bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriophage treatment is effective against carbapenem-resistant
Klebsiella pneumoniae
(KPC) in a neutropenic murine model of gastrointestinal translocation and renal infection
Authors: Zagaliotis Panagiotis , Michalik-Provasek Jordyn , Mavridou Eleftheria , Naing Ethan , Vizirianakis Ioannis S. , Chatzidimitriou Dimitrios , Gill Jason J. , Walsh Thomas J. 
Published: December 2024

ABSTRACT

Carbapenemase-producing
Klebsiella pneumoniae
(KPC) are globally emerging pathogens that cause life-threatening infections. Novel treatment alternatives are urgently needed. We therefore investigated the effectiveness of three novel bacteriophages (Spivey, Pharr, and Soft) in a neutropenic murine model of KPC gastrointestinal colonization, translocation, and disseminated infection. Bacteriophage efficacy was determined by residual bacterial burden of KPC (CFU/g) in kidneys. Parallel studies were conducted of bacteriophage pharmacokinetics and resistance. Treatment of mice with 5 × 10
9
PFU of phage cocktail via intraperitoneal injection was effective in significantly reducing renal KPC CFU by 100-fold (
P
< 0.01) when administered every 24 h and 1000-fold (
P
< 0.01) every 12 h. Moreover, a combination of bacteriophage and ceftazidime-avibactam produced a synergistic effect, resulting in a 10
5
-fold reduction in bacterial burden in cecum and kidney (
P
< 0.001 in both tissues). Prophylactic administration of bacteriophages via oral gavage did not prevent KPC translocation to the kidneys. Bacteriophage decay determined by linear regression of the ln of mean concentrations demonstrated R
2
values in plasma of 0.941, kidney 0.976, and cecum 0.918, with half-lives of t
1/2
= 2.5 h. Furthermore, a phage-resistant mutant displayed increased sensitivity to serum killing
in vitro
, but did not show significant defects in renal infection
in vivo
. A combination of bacteriophages demonstrated significant efficacy alone and synergy with ceftazidime/avibactam in the treatment of experimental disseminated KPC infection in neutropenic mice.
Use of voriconazole to predict susceptibility and resistance to isavuconazole for
Aspergillus fumigatus
using CLSI methods and interpretive criteria
Authors: Winkler Marisa L. , Rhomberg Paul R. , Fedler Kelley A. , Huband Michael D. , Karr Maura , Kimbrough John H. , Castanheira Mariana 
Published: December 2024

ABSTRACT

Aspergillus fumigatus
is a common cause of pulmonary and invasive mold infections among immunocompromised hosts. Mortality in immunocompromised hosts with invasive
Aspergillus
infections (IAI) has been reported to be as high as 80%. Therefore, appropriate therapy is essential in treating IAI. Both isavuconazole and voriconazole are first-line agents in treatment guidelines for IAI, but isavuconazole has favorable properties, often leading it to be preferred over voriconazole, given the lengthy duration of treatment. It is difficult to perform mold antifungal susceptibility testing, which often requires a reference lab and several weeks to determine results. Therefore, use of surrogate markers can be helpful to infer susceptibility when testing is not possible or delayed. We performed isavuconazole and voriconazole broth microdilution susceptibility testing by the Clinical and Laboratory Standards Institute (CLSI) method on a collection of 976 non-duplicate
A. fumigatus
isolates from a global surveillance program between 2017 and 2022. We found that voriconazole and isavuconazole have a very high essential agreement within two doubling dilutions at 99.9% and a categorical agreement of 92.7% with no very major errors, one major error (0.11%), and <10% minor errors. Many of the minor errors were in the setting of voriconazole testing at a MIC of 0.5 mg/L (susceptible) but isavuconazole at 2 mg/L (intermediate). Genetic analysis of
cyp51
genes confirmed that isavuconazole and voriconazole susceptibility testing identified isolates with
cyp51A
and
cyp51B
mutations. Voriconazole can be used to predict the isavuconazole susceptibility testing result when
A. fumigatus
is tested by CLSI broth microdilution methodology.
The palmitoyl-CoA ligase Fum16 is part of a
Fusarium verticillioides
fumonisin subcluster involved in self-protection
Authors: Gherlone Fabio , Jojić Katarina , Huang Ying , Hoefgen Sandra , Valiante Vito , Janevska Slavica 
Published: December 2024

ABSTRACT

Fusarium verticillioides
produces the mycotoxin fumonisin B
1
(FB
1
), which disrupts sphingolipid biosynthesis by inhibiting ceramide synthase and affects the health of plants, animals, and humans. The means by which
F. verticillioides
protects itself from its own mycotoxin are not completely understood. Some fumonisin (
FUM
) cluster genes do not contribute to the biosynthesis of the compound, but their function has remained enigmatic. Recently, we showed that
FUM17
,
FUM18,
and
FUM19
encode two ceramide synthases and an ATP-binding cassette transporter, respectively, which play a role in antagonizing the toxicity mediated by FB
1
. In the present work, we uncovered functions of two adjacent genes,
FUM15
and
FUM16
. Using homologous and heterologous expression systems, in
F. verticillioides
and
Saccharomyces cerevisiae
, respectively, we provide evidence that both contribute to protection against FB
1
. Our data indicate a potential role for the P450 monooxygenase Fum15 in the modification and detoxification of FB
1
since the deletion and overexpression of the respective gene affected extracellular FB
1
levels in both hosts. Furthermore, relative quantification of ceramide intermediates and an
in vitro
enzyme assay revealed that Fum16 is a functional palmitoyl-CoA ligase. It co-localizes together with the ceramide synthase Fum18 to the endoplasmic reticulum, where they contribute to sphingolipid biosynthesis. Thereby,
FUM15-19
constitute a subcluster within the
FUM
biosynthetic gene cluster dedicated to the fungal self-protection against FB
1
.

IMPORTANCE

The study identifies a five-gene
FUM
subcluster (
FUM15-19
) in
Fusarium verticillioides
involved in self-protection against FB
1
.
FUM16
(palmitoyl-CoA ligase),
FUM17,
and
FUM18
(ceramide synthases) enzymatically supplement ceramide biosynthesis, while
FUM19
(ATP-binding cassette transporter) acts as a repressor of the
FUM
cluster. The evolutionary conservation of
FUM15
(P450 monooxygenase) in
Fusarium
and
Aspergillus FUM
clusters is discussed, and its effect on extracellular FB
1
levels in both native (
F. verticillioides
) and heterologous (
Saccharomyces cerevisiae
) hosts is highlighted. These findings enhance our understanding of mycotoxin self-protection mechanisms and could inform strategies for predicting biological activity of unknown secondary metabolites, managing mycotoxin contamination, and developing resistant crop cultivars.
Complete genome sequence of an enterotoxigenic
Bacteroides fragilis
strain 2-078382-3 from an infant with diarrhea
Authors: Lee Eunbi , Kang Heekyoung , Song Hyun Beom , Yeom Jinki 
Published: December 2024

ABSTRACT

This study presents that
Bacteroides fragilis
strain 2-078382-3, isolated from an infant with diarrhea, has a 5.2 million base pair chromosome with a 43.2% GC content and a 5,600 base pairs plasmid pBFP53 with a 39.6% GC content. The strain contains 4,262 genes, including 4,105 coding sequences.
Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample
Authors: Agudelo-Romero Patricia , Caparros-Martin Jose A. , Sharma Abhinav , Saladié Montserrat , Sly Peter D. , Stick Stephen M. , O'Gara Fergal ,   COMBAT study group
Published: December 2024

ABSTRACT

We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for
Stenotrophomonas maltophilia
infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.
Draft genome sequences of six high pH adapted
Marinobacter shengliensis
strains isolated from Mariana forearc serpentinite mud volcanoes
Authors: Elkassas Sabrina M. , Serres Margrethe H. , Navarro Michael , Patterson Amina , Zhivkova Teodora , Petersen Madelyn , Weeks Katelyn , Lang Susan , Seewald Jeffrey , Wheat Geoffrey , Trembath-Reichert Elizabeth , Huber Julie A. 
Published: December 2024

ABSTRACT

Six marine bacterial isolates were obtained from fluid and sediments collected at alkaline serpentinite mud volcanoes of the Mariana forearc to examine life at high pH in a marine environment. Here, we present the draft genome sequences of these six isolates, classified as strains of the species
Marinobacter shengliensis
.
Complete genome sequence of a penicillin-resistant
Fusobacterium necrophorum
subsp.
funduliforme isolate
from a tonsillitis patient
Authors: G C Bibek , Jensen Anders , Wu Chenggang 
Published: December 2024

ABSTRACT

We report the complete genome sequence of a penicillin-resistant
Fusobacterium necrophorum
subsp.
funduliforme
isolate, AJ79, from a tonsillitis patient. The AJ79 genome consists of a chromosome (2,440,359 bp) and plasmid (9,887 bp), providing insights into the genetic basis of penicillin resistance in
F. necrophorum
and its implications for treating tonsillitis.
Not all is lost: resilience of microbiome samples to freezer failures and long-term storage
Authors: Pulido Barriga M. Fabiola , Randolph James W. J. , Glassman Sydney I. 
Published: December 2024

ABSTRACT

Advances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. To evaluate the impact of an unexpected −80°C freezer failure and the recoverability of thawed soil samples, we extracted DNA and compared it to long-term DNA stored at −20°C and original 16S and ITS2 sequencing data collected before the malfunction. Using Illumina MiSeq, we assessed how the freezer failure and long-term storage influenced the resilience of bacterial or fungal richness or community composition and our ability to accurately determine experimental treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient to freezer failure than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at −80°C compared to storage of extracted DNA at −20°C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.

IMPORTANCE
Microbiome studies heavily rely on ultracold freezers for sample storage. Unfortunately, these freezers are prone to frequent malfunctions, resulting in the loss of invaluable samples at laboratories worldwide. Such losses can halt research progress due to potential issues with sample reliability. Our research demonstrates that not all is lost when an unforeseen freezer failure occurs. Samples can still be reliably used to assess treatment effects, which is particularly important for long-term temporal studies where samples cannot be readily obtained again.
Testing loop quantum gravity by quasi-periodic oscillations: rotating blackholes
Authors: Khodagholizadeh Jafar , Jafari Ghadir , Allahyari Alireza , Vahedi Ali 
Published: December 2024

Abstract
We investigate a compelling model of a rotating black hole that is deformed by the effects of loop quantum gravity (LQG). We present a simplified metric and explore two distinct geometries: one in which the masses of the black hole and white hole are equal, and another in which they differ. Our analysis yields the radius of the innermost stable circular orbits (ISCO), as well as the energy and angular momentum of a particle within this framework. Additionally, we find the frequency of the first-order resonance separately. We constrain the model by the quasi-periodic oscillations (QPO) of the X-ray binary GRO J1655-40. We show that

$$\lambda =0.15^{+0.23}_{-0.14}$$

λ
=
0
.

15

-
0.14

+
0.23

at

$$1\sigma $$

1
σ

confidence level for equal mass black hole and white hole geometry. For the other geometry we get

$$\lambda =0.11^{+0.07}_{-0.07}$$

λ
=
0
.

11

-
0.07

+
0.07

at

$$1\sigma $$

1
σ

confidence level. We encounter a degeneracy in the parameter space that hinders our ability to constrain

$$\lambda $$

λ

with greater precision.
Energy conditions in Gauss–Bonnet gravity
Authors: Bajardi Francesco 
Published: December 2024

Abstract
We study the Energy Conditions in modified

$$f(\mathcal {G})$$

f
(
G
)

gravity, with

$$\mathcal {G}$$

G

being the topological Gauss–Bonnet term. Then we use the cosmographic parameters to constrain the functional form of the gravitational action and investigate the possibility to have standard inflation in the early time. Specifically, we select models containing symmetries within the modified

$$f(\mathcal {G})$$

f
(
G
)

theory and obtain conditions for which (i) the energy conditions can be violated and (ii) the magnitude of the slow-roll parameters is small, thus suggesting that under given limits the analyzed theory can potentially trace the cosmic history both at early and at the late times.
Periapsis precession in general stationary and axisymmetric spacetimes
Authors: He Jinhong , Xu Shaofei , Jia Junji 
Published: December 2024

Abstract
This work studies the periapsis shift in the equatorial plane of arbitrary stationary and axisymmetric spacetimes. Two perturbative methods are systematically developed. The first works for small eccentricity but very general orbit size and the second, which is post-Newtonian and includes two variants, is more accurate for orbits of large size but allows general eccentricity. Results from these methods are shown to be equivalent under small eccentricity and large size limits. The periapsis shift of Kerr–Newman, Kerr–Sen and Kerr–Taub-NUT spacetimes is computed to high orders. The electric charge and NUT charge are shown to contribute to the leading order but with opposite signs. The frame-dragging term and high-order effect of spacetime spin are given. The electric and NUT charges of the Earth, Sun and Sgr A* are constrained using the Mercury, satellite and S2 precession data. Periapsis shifts of other spacetimes are obtained too.
Heavy $$K^*$$ mesons with open charm from $$KD^{(*)}D^*$$ interactions
Authors: Ren Xiu-Lei , Khemchandani K. P. , Torres A. Martínez 
Published: December 2024

Abstract
In view of the recent discovery of

$$T_{cc}$$

T

cc

, which can be described as a

$$DD^*$$

D

D
∗

molecular state, we perform a study of the

$$KDD^*$$

K
D

D
∗

system, and its extension to studying

$$KD^*D^*$$

K

D
∗

D
∗

, where

$$D^*D^*$$

D
∗

D
∗

is bound as a spin 1

$$T_{cc}$$

T

cc

-like state, to search for the possible existence of exotic mesons with the open flavors ccs being part of their quark configuration. Considering the additional attractive interactions present in the KD and

$$KD^*$$

K

D
∗

subsystems, where the states

$$D^*_{s0}(2317)$$

D

s
0

∗

(
2317
)

and

$$D_{s1}(2460)$$

D

s
1

(
2460
)

are generated, we solve the Faddeev equations considering the fixed-center approximation for the mentioned three-body systems and find the existence of two doubly charmed

$$K^*$$

K
∗

-like mesons,

$$K_{cc}^*(4309)$$

K

cc

∗

(
4309
)

and

$$K_{cc}^*(4449)$$

K

cc

∗

(
4449
)

, with quantum numbers

$$I(J^P)=1/2\,(1^-)$$

I

(

J
P

)

=
1
/
2

(

1
-

)

. Considering the respective three-body thresholds of the two systems, both

$$K_{cc}$$

K

cc

-states are bound by around 60 MeV. An experimental confirmation will bring evidence for the existence of a degree of exoticity beyond charm +2.
Correspondence Between Alignment Wavelength and Vehicle Response Wavelength of High-Speed Rails
Authors: Liu Xingyu , Shi Jin , Dai Jian , Wang Yingjie , Lu Chaoru 
Published: December 2024

The acceleration of the vehicle body is closely related to the wavelength components of the track, making the design of track alignments crucial for enhancing the comfort of high-speed rail travel. However, research on the effects of long-wavelength deformations on alignment design and their impact on vehicle dynamics remains limited, and existing methodologies fail to effectively calculate the wavelengths of traditional alignments, which consist of linear segments and vertical curves. This study introduces a novel approach for computing long-wavelength track alignments and vehicle response wavelengths using signal decomposition and the Hilbert transform. A comprehensive program is developed to analyze the relationship between alignment and vehicle response wavelengths through correlation coefficients and coherence functions. The results show that traditional alignments have predominant wavelengths exceeding 1 000[Formula: see text]m, which exhibit negligible correlation with vehicle response due to the dominant influence of alignment curvature. In contrast, Fourier series-designed alignments demonstrate a significant correlation with vehicle response, particularly under high-speed conditions. Quantitatively, vehicle response wavelengths are found to range from 1[Formula: see text]000[Formula: see text]m to 5[Formula: see text]000[Formula: see text]m, with Fourier series alignments effectively reducing dynamic impacts. These findings highlight the potential of the proposed approach in optimizing track design for challenging railway sections, providing valuable guidance for improving high-speed railway operations.
Influence of Chromium on Structural, Morphological, Dielectric and Magnetic Properties of M-Type Calcium–Barium Hexagonal Ferrites for Technological Applications
Authors: Zahid Muhammad , Khan Hasan M. 
Published: December 2024

In this work, M-type hexagonal ferrite nanoparticles having the composition [Formula: see text], where [Formula: see text] were fabricated by the sol–gel auto-combustion technique. The influence of chromium doping on structural, dielectric and magnetic characteristics was examined. XRD powder analysis revealed the geometry of single-phase hexaferrite with P63/mmc space group. The magnetoplumbite hexagonal structure was revealed by the X-ray diffraction analysis. Crystallite size, [Formula: see text] & [Formula: see text] lattice parameters, bulk density, X-ray density, cell volume and porosity were assessed. Crystallite size ranged from 39.54[Formula: see text]nm to 42.91[Formula: see text]nm. The X-ray density and bulk density were enhanced while porosity was decreased with the substitution of [Formula: see text]cation. The morphology of the fabricated materials was inspected by the SEM analysis, which displays uniformly scattered particles with hexagonal platelet shape. The value of the dielectric constant is high in the low-frequency regime, and it decreases with increasing frequency. The dielectric constant decreased appreciably with the increase of [Formula: see text]. Such observed dielectric and magnetic features are useful for different technological applications like microwave absorbers, voltage-controlled, dielectric resonators and recording media.
Smoking-Associated Carcinogen–Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation
Authors: Aggarwal Ritesh K. , Sidoli Simone , Wang Jingli , Sahu Srabani , Sanawar Rahul , Gupta Varun , Aluri Srinivas , Sukrithan Vineeth , Vegivinti Charan T.R. , Zavras Phaedon D. , Verma Divij , Gordon-Mitchell Shanisha , Agarwal Beamon , Verma Tanya , Starczynowski Daniel T. , Steidl Ulrich G. , Shastri Aditi , Halmos Balazs , LaFave Lindsay M. , Cheng Haiying , Verma Amit , Zou Yiyu 
Published: December 2024

Abstract

Purpose:
Even though smoking is associated with lung cancer, the exact molecular pathways that link carcinogens with inflammation and oncogenic transformation are not well elucidated. Two major carcinogens in cigarette smoke, nicotine-derived nitrosamine ketone, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and benzo(α)pyrene (BaP), have not been tested in models that mimic inhaled exposure for prolonged periods of time.

Experimental Design:
Mouse models were used for intratracheal delivery of NNK and BaP (NB) for 18 months. Tissue microarrays from human lung cancers were evaluated for IL-1 receptor–associated kinase-4 (IRAK4) expression. Functional effects of IRAK4 inhibition were evaluated in cell lines and xenografts.

Results:
Smoking-associated carcinogen–treated mice developed epithelial dysplasia followed by lung cancers at increased rates relative to controls. Histology revealed myeloid inflammation in murine lung tissues. Lung macrophages showed elevated levels of proinflammatory IL-1β when exposed to cigarette smoking condensate. A key downstream mediator of IL-1β signaling, IRAK4, was overexpressed in murine lung tissues exposed to carcinogens. The majority of human lung cancer samples also exhibited overactivated IRAK4 expression. IRAK4 localized in microtubules in lung cancer cell lines. Using mass spectrometry on isolated microtubules, we observed that IRAK4 inhibition was associated with decreased phosphorylation of tubular motility proteins, including myosin heavy-chain 9. Inhibition of IRAK4 resulted in decreased invasion in lung cancer cell lines and reduced growth of lung cancer xenografts.

Conclusions:
These data demonstrate that smoking-associated carcinogens can be linked to oncogenic transformation via inflammatory IRAK4 activation.
Paradoja de inclusión digital: uso del celular y tecnodependencia en estudiantes universitarios. Estudio de caso
Authors: Melo-Solarte Diego Samir , Narváez-Solarte William , Grisales-Giraldo Jhonathan 
Published: December 2024

(analytical)This study aimed to characterize and determine behavioral patterns regarding cellphone use amonguniversity students. The methodology involved creating an mobile App to capture statistical data from a person’s cellphone, which was installed on 73 students’ cellphones who enrolled in the Faculty of Sciences and Engineering of the Manizales University. The App captured data over a period of three weeks, which was then complemented by 18 interviews. The collected data was processed using the Crisp-DM methodology. The results showed that students used their cellphones for an average of 29.2 minutes each day, unlocking it 43 times per hour. The cellphones were occasionally used for productive activities, but most of the time the focus was on using them for recreational activities. This research on cellphone use revealed behaviors that can contribute to psychological disorders.
Keywords: Cell phone use; technological culture; technological progress; young people.
Authors’ keywords: Techno-dependence; mobile phone addiction.