bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Factor H and anti-Neisserial surface protein A (NspA) antibodies compete for overlapping binding sites on meningococcal NspA
Authors: Raghunathan Dhaarini , Lim Susie Sohee , Moe Gregory R. , Beernink Peter T. 
Published: February 2025

ABSTRACT

Neisserial surface protein A (NspA) is a small, conserved outer membrane protein that has been investigated as a vaccine antigen against meningococcal disease. After NspA had been tested in humans, this antigen was discovered to recruit the human complement regulator Factor H (FH). Previous studies in transgenic mice showed that human FH decreased the protective antibody responses to NspA. The purpose of the present study was to map the binding sites for human FH and anti-NspA antibodies. We found that an anti-NspA monoclonal antibody (mAb), AL-12, inhibits binding of FH to NspA by enzyme-linked immunosorbent assay (ELISA). Based on this result, we tested the roles of the 10 charged residues on the external loops of NspA in binding these two molecules by site-specific mutagenesis and binding experiments. Through ELISA and surface plasmon resonance experiments, we show that three aspartate (D) residues, D77 on loop 2 and D113 and D118 on loop 3, are important for binding human FH. Further, residues D113 and D118, as well as lysine 79 and arginine 109, are involved in binding mAb AL-12, which binds to a conformational epitope. The results have implications for strategies to increase NspA immunogenicity by decreasing binding to human FH, as has been done with other antigens that recruit this complement regulator.
Complete genome sequence of an enterotoxigenic
Bacteroides fragilis
strain 86-5443-2-2 from a piglet
Authors: Lee Eunbi , Yeom Jinki 
Published: February 2025

ABSTRACT

This study presents the genome sequence of
Bacteroides fragilis
strain 86-5443-2-2, isolated from a piglet. The genome of this strain forms a single contig spanning 5.4 million base pairs with a 43.5% GC content and 4,480 genes. Notably, this bacterium possesses two copies of a pathogenic island capable of producing enterotoxins.
Draft genome sequence of
Aspergillus oryzae
(Ahlburg) Cohn ATCC 16868
Authors: Talamantes Becerra Berenice , Hlaing Mya Myintzu , McAuley Catherine M. , Twine Natalie A. , Bauer Denis C. , Shiferaw Terefe Netsanet 
Published: February 2025

ABSTRACT

The draft genome sequence of
Aspergillus oryzae
ATCC 16868 is presented here.
A. oryzae
produces carbohydrase and proteolytic enzymes and is used in the production of fermented food and feed. Genomic data have been utilized to investigate allergenicity and virulence characteristics, contributing to its safety evaluation in food production systems.
Neonatal administration of
Lactiplantibacillus plantarum
ATCC 202195 with or without fructooligosaccharide in Bangladesh: a placebo-controlled randomized trial
Authors: Pell Lisa G. , Qamar Huma , Bassani Diego G. , Heasley Cole , Funk Celine , Chen Chun-Yuan , Shawon Jakaria , O'Callaghan Karen M. , Pullenayegum Eleanor , Hamer Davidson H. , Haque Rashidul , Kabir Mamun , Ahmed Tahmeed , O'Kelly Ciobha , Hossain Md Iqbal , Khan Afreen Z. , Loutet Miranda G. , Islam Mohammad Shahidul , Morris Shaun K. , Shah Prakesh S. , Sherman Philip M. , Sultana Shamima , Mahmud Abdullah Al , Saha Samir K. , Sarker Shafiqul A. , Roth Daniel E. 
Published: February 2025

ABSTRACT

Lactiplantibacillus plantarum
ATCC 202195 (LP202195) plus fructooligosaccharide (FOS) for 7 days was previously shown to colonize the infant intestine up to 6 months of age and reduced sepsis rates among young infants in rural India. In a phase 2 randomized controlled trial in Dhaka, Bangladesh (
N
= 519), neonatal administration of LP202195 for 1 or 7 days, with or without FOS, increased LP202195 stool abundance from 14 to 60 days of age, versus placebo. Abundance progressively declined in the post-administration period and did not persist beyond 2 months of age. FOS did not affect LP202195 abundance or its duration of persistence. All regimens were well-tolerated and safe. The absence of LP202195 colonization was inconsistent with results from a prior trial. Additional large-scale trials of LP202195 ± FOS are needed to establish its efficacy in infants who do not become LP202195-colonized.

IMPORTANCE

Among infants born in Dhaka, Bangladesh, a 7-day regimen of
Lactiplantibacillus plantarum
ATCC 202195 (LP202195) plus fructooligosaccharide (FOS) did not colonize the infant gastrointestinal (GI) tract. The absence of colonization is inconsistent with a prior study of the same synbiotic regimen in India, in which LP202195 was shown to persist in the infant GI tract for up to 6 months. Sustained LP202195 colonization was thought to be required for the probiotic to impart its beneficial impact on newborn sepsis. Therefore, additional trials are warranted to confirm the previously observed effects of LP202195 on infant clinical outcomes in the absence of LP202195 colonization. Moreover, since regimens of LP202195 that did not include FOS were indistinguishable from the synbiotic in terms of colonization, safety, and tolerability, future trials should assess the role of FOS for clinical efficacy; removing FOS would reduce costs, an important consideration for scale-up.

CLINICAL TRIALS

This study has been registered at ClinicalTrials.gov as
NCT05180201
.
Plasmid-borne
mcr-1
and replicative transposition of episomal and chromosomal
bla
NDM-1
,
bla
OXA-69
, and
bla
OXA-23
carbapenemases in a clinical
Acinetobacter baumannii
isolate
Authors: Mmatli Masego , Mbelle Nontombi Marylucy , Osei Sekyere John 
Published: February 2025

ABSTRACT

A multidrug-resistant clinical
Acinetobacter baumannii
isolate with resistance to most antibiotics was isolated from a patient at an intensive care unit. The genetic environment, transcriptome, mobile, and resistome were characterized. The MicroScan system, disc diffusion, and broth microdilution were used to determine the resistance profile of the isolate. A multiplex PCR assay was also used to screen for carbapenemases and
mcr
-1 to -5 resistance genes. Efflux-pump inhibitors were used to evaluate efflux activity. The resistome, mobilome, epigenome, and transcriptome were characterized. There was phenotypic resistance to 22 of the 25 antibiotics tested, intermediate resistance to levofloxacin and nalidixic acid, and susceptibility to tigecycline, which corresponded to the 27 resistance genes found in the genome, most of which occurred in multiple copies through replicative transposition. A plasmid-borne (pR-B2.MM_C3)
mcr-
1 and chromosomal
bla
PER-7
, bla
OXA-69
, bla
OXA-23
(three copies),
bla
ADC-25
,
bla
TEM-1B
, and
bla
NDM-1
were found within composite transposons, ISs, and/or class 1 and 2 integrons on genomic islands. Types I and II methylases and restriction endonucleases were in close synteny to these resistance genes within the genomic islands; chromosomal genomic islands aligned with known plasmids. There was a closer evolutionary relationship between the strain and global strains but not local or regional strains; the resistomes also differed. Significantly expressed/repressed genes (6.2%) included resistance genes, hypothetical proteins, mobile elements, methyltransferases, transcription factors, and membrane and efflux proteins. The genomic evolution observed in this strain explains its adaptability and pandrug resistance and shows its genomic plasticity on exposure to antibiotics.

IMPORTANCE
A pandrug-resistant pathogen that was susceptible to only a single antibiotic, tigecycline, was isolated from a middle-aged patient in an ICU. This pathogen contained two plasmids and had a chromosome that contained portions that were integrated externally from plasmids. These genomic islands were rich with resistance genes, mobile genetic elements, and restriction-modification systems that protected the pathogen and facilitated gene regulation. The strain contained 35 resistance genes and 12 virulence genes. The strain was of closer evolutionary distance to several international strains suggesting that it was imported into South Africa. However, its resistome was unique, suggesting an independent evolution on exposure to antibiotic therapy mediated by epigenomic factors and MGE transposition events. The varied mechanisms available to this strain to overcome antibiotic resistance and spread to other areas and/or transfer its resistance determinants are worrying. This is ultimately a risk to public health, evincing the need for antibiotic stewardship.
Profilin Pfy1 is critical for cell wall integrity and virulence in
Candida albicans
Authors: Sun Xun , Wang Yueqing , Yang Xiaomin , Xiang Xi , Zou Lili , Liu Xiaowen , Luo Gang , Han Qi 
Published: February 2025

ABSTRACT

Profilin is a small actin-binding protein that plays an important role in actin polymerization. However, its functions in
Candida albicans
, the most prevalent fungal pathogen, remain unclear. Here, we report that profilin plays a crucial role in
C. albicans
morphogenesis and virulence. Deletion of profilin results in abnormal morphogenesis and impaired hyphal development. Furthermore,
pfy1Δ/Δ
is hypersensitive to cell wall stress and displays thicker cell wall than wild-type cells, indicative of a critical function of Pfy1 in cell wall integrity. In addition, our findings demonstrate that profilin is required for the virulence of
C. albicans
in a murine model of systemic infection. In conclusion, our work provides a promising target for developing antifungal drugs.

IMPORTANCE

Our research revealed Pfy1 is not only involved in hyphal development but also essential for pseudohyphal formation in response to DNA damage agents methyl methanesulfonate (MMS) and H
2
O
2.
The disruption of
PFY1
resulted in striking morphological defects in both yeast and hyphal forms. Further investigation suggested that profilin plays a role in polarized growth of
Candida albicans
via binding with Act1, and contributes to cell wall remodeling. Both hyphal growth and cell wall integrity are the important virulence factors of
C. albicans
. Thus,
pfy1Δ/Δ
strains significantly reduced mortality rates in mice. These findings suggested that profilin could serve as a target for developing new antifungal drugs possibly for use in combination therapies with caspofungin, for treating invasive candidiasis.
Disrupting the balance: how acne duration impacts skin microbiota assembly processes
Authors: Sun Lang , Wang Qingqun , Huang Jing , Wang Huan , Yu Zheng 
Published: February 2025

ABSTRACT

Growing interest in the impact of microbial balance on health has driven studies on the ecological processes shaping the skin microbiota. Skin diseases, which alter the skin’s local environment, can disrupt the microbial structure and interact with the disease itself. However, research on microbial assembly in diseased skin remains limited. In this study, we applied ecological models to characterize the processes shaping the skin microbiota in acne patients, considering the impact of disease duration on both skin pores and surfaces using bacterial amplicon sequencing. Our results revealed a significant shift in microbial diversity on the skin surface of patients with long-term acne. Further microbial community analyses showed a transition in ecological processes from healthy to diseased skin. Microbial communities on the skin surfaces of healthy controls and individuals with short-duration acne were primarily driven by heterogeneous selection, whereas microbial drift dominated the assembly process in the long-duration groups. Using the Sloan neutral model, we classified amplicon sequence variants (ASVs) into high-effect and low-effect groups based on relative abundance and sample occurrence. High-effect ASVs, likely exerting a greater ecological influence, were predominantly represented by
Cutibacterium
across all acne-affected skin groups, while
Staphylococcus
became enriched among high-effect ASVs in patients with long-term acne. Functional profiling further demonstrated that high-effect ASVs were significantly enriched in motility-related pathways. Additionally, we observed a reduction in microbial network complexity on skin surfaces as disease duration increased. Overall, the ecological dynamics of skin microbial communities may offer valuable insights into the mechanisms underlying disease onset and persistence.

IMPORTANCE
The skin microbiota plays a critical role in acne development, yet the processes governing microbial assembly during acne progression remain poorly understood. Previous studies predominantly focused on factors such as acne severity, location, and duration in relation to skin microbial structure, with little attention given to the ecological mechanisms shaping the communities. In this study, we applied ecological models to investigate the processes influencing microbial assembly of skin microbiota in acne patients with varying disease durations and examined functions of ecologically important non-neutral amplicon sequence variants (ASVs). Our findings reveal a transition in ecological processes from deterministic to neutral processes as acne duration increased, with non-neutral ASVs potentially contributing to acne pathogenicity and persistence. These insights contribute to a deeper understanding of the ecological dynamics underlying acne and indicate that targeting these non-neutral ASVs or their associated functions may serve as the basis for future therapeutic strategies.
Vacuum energy in non-supersymmetric quasi-realistic heterotic-string vacua with fixed moduli
Authors: Basaad Eman , Detraux Luke A. , Avalos Alonzo R. Diaz , Faraggi Alon E. , Percival Benjamin 
Published: February 2025

Abstract
Recently, Baykara et al. (The Quasicrystalline string landscape, 2024; New non-supersymmetric tachyon-free strings, 2024) discussed the existence of quasicrystalline string vacua that contain a single neutral moduli, the dilaton, and studied compactifications of the non-supersymmetric

$$SO(16)\times SO(16)$$

S
O
(
16
)
×
S
O
(
16
)

heterotic-string on these spaces. We discuss a specific class of quasi-realistic string vacua with similar properties that has been known since the late eighties and analyse the vacuum energy in several non-supersymmetric examples that correspond to compactifications of tachyon free ten dimensional vacua as well as compactifications of tachyonic ten dimensional vacua. Our analysis uses the Free Fermionic Formalism of the heterotic-string in four dimensions and employs asymmetric boundary conditions that project all the geometrical moduli by Generalised GSO projections. This methodology produces models with both positive and negative spacetime potential at one-loop.
New axion contribution to the two-photon decays of neutral pions
Authors: Lu Zhen-Yan , Huang Yang , Cheng Ji-Gui , Lu Qi , Wang Shu-Peng 
Published: February 2025

Abstract
The presence of axions introduces new diagrams at one-loop order to the two-photon decays of the neutral pion through axion-pion mixing. In this work, we calculate this correction, missing in all current calculations, in the framework of SU(2) chiral perturbation theory. We show that the correction is proportional to the axion-photon coupling and the square of axion mass, which in turn is strongly suppressed by the axion decay constant for the classical space window but may not be negligible for the QCD axion in the MeV or even larger mass range. On the other hand, in combination with the experimental measurement of the decay width of

$$\pi ^0\rightarrow \gamma \gamma $$

π
0

→
γ
γ

process, this result rules out the standard QCD axion as an explanation for the possible discrepancy between the chiral perturbation theory prediction and the experimental data.
Statistical Analysis of Pond Ash- Bentonite Mixtures: Implications for Liner and Cover Material Design
Authors: Sankar Ganesh K. S. , Ashok Kumar T. 
Published: February 2025

This study investigates the potential use of pond ash (PA) mixed with varying proportions of bentonite (Bt) (10%/ 20%/ 30%) as a landfill liner and cover material. Laboratory test study covers Atterberg limits, compaction, hydraulic conductivity (
k
), and unconfined compressive strength (

q
u

) tests. Further, the test results were analyzed using the probabilistic approach to account for uncertainty. While evaluating the PA-Bt mixtures under liner and cover placement conditions, significant variability was observed in the hydraulic conductivity (
k
) and unconfined compressive strength (

q
u

), with sample coefficients of variation of 197% and 94%, respectively. To better understand and quantify the variability, the probability density function for
k
and

q
u

was identified as a log-normal distribution. The inferential statistical analysis limits
k
and

q
u

standard deviations to 0.66 and 0.17 (key parameters for informed decision-making), respectively. Hypothesis testing was then conducted to assess the suitability of compacted PA-Bt mixtures based on the desired and characteristic values of liner and cover materials. This probabilistic approach allows a more flexible evaluation of placement conditions than deterministic methods, ensuring more reliable performance. Addressing material variability of PA-Bt mixtures enables cost-effective design by exploiting the most probable outcomes.
Transfer of balance performance depends on the specificity of balance training
Authors: Rizzato A. , Faggian S. , Paoli A. , Marcolin G. 
Published: February 2025

This study investigated whether a four-week training on an easy-level unstable board (EL) could induce a transfer of balance performance in a hard-level unstable board (HL) and in an unexpected perturbation-based task. Non-linear center of pressure (CoP) analysis investigated whether training could induce postural control adaptations in trained and untrained tasks. Thirty-four subjects were divided into a training (TR, N=17) and a control (CTRL, N=17) group. Balance was assessed before (T0) and after (T1) a balance training under static and dynamic conditions (EL, HL, and perturbation-based task). A force platform allowed the calculation of CoP displacement while balance performance based on the angular displacement of the unstable boards was assessed with an inertial sensor. From the angular displacement, we calculated three parameters of balance performance: Full Balance (FB), Fine Balance (FiB), and Gross Balance (GB). Stabilogram diffusion analysis (SDA) and sample entropy (SampEn) indirectly assessed neuromuscular control mechanisms. Results showed improvements in the TR from T0 to T1 in balance performance for FB (p<0.001), FiB (p<0.05), and GB (p<0.01) on EL and HL boards. In the perturbation-based task, the earliest CoP response consequent to perturbation improved after training (p<0.01). SampEn and SDA revealed increased automaticity (p<0.05) and efficiency (p<0.05) of balance control in the EL and HL tasks after training. Balance training led to highly task-specific adaptations and improvements that can be transferred between functionally similar balance tasks. Postural strategies learned during training seemed barely transferable to a different balance task, as the unexpected perturbation of the base of support.
Effect of 12 weeks of interval training on skeletal muscle blood flow during single-leg knee extensor exercise in COPD: a non-randomized controlled trial
Authors: Hartmann Jacob P. , Nymand Stine Buus , Hartmeyer Helene Louise , Ryrsø Camilla Koch , Andersen Amalie B. , Mohammad Milan , Rasmussen Iben Elmerdahl , Thomsen Rie Skovly , Durrer Cody Garett , Berg Ronan M. G. , Iepsen Ulrik Winning 
Published: February 2025

High-intensity interval training (HIIT) has shown to improve exercise capacity, symptom burden, and quality of life in COPD patients, but it remains to be investigated if HIIT can counteract limb muscle dysfunction. Therefore, we examined the impact of a 12-week supervised HIIT protocol on muscle oxygen conductance. Eight patients with mild to moderate COPD and eight age-, sex- and BMI-matched controls underwent a 12-week HIIT intervention. Leg blood flow (Q̇leg) and arterio-venous blood samples were collected at rest and during active single-leg knee extensions (KEE) at unloaded (0 watts) and 20% of peak workload (WLpeak) to estimate leg muscle oxygen conductance pre- and post-HIIT. Pre-HIIT, Q̇leg was similar between groups during unloaded KEE (p=0.108) but lower at 20% WLpeak in the COPD group, compared to control group. Q̇leg responses were higher during unloaded KEE (28%, p=0.012) and 20% WLpeak (40%, p<0.001) post-HIIT in the COPD group, whereas no change occurred in the control group. Flow adjusted skeletal muscle O2 conductance was higher in the COPD pre-HIIT but only increased in the control group. Thus, there was no difference in diffusive or convective capacity between groups post- HIIT at submaximal KEE. COPD assessment score decreased by 2.8[1;4] (p=0.003) in the COPD group and V̇O2peak increased in both groups (COPD 192 mL O2/min, p=0.032, control 257 mL O2/min, p=0.004) with no time/group interaction. A 12-week HIIT intervention may improve peripheral exercise capacity in COPD by increasing the vasodilatory function in working muscle, while concurrently improving whole-body exercise capacity and symptom burden.
Mental Fatigue After Aneurysmal Subarachnoid Hemorrhage: A Prospective 5‐Year Follow‐Up Study
Authors: Wenneberg Sandra Bjerkne , Block Linda , Oras Jonatan , Hendén Pia Löwhagen , Liljencrantz Jaquette , Hayden Jane , Hergès Helena Odenstedt 
Published: February 2025

Objectives: Mental fatigue is a common and debilitating symptom following an aneurysmal subarachnoid hemorrhage (aSAH). However, its long‐term prevalence and consequences remain unclear. In this longitudinal pilot study, the Mental Fatigue Scale (MFS) was used to evaluate the prevalence, severity, and dynamics of mental fatigue for up to 5 years and to correlate patient demographics and early complications to the development of mental fatigue.Method: Functional outcomes were scored using the Glasgow Outcome Scale‐Extended (GOSE) during telephone interviews 1, 3, and 5 years after aSAH. The MFS questionnaires (maximum score 42, ≥ 10.5 points indicating mental fatigue) were subsequently sent by mail. Patient admission data and events during the acute phase were recorded.Results: Of 64 included patients, 31 could be assessed at all time points. Mental fatigue (MFS score ≥ 10.5) was present in 58%, 48%, and 52% of the patients at 1, 3, and 5 years, respectively. A significant decrease in the total MFS score was observed between 1 and 5 years (p = 0.025). The proportion of patients experiencing severe mental fatigue halved from 1 to 3 years. The median (range) MFS scores were significantly higher for women (14.5, 0–29.5) than for men (3, 0–17.5) at 1 year (p = 0.043). Compared with patients experiencing loss of consciousness at ictus (LOCi), those without LOCi exhibited a progressive decline in the total MFS score (p = 0.003).Conclusions: Although total MFS scores significantly improved, mental fatigue was a common and persistent symptom affecting half of the patients up to 5 years following aSAH. Mental fatigue was more prevalent in women than men; further, patients who experienced LOCi during the acute phase improved less over time. Our results highlight the importance of evaluating mental fatigue when assessing patient recovery and long‐term outcomes.Trial Registration: Clinical Trial NCT06239142