bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of raffinose family oligosaccharide use in
Bacteroides
species
Authors: Basu Anubhav , Adams Amanda N. D. , Degnan Patrick H. , Vanderpool Carin K. 
Published: September 2024

ABSTRACT

Bacteroides
species are successful colonizers of the human colon and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in polysaccharide utilization loci (PULs). While recent work has uncovered the PULs required for the use of some polysaccharides, how
Bacteroides
utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by α-1,6 bonds to a sucrose (glucose α-1-β-2 fructose) moiety. Previous work showed that an α-galactosidase, BT1871, is required for RFO utilization in
Bacteroides thetaiotaomicron
. Here, we identify two different types of mutations that increase
BT1871
mRNA levels and improve
B. thetaiotaomicron
growth on RFOs. First, a novel spontaneous duplication of
BT1872
and
BT1871
places these genes under the control of a ribosomal promoter, driving high
BT1871
transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase
BT1871
transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in
B. thetaiotaomicron
. Examining the genomes of other
Bacteroides
species, we found homologs of BT1871 in a subset and showed that representative strains of species with a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide.

IMPORTANCE

The gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the microbiota in the colon since they remain undigested by the host. Here, we study how the model commensal organism,
Bacteroides thetaiotaomicron
utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.
Extensive genomic study characterizing three
Paracoccaceae
populations and revealing
Pseudogemmobacter lacusdianii
sp. nov. and
Paracoccus broussonetiae
sp. nov.
Authors: Deng Yang , Li Cong-Jian , Zhang Jing , Liu Wei-Hong , Yu Li-Yan , Zhang Yu-Qin 
Published: September 2024

ABSTRACT

Bacteria within the family
Paracoccaceae
show promising potential for applications in various fields, garnering significant research attention. Three Gram stain-negative bacteria, strains CPCC 101601
T
, CPCC 101403
T
, and CPCC 100767, were isolated from diverse environments: freshwater, rhizosphere soil of
Broussonetia papyrifera
, and the phycosphere, respectively. Analysis of their 16S rRNA gene sequences, compared with those in the GenBank database, indicated that they belong to the family
Paracoccaceae
, with nucleotide similarities of 92.5%–99.9% to all of the
Paracoccaceae
members with valid taxonomic names. Phylogenetic studies based on 16S rRNA gene and whole-genome sequences identified CPCC 101601
T
as a member of the genus
Pseudogemmobacter
, CPCC 101403
T
belonging to the genus
Paracoccus
, and CPCC 100767 as part of the genus
Gemmobacter
. Notably, genomic analysis using average nucleotide identity (ANI; <95%) and digital DNA-DNA hybridization (dDDH; <70%) with their closely related strains suggested that CPCC 101601
T
and CPCC 101403
T
represent new species within their respective genera. Conversely, CPCC 100767 exhibited high ANI (98.5%) and dDDH (87.4%) values with
Gemmobacter fulvus
con5
T
, indicating it belongs to this already recognized species. The in-depth genomic analysis revealed that strains CPCC 101601
T
, CPCC 101403
T
, and CPCC 100767 harbor key genes related to the pathways for denitrifying, MA utilization, and polyhydroxyalkanoate biosynthesis. Moreover, genotyping and phenotyping analysis confirmed that strain CPCC 100767 has the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid, whereas CPCC 101601
T
can only perform the former bioprocess.

IMPORTANCE

Based on polyphasic taxonomic study, two new species,
Pseudogemmobacter lacusdianii
and
Paracoccus broussonetiae,
affiliated with the family
Paracoccaceae
were identified. This expands our understanding of the family
Paracoccaceae
and provides new microbial materials for further studies. Modern genomic techniques such as average nucleotide identity and digital DNA-DNA hybridization were utilized to determine species affiliations. These methods offer more precise results than traditional classification mainly based on 16S rRNA gene analysis. Beyond classification of these strains, the research delved into their genomes and discovered key genes related to denitrification, MA utilization, and polyhydroxyalkanoate biosynthesis. The identification of these genes provides a molecular basis for understanding the environmental roles of these strains. Particularly, strain CPCC 100767 demonstrated the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid. These bioprocess capabilities are of significant practical value, such as in agricultural production for use as biofertilizers or biostimulants.
Barriers and enablers of adherence to high-intensity interval training among patients with cancer: a systematic review and meta-analysis
Authors: Mahdaviani Behnaz , Selk-Ghaffari Maryam , Sarzaeim Mojdeh , Thornton Jane S 
Published: September 2024

Objective
Physical activity confers physical and psychosocial benefits for cancer patients and decreases morbidity and mortality, but adherence varies. High-intensity interval training (HIIT) is time-efficient and may improve adherence. Our aim was to determine barriers and enablers of adherence to HIIT in patients diagnosed with cancer.

Design
Systematic review and meta-analysis.

Data source
PubMed-MEDLINE, Scopus and Web of Science.

Eligibility criteria
Intervention studies including patients diagnosed with any type of cancer, who engaged in HIIT with or without co-intervention in any stage of treatment and have reported outcomes for adherence.

Results
Eight hundred articles were screened and 22 were included (n=807); 19 were included in the meta-analysis (n=755). Weighted adherence to HIIT was 88% (95% CI, 81% to 94%). None of the studies reported serious adverse events. Although being a woman and having breast cancer were associated with lower adherence (p<0.05), age was not (p=0.15). Adherence was significantly lower during the treatment phase in comparison with pre- and post-treatment phases, 83% versus 94% and 96%, respectively (p<0.001). Session time of more than 60 min, when unsupervised and combined with other interventions, was associated with decreased adherence (p<0.05).

Conclusion
Adherence to HIIT programmes among cancer patients varies and is improved when the intervention is supervised, of shorter duration, consists of solely HIIT and not in combination with other exercise and occurs during pre- and post-treatment phases. Strategies to improve adherence to HIIT in specific subpopulations may be needed to ensure all patients with cancer are provided optimal opportunities to reap the benefits associated with physical activity.

PROSPERO registration
CRD42023430180.
Contemporary national and international guidelines on physical activity and sedentary behaviour for people living with chronic conditions, disability and advanced age: a scoping review
Authors: Ranasinghe Mark P , Andersen Harrison , Dempsey Ruby K , Wexler Noah , Davis Rochelle , Francois Monique , Gilbert Stephen , Okely Anthony David , Sherrington Catherine , Dempsey Paddy C 
Published: September 2024

ObjectivesPhysical activity guidelines inform policy and practice in promoting healthier lifestyles. The WHO advocates for distinct recommendations for each country to address variation in needs, resources and context. Specific regional recommendations for three underactive populations facing unique barriers to movement are lacking—people with chronic conditions, disability and advanced age. We review which countries/regions provide specific physical activity guidelines for these populations to identify deficiencies in meeting WHO recommendations and inform future directions for guideline development.DesignScoping review.Data sourcesOVID Medline, PubMed, Scopus, Embase, Web of Science, Google Scholar, ProQuest, CINAHL, Google searches, targeted websites.Eligibility criteriaData sources were searched from database inception to September 2023 to identify community-facing physical activity guidelines at the national/international level for these populations. We recorded, summarised and analysed physical activity guideline recommendations extracted from published guideline documents, organised by population and country/region.Results66 articles were identified, addressing 28 distinct countries/regions, including four international guidelines, published from 2009 to 2023. The WHO guidelines were adopted by 19 countries and the European Union. Across all regions, a lack of specific advice was identified for individuals with chronic conditions (46%), disability (46%) and advanced age (11%). Advice for chronic conditions and disability commonly replicated general adult population advice.ConclusionMany countries/regions do not produce physical activity guidelines specific to populations with chronic conditions and disability. As such, a large proportion of countries/regions failed to meet WHO recommendations, highlighting a lack of customised advice to address unique barriers faced by vulnerable populations.
Applying machine learning approaches for predicting obesity risk using US health administrative claims database
Authors: Choong Casey , Brnabic Alan , Chinthammit Chanadda , Ravuri Meena , Terrell Kendra , Kan Hong 
Published: September 2024

IntroductionBody mass index (BMI) is inadequately recorded in US administrative claims databases. We aimed to validate the sensitivity and positive predictive value (PPV) of BMI-related diagnosis codes using an electronic medical records (EMR) claims-linked database. Additionally, we applied machine learning (ML) to identify features in US claims databases to predict obesity status.Research design and methodsThis observational, retrospective analysis included 692 119 people ≥18 years of age, with ≥1 BMI reading in MarketScan Explorys Claims-EMR data (January 2013–December 2019). Claims-based obesity status was compared with EMR-based BMI (gold standard) to assess BMI-related diagnosis code sensitivity and PPV. Logistic regression (LR), penalized LR with L1 penalty (Least Absolute Shrinkage and Selection Operator), extreme gradient boosting (XGBoost) and random forest, with features drawn from insurance claims, were trained to predict obesity status (BMI≥30 kg/m2) from EMR as the gold standard. Model performance was compared using several metrics, including the area under the receiver operating characteristic curve. The best-performing model was applied to assess feature importance. Obesity risk scores were computed from the best model generated from the claims database and compared against the BMI recorded in the EMR.ResultsThe PPV of diagnosis codes from claims alone remained high over the study period (85.4–89.2%); sensitivity was low (16.8–44.8%). XGBoost performed the best at predicting obesity with the highest area under the curve (AUC; 79.4%) and the lowest Brier score. The number of obesity diagnoses and obesity diagnoses from inpatient settings were the most important predictors of obesity. XGBoost showed an AUC of 74.1% when trained without an obesity diagnosis.ConclusionsObesity prevalence is under-reported in claims databases. ML models, with or without explicit obesity, show promise in improving obesity prediction accuracy compared with obesity codes alone. Improved obesity status prediction may assist practitioners and payors to estimate the burden of obesity and investigate the potential unmet needs of current treatments.
Do healthcare professionals work around safety standards, and should we be worried? A scoping review
Authors: Clark Debbie , Lawton Rebecca , Baxter Ruth , Sheard Laura , O'Hara Jane. K. 
Published: September 2024

BackgroundHealthcare staff adapt to challenges faced when delivering healthcare by using workarounds. Sometimes, safety standards, the very things used to routinely mitigate risk in healthcare, are the obstacles that staff work around. While workarounds have negative connotations, there is an argument that, in some circumstances, they contribute to the delivery of safe care.ObjectivesIn this scoping review, we explore the circumstances and perceived implications of safety standard workarounds (SSWAs) conducted in the delivery of frontline care.MethodWe searched MEDLINE, CINAHL, PsycINFO and Web of Science for articles reporting on the circumstances and perceived implications of SSWAs in healthcare. Data charting was undertaken by two researchers. A narrative synthesis was developed to produce a summary of findings.ResultsWe included 27 papers in the review, which reported on workarounds of 21 safety standards. Over half of the papers (59%) described working around standards related to medicine safety. As medication standards featured frequently in papers, SSWAs were reported to be performed by registered nurses in 67% of papers, doctors in 41% of papers and pharmacists in 19% of papers. Organisational causes were the most prominent reason for workarounds.Papers reported on the perceived impact of SSWAs for care quality. At times SSWAs were being used to support the delivery of person-centred, timely, efficient and effective care. Implications of SSWAs for safety were diverse. Some papers reported SSWAs had both positive and negative implications for safety simultaneously. SSWAs were reported to be beneficial for patients more often than they were detrimental.ConclusionSSWAs are used frequently during the delivery of everyday care, particularly during medication-related processes. These workarounds are often used to balance different risks and, in some circumstances, to achieve safe care.
Early adulthood socioeconomic trajectories contribute to inequalities in adult diet quality, independent of childhood and adulthood socioeconomic position
Authors: Tao Yinhua , Maddock Jane , Howe Laura , Winpenny Eleanor M 
Published: September 2024

Background
Diet is an important risk factor for cardiovascular disease and shows well-established socioeconomic patterning among adults. However, less clear is how socioeconomic inequalities in diet develop across the life course. This study assessed the associations of early adulthood socioeconomic trajectories (SETs) with adult diet quality, adjusting for childhood socioeconomic position (SEP) and testing for mediation by adulthood SEP.

Methods
Participants from the 1970 British Cohort Study with socioeconomic data in early adulthood were included (n=12 434). Diet quality at age 46 years, evaluated using the Mediterranean diet pyramid, was regressed on six previously identified classes of early adulthood SETs between ages 16 and 24 years including a continued education class, four occupation-defined classes and an economically inactive class. Causal mediation analyses tested the mediation of the association via household income and neighbourhood deprivation at age 46 years separately. Models were adjusted for sex, childhood SEP, adolescent diet quality and adolescent health.

Results
The continued education class showed the best diet quality at age 46 years while little difference in diet quality was found among the remaining SET classes. The association between the continued education class and adult diet quality was independent of parental SEP in childhood and was largely not mediated by household income or neighbourhood deprivation (0.7% and 3.7% of the total effect mediated, respectively) in mid-adulthood.

Conclusions
Early adulthood SETs independently contribute to adult diet quality with continuing education associated with better adherence to the Mediterranean diet. Early adulthood therefore represents a sensitive period for intervention to alleviate dietary inequalities in later life.
Primordial black holes and scalar-induced gravitational waves in radiative hybrid inflation
Authors: Afzal Adeela , Ghoshal Anish 
Published: September 2024

AbstractWe study the possibility that primordial black holes (PBHs) can be formed from large curvature perturbations generated during the waterfall phase transition due to the effects of one-loop radiative corrections of Yukawa couplings between the inflaton and a dark fermion in a non-supersymmetric hybrid inflationary model. We obtain a spectral index $$n_s$$

n
s

, and a tensor-to-scalar ratio r, consistent with the current Planck data. Our findings show that the abundance of PBHs is correlated to the dark fermion mass $$m_N$$

m
N

and peak in the GW spectrum. We identify parameter space where PBHs can be the entire dark matter (DM) candidate of the universe or a fraction of it. Our predictions are consistent with any existing constraints of PBH from microlensing, BBN, CMB, etc. Moreover, the scenario is also testable via induced gravitational waves (GWs) from first-order scalar perturbations detectable in future observatories such as LISA and ET. For instance, with inflaton mass $$m \sim 2\times 10^{12}$$

m
∼
2
×

10
12

GeV, $$m_N \sim 5.4\times 10^{15}$$

m
N

∼
5.4
×

10
15

GeV, we obtain PBHs of around $$10^{-13}\, M_\odot $$

10

-
13

M
⊙

mass that can explain the entire abundance of DM and predict GWs with amplitude $$\Omega _\textrm{GW}h^2$$

Ω
GW

h
2

$$\sim 10^{-9}$$

∼

10

-
9

with peak frequency f$$\sim $$
∼
0.1 Hz in LISA. By explicitly estimating fine-tuning we show that the model has very mild tuning. We discuss successful reheating at the end of the inflationary phase via the conversion of the waterfall field into standard model (SM) particles. We also briefly speculate a scenario where the dark fermion can be a possible heavy right-handed neutrino (RHN) which is responsible for generating the SM neutrino masses via the seesaw mechanism. The RHN can be produced due to waterfall field decay and its subsequent decay may also explain the observed baryon asymmetry in the universe via leptogenesis. We find the reheat temperature $$T_R\lesssim 5\times 10^9$$

T
R

≲
5
×

10
9

GeV that explains the matter-anti-matter asymmetry of the universe.
Characterization of neutron-irradiated SiPMs down to liquid nitrogen temperature
Authors: Consuegra Rodríguez Dania , Dolenec Rok , Križan Peter , Korpar Samo , Seljak Andrej , Žontar Dejan , Pestotnik Rok 
Published: September 2024

AbstractPhotodetectors used in future high-energy physics experiments will need to keep sufficient performance during a few years of data-taking despite radiation load, which, for example, in the planned upgrade of the Ring Imaging Cherenkov detectors in Large Hadron Collider beauty (LHCb) experiment is estimated at about 10$$^{13}$$

13

1-MeV neutron equivalent per cm$$^{2}$$

2

(neq/cm$$^{2}$$

2

). Silicon photomultipliers (SiPMs) are considered as candidates for photodetectors for this application. However, their sensitivity to neutron irradiation may seriously compromise their operation, with the increase in dark count rates being the primary limitation after the irradiation. In this work, 1 $$\times $$
×
1 mm$$^{2}$$

2

15 $$\mu $$
μ
m pitch NUV-HD-RH silicon photomultipliers developed by the Fondazione Bruno Kessler were characterized before and after the irradiation. In total, 5 SiPMs were irradiated at the Jožef Stefan Institute TRIGA nuclear reactor with different fluences from 10$$^{9}$$

9

neq/cm$$^{2}$$

2

up to 10$$^{13}$$

13

neq/cm$$^{2}$$

2

. The SiPMs were also annealed at high temperatures and re-characterized after the annealing. For the SiPM characterization in all the cases, current–voltage (I-V curve) measurements, dark count rate measurements, and waveform analysis, including single photon time resolution, were carried out at different controlled temperature steps from room temperature down to the liquid nitrogen temperature. While cooling to − 20$$^{\circ }$$

∘

C was enough for the SiPM irradiated at 10$$^{9}$$

9

neq/cm$$^{2}$$

2

to recover the ability to resolve single photons, by 10$$^{13}$$

13

neq/cm$$^{2}$$

2

, cooling to liquid nitrogen temperature was necessary. With sufficient cooling, the measured single photon time resolution was around 90 ps FWHM for all irradiation levels.
Charged Higgs decay to $$W^{\pm }H$$ at a high energy lepton collider
Authors: Hashemi Majid , Roushandel Laleh 
Published: September 2024

AbstractIn this work, we present a search strategy for heavy charged Higgs boson at compact linear collider (CLIC) as a future $$e^+e^-$$

e
+

e
-

collider. The signal is charged Higgs boson pair production in two Higgs doublet model (2HDM) followed by $$H^{\pm }\rightarrow W^{\pm }H$$

H
±

→

W
±

H

and $$H\rightarrow b\bar{b}$$

H
→
b

b

¯

. Here, H denotes the heavy CP-even neutral Higgs boson of the model. The collider center of mass energy is chosen to be $$\sqrt{s}=1400$$

s

=
1400

GeV as the second stage of CLIC operation. In this case, $$m_{H^+}<\sqrt{s}/2$$

m

H
+

<

s

/
2

can be explored due to the pair production. It is shown that the signal of charged Higgs in the mass range $$250~ \text {GeV}<m_{H^+}< 650~ \text {GeV}$$

250

GeV
<

m

H
+

<
650

GeV

in fully hadronic final state, containing four b-jets from neutral Higgs and four jets from W bosons, can well be observed on top of the standard model background. Finally $$5\sigma $$

5
σ

contours are presented in $$(m_{H^{\pm }},m_{H})$$

(

m

H
±

,

m
H

)

space for different $$\tan \beta $$

tan
β

values.
Climbing over the potential barrier during inflation via null energy condition violation
Authors: Pan Shi , Cai Yong , Piao Yun-Song 
Published: September 2024

AbstractThe violation of the null energy condition (NEC) may play a crucial role in enabling a scalar field to climb over high potential barriers, potentially significant in the very early universe. We propose a single-field model where the universe sequentially undergoes a first stage of slow-roll inflation, NEC violation, and a second stage of slow-roll inflation. Through the NEC violation, the scalar field climbs over high potential barriers, leaving unique characteristics on the primordial gravitational wave power spectrum, including a blue-tilted nature in the middle-frequency range and diminishing oscillation amplitudes at higher frequencies. Additionally, the power spectrum exhibits nearly scale-invariant behavior on both large and small scales.