bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Factors Associated With Accelerometer Validity Among Ethnically Diverse Toddlers
Authors: Crumbley Christine , Cepni Aliye B. , Taylor Ashley , Thompson Debbe , Moran Nancy E. , Olvera Norma , O’Connor Daniel P. , Johnston Craig A. , Ledoux Tracey A. 
Published: September 2023

Purpose: Studying physical activity in toddlers using accelerometers is challenging due to noncompliance with wear time (WT) and activity log (AL) instructions. The aims of this study are to examine relationships between WT and AL completion and (1) demographic and socioeconomic variables, (2) parenting style, and (3) whether sedentary time differs by AL completion. Methods: Secondary analysis was performed using baseline data from a community wellness program randomized controlled trial for parents with toddlers (12–35 mo). Parents had toddlers wear ActiGraph wGT3x accelerometers and completed ALs. Valid days included ≥600-minute WT. Analysis of variance and chi-square analyses were used. Results: The sample (n = 50) comprised racial and ethnically diverse toddlers (mean age = 27 mo, 58% male) and parents (mean age = 31.7 y, 84% female). Twenty-eight families (56%) returned valid accelerometer data with ALs. Participants in relationships were more likely to complete ALs (P < .05). Toddler sedentary time did not differ between those with ALs and those without. Conclusions: We found varied compliance with WT instructions and AL completion. Returned AL quality was poor, presenting challenges in correctly characterizing low-activity counts to improve internal validity of WT and physical activity measures. Support from marital partners may be important for adherence to study protocols.
Association of Recess Provision With Accelerometer-Measured Physical Activity and Sedentary Time in a Representative Sample of 6- to 11-Year-Old Children in the United States
Authors: Clevenger Kimberly A. , McKee Katherine L. , McNarry Melitta A. , Mackintosh Kelly A. , Berrigan David 
Published: September 2023

Purpose: To assess the association between the amount of recess provision and children’s accelerometer-measured physical activity (PA) levels. Methods: Parents/guardians of 6- to 11-year-olds (n = 451) in the 2012 National Youth Fitness Survey reported recess provision, categorized as low (10–15 min; 31.9%), medium (16–30 min; 48.0%), or high (>30 min; 20.1%). Children wore a wrist-worn accelerometer for 7 days to estimate time spent sedentary, in light PA, and in moderate to vigorous PA using 2 different cut points for either activity counts or raw acceleration. Outcomes were compared between levels of recess provision while adjusting for covariates and the survey’s multistage, probability sampling design. Results: Children with high recess provision spent less time sedentary, irrespective of type of day (week vs weekend) and engaged in more light or moderate to vigorous PA on weekdays than those with low recess provision. The magnitude and statistical significance of effects differed based on the cut points used to classify PA (eg, 4.7 vs 11.9 additional min·d−1 of moderate to vigorous PA). Conclusions: Providing children with >30 minutes of daily recess, which exceeds current recommendations of ≥20 minutes, is associated with more favorable PA levels and not just on school days. Identifying the optimal method for analyzing wrist-worn accelerometer data could clarify the magnitude of this effect.
The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea
Authors: Liu Wei-Wei , Pan Piaopiao , Zhou Ning-Yi 
Published: September 2023

ABSTRACT

Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaK
ANME
) and benzoate-CoA ligase (BadA
ANME
) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA
in vitro,
respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments.

IMPORTANCE
ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.
A sensitive mass spectrometry-based method to identify common respiratory pathogens in children
Authors: Hu Lixin , Zhang Shenyan , Song Wenqi , Dong Fang , Xie Zhengde , Chen Xiangpeng , Liu Meng , Cui Baoxue , Zhang Yunheng , Zhang Rui , Wang Qingtao 
Published: September 2023

ABSTRACT
Public health threats posed by emerging respiratory infections are a significant concern, particularly in children and infants. Traditional culture-based detection methods are time-consuming and typically require 1–3 days. Herein, we developed and evaluated a 23-plex common respiratory pathogen mass spectrometry assay that enables the simultaneous detection of 18 common respiratory pathogens in children. This assay combines matrix-assisted laser desorption/ionization time of flight mass spectrometry with multiplex reverse transcription-PCR and targets 11 bacterial and 7 viral pathogens (including 10 subtypes), and two internal controls. The detection limit of the common respiratory pathogen mass spectrometry assay was as low as 1 copy/µL, with no cross-reactivity with other organisms. We assessed the clinical performance of the common respiratory pathogen mass spectrometry assay using respiratory samples from 450 children. The total 450 clinical specimens underwent analysis via matrix-assisted laser desorption/ionization time of flight mass spectrometry, and the outcomes were juxtaposed with those derived from real-time reverse-transcriptase PCR conducted concurrently. The concordance between these methods was 96.0%, and the multiple infection identification rate was 7.1%. This innovative approach enables the simultaneous analysis of numerous outcomes from a solitary examination across 192 specimens within a timeframe of approximately 7 hours, with a dramatically reduced sample use and cost. In summary, the common respiratory pathogen mass spectrometry assay is a sensitive, accurate, and cost-effective method for detecting common respiratory pathogens in children and has the potential to revolutionize the diagnosis of respiratory tract infections.

IMPORTANCE
This study aimed to present and evaluate a novel co-detection method that enables the simultaneous identification of 11 bacterial and 7 viral pathogens in about 7 hours using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Our approach utilizes a combination of multiplex reverse transcription-PCR and matrix-assisted laser desorption/ionization time of flight mass spectrometry, which overcomes the limitations of conventional assays, which include a long assessment time, technical difficulty, and high costs. As a screening method for common respiratory pathogens in children, common respiratory pathogen mass spectrometry assay has the potential to revolutionize the diagnosis of respiratory tract infections by providing an accurate etiological diagnosis. The common respiratory pathogen mass spectrometry assay is expected to be a critical tool for the diagnosis of respiratory infections in children, offering a more efficient, cost-effective, and accurate approach for the detection of common respiratory pathogens.
Viral and cellular telomerase RNAs possess host-specific anti-apoptotic functions
Authors: Kheimar Ahmed , Trapp-Fragnet Laetitia , Conradie Andelé M. , Bertzbach Luca D. , You Yu , Sabsabi Mohammad A. , Kaufer Benedikt B. 
Published: September 2023

ABSTRACT
Human telomerase RNA (hTR) is overexpressed in many cancers and protects T cells from apoptosis in a telomerase-independent manner. The most prevalent cancer in the animal kingdom is caused by the highly oncogenic herpesvirus Marek’s disease virus (MDV). MDV encodes a viral telomerase RNA (vTR) that plays a crucial role in MDV-induced tumorigenesis and shares all four conserved functional domains with hTR. In this study, we assessed whether hTR drives tumor formation in this natural model of herpesvirus-induced tumorigenesis. Therefore, we replaced vTR with hTR in the genome of a highly oncogenic MDV. Furthermore, we investigated the anti-apoptotic activity of vTR, hTR, and their counterpart in the chicken [chicken telomerase RNA (cTR)]. hTR was efficiently expressed and did not alter replication of the recombinant virus. Despite its conserved structure, hTR did not complement the loss of vTR in virus-induced tumorigenesis. Strikingly, hTR did not inhibit apoptosis in chicken cells, but efficiently inhibited apoptosis in human cells. Inverse host restriction has been observed for vTR and cTR in human cells. Our data revealed that vTR, cTR, and hTR possess conserved but host-specific anti-apoptotic functions that likely contribute to MDV-induced tumorigenesis.

IMPORTANCE
hTR is overexpressed in many cancers and used as a cancer biomarker. However, the contribution of hTR to tumorigenesis remains elusive. In this study, we assessed the tumor-promoting properties of hTR using a natural virus/host model of herpesvirus-induced tumorigenesis. This avian herpesvirus encodes a telomerase RNA subunit (vTR) that plays a crucial role in viral tumorigenesis and shares all conserved functional domains with hTR. Our data revealed that vTR and cellular TRs of humans and chickens possess host-specific anti-apoptotic functions. This provides important translational insights into therapeutic strategies, as inhibition of apoptosis is crucial for tumorigenesis.
Efflux pump inhibitory potential of indole derivatives as an arsenal against
norA
over-expressing
Staphylococcus aureus
Authors: Chandal Nishtha , Tambat Rushikesh , Kalia Ritu , Kumar Gautam , Mahey Nisha , Jachak Sanjay , Nandanwar Hemraj 
Published: September 2023

ABSTRACT

NorA, an extensively studied efflux pump in
Staphylococcus aureus
, has been connected to fluoroquinolone, antiseptic, and disinfection resistance. Several studies have also emphasized how efflux pumps, including NorA, function as the first line of defense of
S. aureus
against antibiotics. In this study, we have screened some chemically synthesized indole derivatives for their activity as efflux pump inhibitors (EPIs). The derivative SMJ-5 was found to be a potent NorA efflux pump inhibitor among the screened indole derivatives, owing to increased ethidium bromide and norfloxacin accumulation in
norA
over-expressing
S. aureus
. The combination of SMJ-5 and ciprofloxacin demonstrated the eradication of
S. aureus
biofilm and prolonged the post-antibiotic effect more than ciprofloxacin alone. SMJ-5 was able to inhibit staphyloxanthin virulence. In
in vitro
time-kill trials and
in vivo
efficacy investigations, the combination enhanced the bactericidal activity of ciprofloxacin against
S. aureus
. Additionally, reverse transcription PCR results revealed that SMJ-5 also inhibits the NorA efflux pump indirectly at the transcriptional level.

IMPORTANCE

The NorA efflux pump is the most effective resistance mechanism in
S. aureus
. The clinical importance of NorA efflux pumps is demonstrated by the expression of pump genes in
S. aureus
strains in response to fluoroquinolones and biocides. Along with the repercussions of decreased fluoroquinolone sensitivity, increasing expression of efflux pump genes by their substrate necessitates the importance of efflux pump inhibitors. Reserpine and verapamil are clinically used to treat ailments and have proven NorA inhibitors, but, unfortunately, the concentration needed for these drugs to inhibit the pump is not safe in clinical settings. In the current study, we have screened some indole derivatives, and among them, SMJ-5 was reported to potentiate norfloxacin and ciprofloxacin at their sub-inhibitory concentration by inhibiting the
norA
gene transcriptionally. Here we highlight the promising points of this study, which could serve as a model to design a therapeutic EPI candidate against
norA
over-expressing
S. aureus
.
Cesin, a short natural variant of nisin, displays potent antimicrobial activity against major pathogens despite lacking two C-terminal macrocycles
Authors: Guo Longcheng , Wambui Joseph , Wang Chenhui , Muchaamba Francis , Fernandez-Cantos Maria Victoria , Broos Jaap , Tasara Taurai , Kuipers Oscar P. , Stephan Roger 
Published: September 2023

ABSTRACT

Nisin is a widely used lantibiotic owing to its potent antimicrobial activity and its food-grade status. Its mode of action includes cell wall synthesis inhibition and pore formation, which are attributed to the lipid II binding and pore-forming domains, respectively. We discovered cesin, a short natural variant of nisin, produced by the psychrophilic anaerobe
Clostridium estertheticum
. Unlike other natural nisin variants, cesin lacks the two terminal macrocycles constituting the pore-forming domain. The current study aimed at heterologous expression and characterization of the antimicrobial activity and physicochemical properties of cesin. Following the successful heterologous expression of cesin in
Lactococcus lactis
, the lantibiotic demonstrated a broad and potent antimicrobial profile comparable to that of nisin. Determination of its mode of action using lipid II and lipoteichoic acid binding assays linked the potent antimicrobial activity to lipid II binding and electrostatic interactions with teichoic acids. Fluorescence microscopy showed that cesin lacks pore-forming ability in its natural form. Stability tests have shown the lantibiotic is highly stable at different pH values and temperature conditions, but that it can be degraded by trypsin. However, a bioengineered analog, cesin R15G, overcame the trypsin degradation, while keeping full antimicrobial activity. This study shows that cesin is a novel (small) nisin variant that efficiently kills target bacteria by inhibiting cell wall synthesis without pore formation.

IMPORTANCE

The current increase in antibiotic-resistant pathogens necessitates the discovery and application of novel antimicrobials. In this regard, we recently discovered cesin, which is a short natural variant of nisin produced by the psychrophilic
Clostridium estertheticum
. However, its suitability as an antimicrobial compound was in doubt due to its structural resemblance to nisin(1–22), a bioengineered short variant of nisin with low antimicrobial activity. Here, we show by heterologous expression, purification, and characterization that the potency of cesin is not only much higher than that of nisin(1–22), but that it is even comparable to the full-length nisin, despite lacking two C-terminal rings that are essential for nisin’s activity. We show that cesin is a suitable scaffold for bioengineering to improve its applicability, such as resistance to trypsin. This study demonstrates the suitability of cesin for future application in food and/or for health as a potent and stable antimicrobial compound.
Infections in autoimmune pulmonary alveolar proteinosis: a large retrospective cohort
Authors: Mabo Axelle , Borie Raphael , Wemeau-Stervinou Lidwine , Uzunhan Yurdagül , Gomez Emmanuel , Prevot Gregoire , Reynaud-Gaubert Martine , Traclet Julie , Bergot Emmanuel , Cadranel Jacques , Marchand-Adam Sylvain , Bergeron Anne , Blanchard Elodie , Bondue Benjamin , Bonniaud Philippe , Bourdin Arnaud , Burgel Pierre Regis , Hirschi Sandrine , Marquette Charles Hugo , Quétant Sébastien , Nunes Hilario , Chenivesse Cécile , Crestani Bruno , Guirriec Yoann , Monnier Delphine , Ménard Cédric , Tattevin Pierre , Cottin Vincent , Luque Paz David , Jouneau Stéphane 
Published: September 2023

BackgroundAutoimmune pulmonary alveolar proteinosis (aPAP) is a rare disease, predisposing to an increased risk of infection. A complete picture of these infections is lacking.Research questionDescribe the characteristics and clinical outcomes of patients diagnosed with aPAP, and to identify risk factors associated with opportunistic infections.MethodsWe conducted a retrospective cohort including all patients diagnosed with aPAP between 2008 and 2018 in France and Belgium. Data were collected using a standardised questionnaire including demographics, comorbidities, imaging features, outcomes and microbiological data.ResultsWe included 104 patients, 2/3 were men and median age at diagnosis was 45 years. With a median follow-up of 3.4 years (IQR 1.7–6.6 years), 60 patients (58%), developed at least one infection, including 23 (22%) with opportunistic infections.Nocardiaspp was the main pathogen identified (n=10). Thirty-five (34%) patients were hospitalised due to infection. In univariate analysis, male gender was associated with opportunistic infections (p=0.04, OR=3.88; 95% CI (1.02 to 22.06)). Anti-granulocyte macrophage colony-stimulating factor antibody titre at diagnosis was significantly higher among patients who developed nocardiosis (1058 (316–1591) vs 580 (200–1190), p=0.01). Nine patients had died (9%), but only one death was related to infection.InterpretationPatients with aPAP often presented with opportunistic infections, especially nocardiosis, which highlights the importance of systematic search for slow-growing bacteria in bronchoalveolar lavage or whole lung lavage.
Management impacts on organic carbon under continuous perennial grass, perennial grass-legume mixture, and annual cereals on a thick Black Chernozemic soil
Authors: Mapfumo E. , Baron V.S. , Lemke R. , Naeth M.A. , Chanasyk D.S. , Dick Campbell 
Published: September 2023

Impacts of annual and perennial pasture management on soil organic carbon (SOC) and equivalent SOC stocks (equal soil mass basis) were investigated in two trials [CAESA (1994–1997) and BMP (2008–2012) trials] conducted on the same experimental paddocks at Lacombe, AB. The original site was broken from perennial grass in 1992, and the CAESA trial established in 1993. Between 1994 and 1997, half of the paddocks included winter triticale and a mixture of triticale and spring barley; half included smooth and meadow bromegrass; and each paddock was light, medium, or heavily grazed. The BMP trial (2008–2012) on the same paddocks included fertilized, direct seeded barley as silage; grazing and haying of unfertilized meadow bromegrass, fertilized meadow bromegrass, and meadow bromegrass and alfalfa mixture; and unfertilized oldgrass that was continuous since 1994. Between trials (1998–2007), all paddocks received no fertilizer. In the 0–15 cm depth, SOC under oldgrass was constant between 1994 and 2012 and averaged 88 Mg C ha−1. Under barley silage, SOC decreased from 89 to 72 Mg C ha−1 by 2012. Between 1994 and 2012, SOC decreased in all treatments re-established on original annual forage (1994–1998) but not to the level of barley silage. Light fraction carbon was the highest under oldgrass and the lowest under barley silage. Overall, oldgrass with no fertilizer inputs maintained a constant SOC, although annuals reduced SOC stocks. Re-establishment of perennial grass with grazing may therefore reduce SOC loss, whereas haying perennial grass may not reduce SOC loss.
Direct detection of electroweak dark matter
Authors: Amintaheri Ramtin 
Published: September 2023

AbstractTeV-scale dark matter is well motivated by notions of naturalness as the new physics threshold is expected to emerge in the TeV regime. We generalise the Standard Model by including an arbitrary SU(2) multiplet of dark matter particles in non-chiral representation. The pseudo-real representations can be viable DM candidates if one considers a higher-dimensional operator which induces mass-splitting, and avoids the tree-level inelastic scattering through Z-boson exchange. These effective operators give rise to sizable contributions from Higgs mediated dark matter interactions with quarks and gluons. A linear combination of the effective couplings named $$\lambda $$
λ
is identified as the critical parameter in determining the magnitude of the cross-section. When $$\lambda $$
λ
is smaller than the critical value, the theory behaves similar to the known renormalisable model, and the scattering rate stays below the current experimental reach. Nevertheless, above the criticality, the contribution from the higher-dimensional operators significantly changes the phenomenology. The scattering amplitude of pseudo-real models will be coherently enhanced, so that it would be possible for next generation large-exposure experiments to fully probe these multiplets. We studied the parameter space of the theory, taking into account both indirect astrophysical and direct search constraints. It is inferred that multi-TeV mass scale remains a viable region, quite promising for forthcoming dark matter experiments.
A bias using the ages of the oldest astrophysical objects to address the Hubble tension
Authors: Costa André A. , Ren Zelin , Yin Zhixiang 
Published: September 2023

AbstractRecently different cosmological measurements have shown a tension in the value of the Hubble constant, $$H_0.$$

H
0

.

Assuming the $$\Lambda $$
Λ
CDM model, the Planck satellite mission has inferred the Hubble constant from the cosmic microwave background (CMB) anisotropies to be $$H_0 = 67.4 \pm 0.5 \, \text {km} \, \text {s}^{-1} \, \text {Mpc}^{-1}.$$

H
0

=
67.4
±
0.5

km

s

-
1

Mpc

-
1

.

On the other hand, low redshift measurements such as those using Cepheid variables and supernovae Type Ia (SNIa) have obtained a significantly larger value. For instance, Riess et al. reported $$H_0 = 73.04 \pm 1.04 \, \text {km} \, \text {s}^{-1} \, \text {Mpc}^{-1},$$

H
0

=
73.04
±
1.04

km

s

-
1

Mpc

-
1

,

which is $$5\sigma $$

5
σ

apart of the prediction from Planck observations. This tension is a major problem in cosmology nowadays, and it is not clear yet if it comes from systematic effects or new physics. The use of new methods to infer the Hubble constant is therefore essential to shed light on this matter. In this paper, we discuss using the ages of the oldest astrophysical objects (OAO) to probe the Hubble tension. We show that, although this data can provide additional information, the method can also artificially introduce a tension. Reanalyzing the ages of 114 OAO, we obtain that the constraint in the Hubble constant goes from slightly disfavoring local measurements to favoring them.