mean absolute error and root mean square error are less than 1% and the method has high-estimation accuracy and robustness.
A Moving Horizon Estimation for a Class of Soft Continuum Manipulators
Authors: Bastos Guaraci 
Published: June 2024

Abstract
This work proposes a formulation for the moving horizon estimation technique considering both states and parameters obtained simultaneously with reduced estimation issues. The parameters can be either constant or time-varying, while states are related to complex output trajectories related to underactuated systems. Particularly, the proposed formulation considers additional equality constraints as a counterpart of the dynamics tube-model predictive control. Thus, it becomes less dependent on probabilistic information, such as probability density function and covariance of the process noise. In addition, the calibration of the method parameters has less sensitivity and driven by the tube constraints. The proposed approach can be applied in different systems; however, here it is detailed for a class of soft continuum manipulators with fluidic actuation through a variable flowrate and demonstrated with numerical simulations in planar motion. Results indicate robustness of the algorithm estimation in a challenging scenario arising from underactuation as well as in the presence of uncertainty and external disturbance, while simultaneously states and a vector of structural parameters are coherently estimated.
Infrared Emission for Heat Radiation From Micro-Cone Textured Metallic Sheet Device With Semi-Regular Alignment
Authors: Aizawa Tatsuhiko , Nakata Hiroki , Nasu Takeshi 
Published: June 2024

Abstract
A micro-cone textured copper sheet was fabricated as an emitter of electromagnetic waves in the near-infrared (IR) to the far-IR wavelengths. The micro-cone texture was aligned in semiregular by varying the micro-cone size parameters. The micro-cone height (H) was varied from 0.5 μm to 4 μm in average. Scanning electron microscopy (SEM) analysis was utilized to characterize the microstructure of micro-cone textures and to measure the population of micro-cone height (H), its root diameter (B), and pitch (D) with aid of the image processing and computational geometry. This emittance was measured by Fourier transformation-infrared (FT-IR) to investigate the micro-cone size effect on the resonant wavelengths for IR-emission. This height population P(H) was compared to the IR emission spectrum, which was measured by the FT-IR. Even varying the average height of micro-cone textures, the IR-emission wavelength (λ) abided by the resonance condition by λ ∼ 2 × H within the standard deviation of heights and wavelengths. The radiation heat flux from this emitter to objective body in vacuum was experimentally estimated to describe the heat transportation from this microtextured emitter. Through the heat radiation experiment in vacuum, the emitted heat flux was estimated to be 58 W/m2 by the one-dimensional heat balance between the heating rate of objective body and the radiated heat flux.
Random forest machine-learning algorithm classifies white- and brown-rot fungi according to the number of the genes encoding Carbohydrate-Active enZyme families
Authors: Hasegawa Natsuki , Sugiyama Masashi , Igarashi Kiyohiko 
Published: June 2024

ABSTRACT

Wood-rotting fungi play an important role in the global carbon cycle because they are the only known organisms that digest wood, the largest carbon stock in nature. In the present study, we used linear discriminant analysis and random forest (RF) machine learning algorithms to predict white- or brown-rot decay modes from the numbers of genes encoding Carbohydrate-Active enZymes with over 98% accuracy. Unlike other algorithms, RF identified specific genes involved in cellulose and lignin degradation, including auxiliary activities (AAs) family 9 lytic polysaccharide monooxygenases, glycoside hydrolase family 7 cellobiohydrolases, and AA family 2 peroxidases, as critical factors. This study sheds light on the complex interplay between genetic information and decay modes and underscores the potential of RF for comparative genomics studies of wood-rotting fungi.

IMPORTANCE
Wood-rotting fungi are categorized as either white- or brown-rot modes based on the coloration of decomposed wood. The process of classification can be influenced by human biases. The random forest machine learning algorithm effectively distinguishes between white- and brown-rot fungi based on the presence of Carbohydrate-Active enZyme genes. These findings not only aid in the classification of wood-rotting fungi but also facilitate the identification of the enzymes responsible for degrading woody biomass.
DarA—the central processing unit for the integration of osmotic with potassium and amino acid homeostasis in
Bacillus subtilis
Authors: Warneke Robert , Herzberg Christina , Weiß Martin , Schramm Thorben , Hertel Dietrich , Link Hannes , Stülke Jörg 
Published: June 2024

ABSTRACT

Cyclic di-adenosine monophosphate (c-di-AMP) is a second messenger involved in diverse metabolic processes including osmolyte uptake, cell wall homeostasis, as well as antibiotic and heat resistance. This study investigates the role of the c-di-AMP receptor protein DarA in the osmotic stress response in
Bacillus subtilis
. Through a series of experiments, we demonstrate that DarA plays a central role in the cellular response to osmotic fluctuations. Our findings show that DarA becomes essential under extreme potassium limitation as well as upon salt stress, highlighting its significance in mediating osmotic stress adaptation. Suppressor screens with
darA
mutants reveal compensatory mechanisms involving the accumulation of osmoprotectants, particularly potassium and citrulline. Mutations affecting various metabolic pathways, including the citric acid cycle as well as glutamate and arginine biosynthesis, indicate a complex interplay between the osmotic stress response and metabolic regulation. In addition, the growth defects of the
darA
mutant during potassium starvation and salt stress in a strain lacking the high-affinity potassium uptake systems KimA and KtrAB can be rescued by increased affinity of the remaining potassium channel KtrCD or by increased expression of
ktrD,
thus resulting in increased potassium uptake. Finally, the
darA
mutant can respond to salt stress by the increased expression of MleN , which can export sodium ions.

IMPORTANCE

Environmental bacteria are exposed to rapidly changing osmotic conditions making an effective adaptation to these changes crucial for the survival of the cells. In Gram-positive bacteria, the second messenger cyclic di-AMP plays a key role in this adaptation by controlling (i) the influx of physiologically compatible organic osmolytes and (ii) the biosynthesis of such osmolytes. In several bacteria, cyclic di-adenosine monophosphate (c-di-AMP) can bind to a signal transduction protein, called DarA, in
Bacillus subtilis
. So far, no function for DarA has been discovered in any organism. We have identified osmotically challenging conditions that make DarA essential and have identified suppressor mutations that help the bacteria to adapt to those conditions. Our results indicate that DarA is a central component in the integration of osmotic stress with the synthesis of compatible amino acid osmolytes and with the homeostasis of potassium, the first response to osmotic stress.
A broadly neutralizing human monoclonal antibody generated from transgenic mice immunized with HCMV particles limits virus infection and proliferation
Authors: Atanasoff Kristina E. , Parsons Andrea J. , Ophir Sabrina I. , Lurain Nell , Kraus Thomas , Moran Thomas , Duty J. Andrew , Tortorella Domenico 
Published: June 2024

ABSTRACT

Human cytomegalovirus (HCMV) is a β-herpesvirus that poses severe disease risk for immunocompromised patients who experience primary infection or reactivation. Development and optimization of safe and effective anti-HCMV therapeutics is of urgent necessity for the prevention and treatment of HCMV-associated diseases in diverse populations. The use of neutralizing monoclonal antibodies (mAbs) to limit HCMV infection poses a promising therapeutic strategy, as anti-HCMV mAbs largely inhibit infection by targeting virion glycoprotein complexes. In contrast, the small-molecule compounds currently approved for patients (e.g., ganciclovir, letermovir, and maribavir) target later stages of the HCMV life cycle. Here, we present a broadly neutralizing human mAb, designated 1C10, elicited from a VelocImmune mouse immunized with infectious HCMV particles. Clone 1C10 neutralizes infection after virion binding to cells by targeting gH/gL envelope complexes and potently reduces infection of diverse HCMV strains in fibroblast, trophoblast, and epithelial cells. Antibody competition assays found that 1C10 recognizes a region of gH associated with broad neutralization and binds to soluble pentamer in the low nanomolar range. Importantly, 1C10 treatment significantly reduced virus proliferation in both fibroblast and epithelial cells. Further, the combination treatment of mAb 1C10 with ganciclovir reduced HCMV infection and proliferation in a synergistic manner. This work characterizes a neutralizing human mAb for potential use as a HCMV treatment, as well as a possible therapeutic strategy utilizing combination-based treatments targeting disparate steps of the viral life cycle. Collectively, the findings support an antibody-based therapy to effectively treat patients at risk for HCMV-associated diseases.

IMPORTANCE
Human cytomegalovirus is a herpesvirus that infects a large proportion of the population and can cause significant disease in diverse patient populations whose immune systems are suppressed or compromised. The development and optimization of safe anti-HCMV therapeutics, especially those that have viral targets and inhibition mechanisms different from current HCMV treatments, are of urgent necessity to better public health. Human monoclonal antibodies (mAbs) that prevent HCMV entry of cells were identified by immunizing transgenic mice and screened for broad and effective neutralization capability. Here, we describe one such mAb, which was found to target gH/gL envelope complexes and effectively limit HCMV infection and dissemination. Further, administration of the antibody in combination with the antiviral drug ganciclovir inhibited HCMV in a synergistic manner, highlighting this approach and the use of anti-HCMV mAbs more broadly, as a potential therapeutic strategy for the treatment of diverse patient populations.
Genomic and epidemiological evidence for the emergence of a
L. infantum/L. donovani
hybrid with unusual epidemiology in northern Italy
Authors: Bruno F. , Castelli G. , Li B. , Reale S. , Carra E. , Vitale F. , Scibetta S. , Calzolari M. , Varani S. , Ortalli M. , Franceschini E. , Gennari W. , Rugna G. , Späth G. F. 
Published: June 2024

ABSTRACT

Leishmania
(
L
.)
infantum
is one of the main causative agents of animal and human leishmaniasis across many endemic areas in South America, Europe, North Africa, and Asia. Despite its clinical significance, little is known about the genetic diversity of
L. infantum
circulating in a given endemic area. Here, we investigate this important open question by applying a comparative genomics approach to seven
L. infantum
isolates from different hosts and Italian regions, including the northern part of the country (Emilia-Romagna, RER), Sicily, and Sardinia, as an initial attempt to explore the breadth of parasite genetic heterogeneity in Italy. Additionally, microsatellite analysis was carried out to compare the isolates from RER with other 70
L
.
infantum
strains from the same region as well as 65 strains belonging to the
L. donovani
complex from other countries. We revealed important karyotypic instability and identified strain-specific changes in gene dosage, which affected important virulence factors such as amastins and surface antigen-like proteins. Single nucleotide polymorphism-based clustering analysis of these genomes together with over 80 publicly available
L. infantum
and
L. donovani
genomes placed the Italian isolates into three geographically distinct clusters within the Mediterranean basin and uncovered three isolates clustering with putative
L. infantum/L. donovani
hybrids isolated in Cyprus. As judged by microsatellite profiling, these hybrid isolates are representative of a sub-population of parasites circulating in northern Italy that preferentially infect humans but not dogs. Our results place Italy at the crossroads of
L. infantum
infection in the Mediterranean and call attention to the public health risk represented by the introduction of non-European
Leishmania
species.

IMPORTANCE

This study closes important knowledge gaps with respect to
Leishmania (L.) infantum
genetic heterogeneity in a given endemic country, as exemplified here for Italy, and reveals genetic hybridization as a main cause for re-emerging human leishmaniasis in northern Italy. The observed high diversity of
Leishmania
parasites on the Italian peninsula suggests different geographical origins, with genomic adaptation to various ecologies affecting both pathogenicity and transmission potential. This is documented by the discovery of a putative
L. infantum
/
L. donovani
hybrid strain, which has been shown to preferentially infect humans but not dogs. Our results provide important information to health authorities, which need to consider the public health risk represented by the introduction of new
Leishmania
species into EU countries due to population displacement or travel from countries where exotic/allochthonous parasite species are endemic.
Mriyaviruses: small relatives of giant viruses
Authors: Yutin Natalya , Mutz Pascal , Krupovic Mart , Koonin Eugene V. 
Published: June 2024

ABSTRACT

The phylum
Nucleocytoviricota
consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35–45 kb that appear to be related to the
Nucleocytoviricota
. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCPs) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the
Nucleocytoviricota
and accordingly would comprise a class which we propose to name “
Mriyaviricetes
” (after Ukrainian “mriya,” dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the
Nucleocytoviricota
. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family
Yaraviridae
and proposed new family “
Gamadviridae.
” The previously characterized members of these families, yaravirus and
Pleurochrysis
sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the
Nucleocytoviricota
, and RNA polymerase subunits encoded by all cytoplasmic viruses among the
Nucleocytoviricota
, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.

IMPORTANCE

The origin of giant viruses of eukaryotes that belong to the phylum
Nucleocytoviricota
is not thoroughly understood and remains a matter of major interest and debate. Here, we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35–45 kilobases that appear to comprise a distinct class within the phylum
Nucleocytoviricota
that we provisionally named “
Mriyaviricetes
.” Mriyaviruses appear to be the closest identified relatives of the ancestors of the
Nucleocytoviricota
. Analysis of proteins encoded in mriyavirus genomes suggests that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members of
Nucleocytoviricota
.
Multicenter retrospective genomic characterization of carbapenemase-producing
Acinetobacter baumannii
isolates from Jiangxi patients 2021–2022: identification of a novel international clone, IC11
Authors: Xu An , Li Min , Hang Yaping , Zeng Lingbing , Zhang Xuefei , Hu Yiyi , Guo Qinglan , Wang Minggui 
Published: June 2024

ABSTRACT

This study aimed to characterize carbapenem-resistant
Acinetobacter baumannii
(CRAB) isolates from Jiangxi patients using whole-genome sequencing (WGS). We subjected 100 clinical CRAB strains isolated from the three local largest teaching hospitals to WGS and antimicrobial susceptibility testing. Molecular epidemiology was investigated using multilocus sequence typing, core genome multilocus typing, core genome single-nucleotide polymorphism phylogeny, and pulsed-field gel electrophoresis. The most prevalent acquired carbapenemase was
bla
OXA-23
, predominant in all isolates (100%). Isolates belonging to the dominating international clone IC2 accounted for 92% of all isolates. International IC11 (ST164
Pas
/ST1418
Ox
) clone was found in an additional 8% (eight isolates), with seven isolates (87.5%) carrying an acquired additional
bla
NDM-1
carbapenemase. The
oxa23
-associated Tn
2009
, either alone or in a tandem repeat structure containing four copies of
bla
OXA-23
, was discovered in 62% (57 isolates) of IC2. The
oxa23
-associated Tn
2006
was identified in 38% (35 isolates) of IC2 and all IC11 isolates. A putative conjugative RP-T1 (formerly RepAci6) plasmid with
bla
OXA-23
in Tn
2006
within AbaR4, designated pSRM1.1, was found in IC2
A. baumannii
strain SRM1. The
bla
NDM-1
gene found in seven IC11 isolates was located on a novel Tn
6924
-like transposon, a first-time report in IC11. These findings underscore the significant importance of real-time surveillance to prevent the further spread of CRAB.

IMPORTANCE

Carbapenem-resistant
Acinetobacter baumannii
(CRAB) is notorious for causing difficult-to-treat infections. To elucidate the molecular and clinical epidemiology of CRAB in Jiangxi, clinical CRAB isolates were collected and underwent whole-genome sequencing and antibiotic susceptibility phenotyping. Key findings included the predominance of OXA-23-producing IC2
A. baumannii
, marked by the emergence of OXA-23 and NDM-1-producing IC11 strains.
A limited concentration range of diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, promotes the
in vitro
gene expression with bacterial ribosomes
Authors: Takasu Rena , Izu Takashi , Nakabachi Atsushi 
Published: June 2024

ABSTRACT

Diaphorin is a polyketide produced by “
Candidatus
Profftella armatura” (
Gammaproteobacteria: Burkholderiales
), an obligate symbiont of a devastating agricultural pest, the Asian citrus psyllid
Diaphorina citri
(Hemiptera: Psyllidae). Physiological concentrations of diaphorin, which
D. citri
contains at levels as high as 2–20 mM, are inhibitory to various eukaryotes and
Bacillus subtilis
(
Firmicutes: Bacilli
) but promote the growth and metabolic activity of
Escherichia coli
(
Gammaproteobacteria: Enterobacterales
). Our previous study demonstrated that 5-mM diaphorin, which exhibits significant inhibitory and promoting effects on cultured
B. subtilis
and
E. coli
, respectively, inhibits
in vitro
gene expression utilizing purified
B. subtilis
and
E. coli
ribosomes. This suggested that the adverse effects of diaphorin on
B. subtilis
are partly due to its influence on gene expression. However, the result appeared inconsistent with the positive impact on
E. coli
. Moreover, the diaphorin concentration in bacterial cells, where genes are expressed
in vivo
, may be lower than in culture media. Therefore, the present study analyzed the effects of 50 and 500 µM of diaphorin on bacterial gene expression using the same analytical method. The result revealed that this concentration range of diaphorin, in contrast to 5-mM diaphorin, promotes the
in vitro
translation with the
B. subtilis
and
E. coli
ribosomes, suggesting that the positive effects of diaphorin on
E. coli
are due to its direct effects on translation. This study demonstrated for the first time that a pederin-type compound promotes gene expression, establishing a basis for utilizing its potential in pest management and industrial applications.

IMPORTANCE

This study revealed that a limited concentration range of diaphorin, a secondary metabolite produced by a bacterial symbiont of an agricultural pest, promotes cell-free gene expression utilizing substrates and proteins purified from bacteria. The unique property of diaphorin, which is inhibitory to various eukaryotes and
Bacillus subtilis
but promotes the growth and metabolic activity of
Escherichia coli
, may affect the microbial flora of the pest insect, potentially influencing the transmission of devastating plant pathogens. Moreover, the activity may be exploited to improve the efficacy of industrial production by
E. coli,
which is often used to produce various important materials, including pharmaceuticals, enzymes, amino acids, and biofuels. This study elucidated a part of the mechanism by which the unique activity of diaphorin is expressed, constructing a foundation for applying the distinct property to pest management and industrial use.