bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis of strain
Priestia megaterium
B1 reveals conserved potential for adaptation to endophytism and plant growth promotion
Authors: Mahmoud Fatma M. , Pritsch Karin , Siani Roberto , Benning Sarah , Radl Viviane , Kublik Susanne , Bunk Boyke , Spröer Cathrin , Schloter Michael 
Published: June 2024

ABSTRACT

In our study, we aimed to explore the genomic and phenotypic traits of
Priestia megaterium
strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of
P. megaterium
strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.

IMPORTANCE

Both genomic and phenotypic analyses yielded valuable insights into the capacity of
P. megaterium
B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that
P. megaterium
members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.
Long-term effectiveness, safety, and tolerability of doravirine in antiretroviral-experienced people with HIV in real life
Authors: Mejías-Trueba Marta , Gutierrez-Valencia Alicia , Llaves-Flores Silvia , Roca-Oporto Cristina , Herrero Marta , Sotomayor de la Piedra César , Lopez-Cortes Luis F. , Espinosa Nuria 
Published: June 2024

ABSTRACT

Real-life data on doravirine (DOR) in different drug combinations are limited. We evaluated the effectiveness of DOR plus two nucleos(t)ide reverse transcriptase inhibitors (NRTI), mainly abacavir/lamivudine, and dual therapies in people with HIV (PWH), mostly virologically suppressed. Ambispective observational study that enrolled adults PWH who initiated a DOR-based regimen from September 2020 to February 2022 at a referral center in Spain. Participants were grouped as follows: A, received DOR plus two NRTI; B, dual therapy (DT) with DOR plus dolutegravir (DTG) or darunavir/cobicistat (DRVc); C, DOR plus ≥two antiretroviral drugs. The primary endpoints were treatment effectiveness at week 48 by intention-to-treat (ITT) and per-protocol analysis (OT). A cohort of 187 participants, 91% virologically suppressed, were analyzed after a median follow-up of 112 weeks (80–136). Group A received DOR plus abacavir/lamivudine (ABV/3TC) (
n
= 109) or tenofovir/emtricitabine (TFV/3TC) (
n
= 45). At week 48, the effectiveness of DOR plus ABV/3TC by ITT was 90.8% (CI
95
, 88.0–93.6), better than with TFV/FTC [73.3% (66.7–79.9);
P
= 0.003]. Only one virologic failure was observed. Mild adverse effects were the cause of treatment discontinuation in 7.8%, followed by switching to a single-tablet regimen. In group B, the effectiveness by ITT was 92.9% (CI
95
, 88.0–97.8) at week 48. No adverse effects or virologic failure were registered in this group. DOR plus two NRTI or DT have long-term effectiveness and safety as a switching option for PWH, mostly virologically suppressed. The DOR plus ABV/3TC combination has shown even better effectiveness than TFV/FTC.

IMPORTANCE
DOR-based regimens have shown long-term effectiveness and safety in PWH, mostly virologically suppressed. The combination of DOR plus ABV/3TC has shown even better safety and effectiveness than TFV/FTC. DOR plus two NRTI offers cost benefits compared to other regimens.
Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy
Authors: Hilliam Yasmin , Armbruster Catherine R. , Rapsinski Glenn J. , Marshall Christopher W. , Moore John , Koirala Junu , Krainz Leah , Gaston Jordan R. , Cooper Vaughn S. , Lee Stella E. , Bomberger Jennifer M. 
Published: June 2024

ABSTRACT

Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has revolutionized the treatment of cystic fibrosis (CF) for most affected individuals but the effects of treatment on sinus microbiota are still unknown. Changes to the airway microbiota in CF are associated with disease state and alterations to the bacterial community after ETI initiation may require changes to clinical management regimens. We collected sinus swab samples from the middle meatus in an observational study of 38 adults with CF and chronic rhinosinusitis (CRS) from 2017 to 2021 and captured the initiation of ETI therapy. We performed 16S and custom amplicon sequencing to characterize the sinus microbiota pre- and post-ETI. Real-time quantitative PCR (RT-qPCR) was performed to estimate total bacterial abundance. Sinus samples from people with CF (pwCF) clustered into three community types, dependent on the dominant bacterial organism: a
Pseudomonas
-dominant,
Staphylococcus
-dominant, and mixed dominance cluster. Shannon’s diversity index was low and not significantly altered post-ETI. Total bacterial load was not significantly lowered post-ETI.
Pseudomonas
spp. abundance was significantly reduced post-ETI, but eradication was not observed.
Staphylococcus
spp. became the dominant organism in most individuals post-ETI and we showed the presence of methicillin-resistant
Staphylococcus aureus
(MRSA) in the sinus both pre- and post-ETI. We also demonstrated that the sinus microbiome is predictive of the presence of
Pseudomonas
spp.,
Staphylococcus
spp., and
Serratia
spp. in the sputum.
Pseudomonas
spp. and
Staphylococcus
spp., including MRSA, persist in the sinuses of pwCF after ETI therapy, indicating that these pathogens will continue to be important in CF airway disease management in the era of highly effective modulator therapies (HEMT).

IMPORTANCE

Highly effective modulator therapies (HEMT), such as elexacaftor/tezacaftor/ivacaftor (ETI), for cystic fibrosis (CF) have revolutionized patient care and quality of life for most affected individuals. The effects of these therapies on the microbiota of the airways are still unclear, though work has already been published on changes to microbiota in the sputum. Our study presents evidence for reduced relative abundance of
Pseudomonas
spp. in the sinuses following ETI therapy. We also show that
Staphylococcus
spp. becomes the dominant organism in the sinus communities of most individuals in this cohort after ETI therapy. We identified methicillin-resistant
Staphylococcus aureus
(MRSA) in the sinus microbiota both pre- and post-therapy. These findings demonstrate that pathogen monitoring and treatment will remain a vital part of airway disease management for people with cystic fibrosis (pwCF) in the era of HEMT.
In vitro
identification of underutilized β-lactam combinations against methicillin-resistant
Staphylococcus aureus
bacteremia isolates
Authors: Davis Kathleen P. , McDermott Laura A. , Snydman David R. , Aldridge Bree B. 
Published: June 2024

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) bacteremia is a serious clinical challenge with high mortality rates. Antibiotic combination therapy is currently used in cases of persistent infection; however, the limited development of new antibiotics will likely increase the need for combination therapy, and better methods are needed for identifying effective combinations for treating persistent bacteremia. To identify pairwise combinations with the most consistent potential for benefit compared to monotherapy with a primary anti-MRSA agent, we conducted a systematic study with an
in vitro
high-throughput methodology. We tested daptomycin and vancomycin each in combination with gentamicin, rifampicin, cefazolin, and oxacillin, and ceftaroline with daptomycin, gentamicin, and rifampicin. Combining cefazolin with daptomycin lowered the daptomycin concentration required to reach 95% growth inhibition (IC
95
) for all isolates tested and lowered daptomycin IC
95
below the sensitivity breakpoint for five out of six isolates that had daptomycin minimum inhibitory concentrations at or above the sensitivity breakpoint. Similarly, vancomycin IC
95
s were decreased when vancomycin was combined with cefazolin for 86.7% of the isolates tested. This was a higher percentage than was achieved by adding any other secondary antibiotic to vancomycin. Adding rifampicin to daptomycin or vancomycin did not always reduce IC
95
s and failed to produce synergistic interaction in any of the isolates tested; the addition of rifampicin to ceftaroline was frequently synergistic and always lowered the amount of ceftaroline required to reach the IC
95
. These analyses rationalize further
in vivo
evaluation of three drug pairs for MRSA bacteremia: daptomycin+cefazolin, vancomycin+cefazolin, and ceftaroline+rifampicin.

IMPORTANCE

Bloodstream infections caused by methicillin-resistant
Staphylococcus aureus
(MRSA) have a high mortality rate despite the availability of vancomycin, daptomycin, and newer antibiotics including ceftaroline. With the slow output of the antibiotic pipeline and the serious clinical challenge posed by persistent MRSA infections, better strategies for utilizing combination therapy are becoming increasingly necessary. We demonstrated the value of a systematic high-throughput approach, adapted from prior work testing antibiotic combinations against tuberculosis and other mycobacteria, by using this approach to test antibiotic pairs against a panel of MRSA isolates with diverse patterns of antibiotic susceptibility. We identified three antibiotic pairs—daptomycin+cefazolin, vancomycin+cefazolin, and ceftaroline+rifampicin—where the addition of the second antibiotic improved the potency of the first antibiotic across all or most isolates tested. Our results indicate that these pairs warrant further evaluation in the clinical setting.
Agreement between two real-time commercial PCR kits and an in-house real-time PCR for diagnosis of mucormycosis
Authors: Rafanomezantsoa Lovanirina Clémencia , Sabourin Estelle , Guennouni Sebbouh Nadia , Sitterlé Emilie , Ben Halima Nada , Raveloarisaona Yannick Sonjah , Quesne Gilles , Dannaoui Eric , Bougnoux Marie-Elisabeth 
Published: June 2024

ABSTRACT

Mucormycosis is a severe and emerging invasive fungal infection associated with high mortality rates. Early diagnosis is crucial for initiating specific antifungal treatment, with molecular tools currently representing the most efficient diagnostic approach. Presently, a standardized in-house real-time PCR method is widely employed for diagnosing mucormycosis. Our study aimed to evaluate the agreement for the Mucorales DNA detection between two commercial real-time PCR assays—the Fungiplex Mucorales Real-Time PCR Kit and the MycoGENIE
Aspergillus-Mucorales
spp. Real-Time PCR Kit—in comparison with the in-house PCR. We retrospectively analyzed 58 samples previously identified as positive for Mucorales using the in-house PCR. These samples, obtained from 22 patients with proven or probable mucormycosis, were tested with both commercial kits. Additionally, samples from 40 patients without mucormycosis served as negative controls. Our findings revealed that the MycoGENIE Kit demonstrated superior performance in detecting Mucorales DNA in samples identified as positive by the in-house PCR. Notably, we observed minimal variability in cycle threshold (CT) values when comparing the results of the MycoGENIE Kit with those of the in-house PCR, with an average difference of 1.8 cycles. In contrast, the Fungiplex Kit exhibited a larger discrepancy in CT values compared to the in-house PCR, with an average difference of 4.1 cycles. The MycoGENIE Kit exhibited very good agreement (kappa of 0.82) with the in-house PCR for detecting Mucorales DNA across various sample types. These findings are important for the choice of kits that could be used to diagnose mucormycosis in clinical microbiology laboratories.

IMPORTANCE
Early diagnosis of mucormycosis is crucial for initiating effective treatment. The detection of Mucorales DNA by PCR in serum has revolutionized the diagnosis of this infection. However, the use of in-house methods can be time consuming. The availability of a commercial kit eliminates the need for in-house assay development, reducing laboratory workload and ensuring consistent performance across different healthcare settings. Currently, there are several commercial assays available, but many have limited evaluation. In this study, we compared two commercial kits and found that the MycoGENIE Kit offers a promising alternative to the in-house method.
Comparative performance of the Platelia
Aspergillus
Antigen and
Aspergillus
Galactomannan antigen Virclia Monotest immunoassays in serum and lower respiratory tract specimens: a “real-life” experience
Authors: Albert Eliseo , Alcaraz María Jesús , Giménez Estela , Clari María Ángeles , Torres Ignacio , Colomina Javier , Olea Beatriz , Tormo Mar , Piñana José Luis , Oltra Rosa , Signes-Costa Jaime , Carbonell Nieves , Solano Carlos , Navarro David 
Published: June 2024

ABSTRACT

The Platelia Aspergillus Antigen immunoassay is the “gold standard” for Aspergillus galactomannan (GLM) measurement in sera and bronchoalveolar lavage (BAL) for the diagnosis of invasive pulmonary aspergillosis (IPA). We evaluated the performance of the Aspergillus GLM antigen Virclia Monotest compared to the Platelia assay. A total of 535 specimens [320 sera, 86 bronchial aspirates (BAs), 70 BAL, and 59 tracheal aspirates (TAs)] from 177 adult patients (72 hematological, 32 Intensive Care Unit, and 73 hospitalized in other wards) were processed for GLM testing upon clinical request. One patient had proven IPA, and 11 had probable disease. After excluding indeterminate Virclia results (
n
= 38), 396 specimens yielded concordant results (56 positive and 340 negative) and 101 discordant results (Virclia positive/Platelia negative,
n
= 95). The overall agreement between immunoassays was higher for sera (
κ
0.56) than for BAL (
κ
≤ 0.24) or BAS and TA (
κ
≤ 0.22). When considering all specimen types in combination, the overall sensitivity and specificity of the Virclia assay for the diagnosis of proven/probable IPA were 100% and 65%, respectively, and for the Platelia immunoassay, sensitivity and specificity were 91.7% and 89.4%, respectively. The correlation between index values by both immunoassays was strong for serum/BAL (
ρ
= 0.73;
P
< 0.001) and moderate for BAS/TA (Rho = 0.52;
P
= 0.001). The conversion of Virclia index values into the Platelia index could be derived by the formula
y
= (11.97 *
X
)/3.62 +
X
). Data from GLM-positive serum/BAL clinical specimens fitted the regression model optimally (
R
2
= 0.94), whereas that of BAS and TA data did not (
R
2
= 0.11). Further studies are needed to determine whether the Virclia assay may be an alternative to the Platelia assay for GLM measurement in sera and lower respiratory tract specimens.

IMPORTANCE
Galactomannan detection in serum or bronchoalveolar fluid specimens is pivotal for the diagnosis of invasive pulmonary aspergillosis (IPA). The Platelia Aspergillus Antigen immunoassay has become the “gold standard” for Aspergillus GLM measurement. Here, we provide data suggesting that the Virclia Monotest assay, which displays several operational advantages compared with the Platelia assay, may become an alternative to the Platelia assay, although further studies are needed to validate this assumption. We also provide a formula allowing the conversion of Virclia index values into Platelia values. The study may contribute toward positioning the Virclia assay within the diagnostic algorithm of IPA.
Seasonal patterns and key chemical predictors of dissolved greenhouse gases in small prairie pothole ponds
Authors: Miranda Lauren T. , Whitfield Colin J. 
Published: June 2024

Shallow ponds can provide ideal conditions for production of greenhouse gases (GHGs) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), and thus are important to include in global and regional GHG budgets. The Canadian Prairie Pothole Region contains millions of shallow natural ponds, and we investigated GHG dynamics in 145 ponds across the region. Ponds were consistently supersaturated with CH4, often supersaturated with CO2 (57% occurrence), and often undersaturated with N2O (65% occurrence). Spring measurements showed higher N2O saturation ( p = 0.0037) than summer, while summer had higher CH4 ( p < 0.001) and CO2 ( p = 0.023) saturation than spring. Ponds exhibited large physicochemical variation, yet sulfate concentration and pH were strong predictors of dissolved CH4 and CO2, respectively. No predictor was identified for N2O. The link between sulfate and CH4 has important implications as dissolved CH4 in low sulfate (<178 mg L−1) systems was much more responsive to changes in temperature. This research fills an important knowledge gap about the GHG dynamics of prairie pothole ponds and the role of water chemistry for diffuse GHG release. Our work can also be used in ongoing efforts to describe ecosystem services (or disservices) assigned to ponds in this agriculture-dominated region.
The impact of different unravelings in a monitored system of free fermions
Authors: Piccitto Giulia , Rossini Davide , Russomanno Angelo 
Published: June 2024

AbstractWe consider a free-fermion chain undergoing dephasing, described by two different random-measurement protocols (unravelings): a quantum-state-diffusion and a quantum-jump one. Both protocols keep the state in a Slater-determinant form, allowing to address quite large system sizes. We find a bifurcation in the distribution of the measurement operators along the quantum trajectories, that’s to say, there is a point where the shape of this distribution changes from unimodal to bimodal. The value of the measurement strength where this phenomenon occurs is similar for the two unravelings, but the distributions and the transition have different properties reflecting the symmetries of the two measurement protocols. We also consider the scaling with the system size of the inverse participation ratio of the Slater-determinant components and find a power-law scaling that marks a multifractal behaviour, in both unravelings and for any nonvanishing measurement strength.Graphical abstractPosition of the maxima ofPnvs$$\gamma $$γfor the QSD protocol. The two maxima stem continuously and symmetrically at the bifurcation point$$\gamma $$γQSD$$\sim 0.2$$∼0.2, with a discontinuity of the derivative.
Gluon GTMDs at nonzero skewness and impact parameter dependent parton distributions
Authors: Tan Chentao , Lu Zhun 
Published: June 2024

AbstractWe investigate the leading twist generalized transverse momentum dependent parton distributions (GTMDs) of the unpolarized and longitudinally polarized gluons in the nucleon. We adopt a light-front gluon-triquark model for the nucleon motivated by soft-wall AdS/QCD. The gluon GTMDs are defined through the off-forward gluon-gluon generalized correlator and are expressed as the overlap of light-cone wave functions. The GTMDs can be employed to provide the generalized parton distributions (GPDs) by integrating out the transverse momentum. The Fourier transform of the GPDs encodes the parton distributions in the transverse position space, namely, the impact parameter dependent parton distributions (IPDs). We also calculate the three gluon IPDs corresponding to the GPDs $$H^g$$

H
g

, $$E^g$$

E
g

and $$\widetilde{H}^g$$

H
~

g

, and present their dependence on x and $$b_\perp $$

b
⊥

, respectively.
Classical acceleration temperature from evaporated black hole remnants and accelerated electron-mirror radiation
Authors: Lin Kuan-Nan , Ievlev Evgenii , Good Michael R. R. , Chen Pisin 
Published: June 2024

AbstractWe investigate the radiation from accelerating electrons with asymptotic constant velocity and their analog signatures as evaporating black holes with left-over remnants. We find high-speed electrons, while having a high temperature, correspond to low-temperature analog remnants.
Superoscillations in high energy physics and gravity
Authors: Addazi Andrea , Gan Qingyu 
Published: June 2024

AbstractWe explore superoscillations within the context of classical and quantum field theories, presenting novel solutions to Klein–Gordon’s, Dirac’s, Maxwell’s and Einstein’s equations. In particular, we illustrate a procedure of second quantization of fields and how to construct a Fock space which encompasses Superoscillating states. Furthermore, we extend the application of superoscillations to quantum tunnelings, scatterings and mixings of particles, squeezed states and potential advancements in laser interferometry, which could open new avenues for experimental tests of quantum gravity effects. By delving into the relationship among superoscillations and phenomena such as Hawking radiation, the black hole (BH) information and the Firewall paradox, we propose an alternative mechanism for information transfer across the BH event horizon.
Imaging of the superficial white matter in health and disease
Authors: Van Dyken Peter C. , Khan Ali R. , Palaniyappan Lena 
Published: June 2024

Abstract
The superficial white matter, the layer of white matter immediately deep to the cortical grey matter, is a highly complex, heterogeneous tissue region comprising dense meshes of neural fibres, a robust population of interstitial neurons, and ongoing glial activity and myelination. It originates from the histologically distinct, developmentally vital subplate in the foetal brain, maintains thalamo-cortical connections throughout adult life, and is a necessary passage for all axons passing between the grey and white matter. Despite these features, the superficial white matter is among the most poorly understood regions of the brain, in part due to its complex makeup and the resulting difficulty of its study. In this review, we present our current knowledge of superficial white matter (SWM) anatomy, development, and response to disease. We discuss the unique challenges encountered in the neuroimaging of this region, including the lack of standard definition and the non-specificity of neuroimaging markers amplified by the complexity of the tissue. We discuss recent innovations and offer potential pathways forward.