bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomy of
Pseudomonas
spp. determines interactions with
Bacillus subtilis
Authors: Lyng Mark , Þórisdóttir Birta , Sveinsdóttir Sigrún H. , Hansen Morten L. , Jelsbak Lars , Maróti Gergely , Kovács Ákos T. 
Published: September 2024

ABSTRACT

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on
Bacillus subtilis
pellicle formation in two types of media and found a predictor for interaction outcome in
Pseudomonas
taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with
Pseudomonas capeferrum
,
Pseudomonas entomophila
, and
Pseudomonas protegens
, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of
B. subtilis
. Non-inhibiting strains were closely related to
Pseudomonas trivialis
and
Pseudomonas lini
. Using such a non-inhibiting isolate,
Pseudomonas
P9_31, which increased
B. subtilis
pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between
B. subtilis
and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

IMPORTANCE

There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other’s growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720
Pseudomonas
isolates, and their impact on the biofilm formation of
Bacillus subtilis
was tested. The aim was to determine whether a majority of
Pseudomonas
will promote or inhibit the biofilms of
B. subtilis
in the co-cultures. This study reports that
Pseudomonas
taxonomy is a good predictor of interaction outcome, and only a minority of
Pseudomonas
isolates promote
Bacillus
biofilm establishment.
A specific and ultrasensitive Cas12a/crRNA assay with recombinase polymerase amplification and lateral flow biosensor technology for the rapid detection of
Streptococcus pyogenes
Authors: Cheng Yu , Lyu Jiawen , Han Jiangfeng , Feng Long , Li Xiangmei , Li Pei , Zhang Shanfeng , Zang Wenqiao 
Published: September 2024

ABSTRACT

The potential of CRISPR/Cas systems for nucleic acid detection in novel biosensing applications is remarkable. The current clinical diagnostic detection of
Streptococcus pyogenes
(
S. pyogenes
) is based on serological identification, culture, and PCR. We report a rapid, simple, and sensitive method for detecting and screening for
S. pyogenes
. This novel method is a promising supplemental test. After 10 min of the sample processing and 10 min of recombinase polymerase amplification, followed by 10 min of Cas12 reaction and 3 min of lateral flow biosensor (LFB) readout, a visible outcome can be observed without the need for magnification within 33 min. This platform is robust, inexpensive, and appropriate for on-site testing. A new technique for detection was created using CRISPR-Cas12a technology, which includes two measurements: a fluorescent-CRISPR-
S. pyogenes
test and a LFB-CRISPR-
S. pyogenes
test. An approach utilizing CRISPR Cas12a was developed, and the accuracy and precision of this technique were assessed. The LoD for the fluorescence-CRISPR-
S. pyogenes
assay was 1 copy/μL, and the technique effectively differentiated
S. pyogenes
from other microorganisms. Moreover, the detection outcomes were presented in a user-friendly manner using lateral flow biosensor strips. Conclusion: A rapid and sensitive Cas12a/crRNA assay using recombinase RPA and LFB was developed to detect
S. pyogenes
. The Cas12a/crRNA-based assay exhibited high specificity among different bacteria strains and extremely high sensitivity. The accuracy and rapidity of this method make it a promising tool for
S. pyogenes
detection and screening.

IMPORTANCE

Patients may experience a range of symptoms due to
Streptococcus pyogenes
infections, including superficial skin infections, pharyngitis, and invasive diseases in subcutaneous tissues like streptococcal toxic shock syndrome. At present, the clinical diagnostic detection of
S. pyogenes
is based on serological identification, culture, and PCR. These detection methods are time-consuming and require sophisticated equipment, making these methods challenging for routine laboratories. Thus, there is a need for a detection platform that is capable of quickly and accurately identifying
S. pyogenes
. In this study, a rapid and sensitive Cas12a/crRNA assay using recombinase RPA and LFB was developed to detect
S. pyogenes
. The Cas12a/crRNA-based assay exhibited high specificity among different bacteria strains and extremely high sensitivity. This method probably plays an important role for
S. pyogenes
detection and screening.
Phenotypic and genomic comparison of three human outbreak and one cattle-associated Shiga toxin-producing
Escherichia coli
O157:H7
Authors: Peroutka-Bigus Nathan , Nielsen Daniel W. , Trachsel Julian , Mou Kathy T. , Sharma Vijay K. , Kudva Indira T. , Loving Crystal L. 
Published: September 2024

ABSTRACT

Escherichia coli
O157:H7-adulterated food products are associated with disease outbreaks in humans. Although cattle feces are a source for
E. coli
O157:H7 contamination, it is unclear if human-associated outbreak isolates differentially colonize and shed in the feces of cattle from that of non-outbreak isolates. It is also unclear if phenotypes, such as biofilm formation, cell attachment, or toxin production, differentiate environmental
E. coli
O157:H7 isolates from those associated with human illness. The objective of this study was to compare the genotypes and phenotypes of a diverse set of
E. coli
O157:H7 isolates, with the intent of identifying differences that could inform cattle colonization and fecal shedding, along with virulence potential in humans. Isolates differed in attachment phenotypes on human Caco-2 cells and bovine-derived recto-anal junction squamous epithelial cells, with curli having a strong impact on attachment to the human-derived cell line. The prototypical
E. coli
O157 isolate EDL933 had the greatest expression of the adhesin gene
iha
, yet it had decreased expression of the virulence genes
stx2
,
eae
, and
ehxA
compared the lineage I/II isolates RM6067W and/or FRIK1989. Strong or weak biofilm production was not associated with significant differences in cattle colonization or shedding, suggesting biofilms may not play a major role in cattle colonization. No significant differences in cattle colonization and fecal shedding were detected, despite genomic and
in vitro
phenotypic differences. The outbreak isolate associated with the greatest incidence of hemolytic uremic syndrome, RM6067W, induced the greatest Vero cell cytotoxicity and had the greatest
stx2
gene expression.

IMPORTANCE

Foodborne illness has major impacts on global health and imposes financial hardships on food industries.
Escherichia coli
serotype O157:H7 is associated with foodborne illness. Cattle feces are a source of
E. coli
O157:H7, and routine surveillance has led to an abundance of
E. coli
O157:H7 genomic data. The relationship between
E. coli
O157:H7 genome and phenotype is not clearly discerned for cattle colonization/shedding and improved understanding could lead to additional strategies to limit
E. coli
O157:H7 in the food chain. The goal of the research was to evaluate genomic and phenotypic attributes of
E. coli
O157:H7 associated with cattle colonization and shedding, environmental persistence, and human illness. Our results indicate variations in biofilm formation and
in vitro
cellular adherence was not associated with differences in cattle colonization or shedding. Overall, processes involved in cattle colonization and various phenotypes in relation to genotype are complex and remain not well understood.
The timing and duration of large-scale carbon release in the Early Jurassic
Authors: Kemp David B. , Ramezani Jahandar , Izumi Kentaro , Al-Suwaidi Aisha , Huang Chunju , Chen Wenhan , Zhu Yuqing 
Published: September 2024

Abstract
The Toarcian oceanic anoxic event (T-OAE, ca. 183 Ma) in the Early Jurassic was one of the most significant warming events of the Phanerozoic, associated with large-scale carbon emissions, mass extinction, and perturbations to hydrology and ocean chemistry. However, the age and duration of this hyperthermal have long been uncertain, hindering our understanding of the timing and pace of carbon release and the associated environmental and biotic changes. We present high-precision radioisotopic dates bracketing a biostratigraphically constrained record of the T-OAE in Japan. Our geochronology reveals an unexpectedly short T-OAE duration of ∼300 k.y. and a temporal coincidence with Ferrar large igneous province (LIP) magmatism. Our dates refute previous work linking the T-OAE to the earlier Karoo LIP, which was coincident with an earlier carbon cycle perturbation at the Pliensbachian–Toarcian boundary. Our results suggest both events were driven by extremely rapid (perhaps sub-millennial scale) thermogenic carbon degassing during LIP sill intrusion.
Comparative efficacy of pharmacological and non-pharmacological interventions for mitigating pain and anxiety associated with venipuncture: a randomised controlled trial
Authors: Suleman Sherzad Khudeida , Yahya Nizer , Nilsson Stefan , Enskär Karin 
Published: September 2024

BackgroundVenipuncture is one of the most commonly performed medical procedures in paediatric care, but it can also be one of the most painful and distressing experiences for patients. Finding effective strategies to manage pain and fear associated with venipuncture is crucial for improving the paediatric patient experience and promoting positive health outcomes. This study aimed to evaluate the efficacy of a combined approach using a topical analgesic cream (TKTX cream) and a distraction technique (Trace Image and Colouring for Kids-Book, TICK-B) in reducing pain intensity and fear levels in children undergoing venipuncture procedures.MethodsWe conducted this randomised controlled trial among 176 children aged 6–12 years undergoing venipuncture. Participants were randomly assigned to four groups: TICK-B, TKTX cream, TICK-B+TKTX cream and a control group. Pain and fear were measured using the Wong-Baker FACES Pain Rating Scale and Children’s Fear Scale. The study was carried out from 20 February 2024 to 1 June 2024 at the emergency unit of Heevi paediatric teaching hospital in the Kurdistan region of Iraq. In the intervention groups, TICK-B was applied for 2–3 min before needle insertion, and TKTX cream was applied 20 min before the venipuncture procedure. All outcome measures were evaluated 2–3 min after the completion of the venipuncture procedure.ResultsThe combined TICK-B (colouring book) and TKTX cream (topical anaesthetic) intervention was the most effective in reducing both pain intensity (mean score 2.80 vs 7.24 in the control, p<0.001) and fear levels (mean score 0.93 vs 2.83 in the control, p<0.001) during and after venipuncture procedures compared with individual interventions and control.ConclusionsThe combined TICK-B distraction and TKTX cream topical anaesthetic intervention was the most effective in reducing pain intensity and fear during and after venipuncture in children, providing a practical strategy for healthcare providers to optimise needle procedure management.Trial registration numberNCT06326125.
Genome-wide association studies for growth and feed efficiency traits in American mink
Authors: Davoudi Pourya , Do Duy Ngoc , Rathgeber Bruce , Colombo Stefanie , Sargolzaei Mehdi , Plastow Graham , Wang Zhiquan , Miar Younes 
Published: September 2024

The objective of this study was to identify potential genetic variants and positional candidate genes associated with growth and feed efficiency traits in American mink. Genome-wide association studies (GWAS) were performed using deregressed estimated breeding values of 1037–1872 individuals (as pseudophenotypes), genotyped with the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array. A total of 42 SNPs located on 11 different chromosomes were significantly (false discovery rate < 0.01) associated with six growth and feed efficiency traits. Furthermore, 153 genes were identified within 1-Mb windows flanking these significant SNPs. Several positional candidate genes such as TUBB, CDKN1A, SRSF3, GPRC6A, RFX6, and KPNA5 were previously associated with feed efficiency and growth traits in other livestock species. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that these genes were involved in lipid metabolism, hormone signaling and regulation, and muscle development. To our knowledge, this is the first GWAS to identify genetic variants and biological mechanisms associated with growth and feed efficiency traits in American mink. These findings provide a biological foundation for improving these traits using genomic selection programs to select more efficient mink.
$$A_4$$ modular invariance and the strong CP problem
Authors: Petcov S. T. , Tanimoto M. 
Published: September 2024

AbstractWe present simple effective theory of quark masses, mixing and CP violation with level $$N=3$$

N
=
3

($$A_4$$

A
4

) modular symmetry, which provides solution to the strong CP problem without the need for an axion. The vanishing of the strong CP-violating phase $${\bar{\theta }}$$

θ

¯

is ensured by assuming CP to be a fundamental symmetry of the Lagrangian of the theory. The CP symmetry is broken spontaneously by the vacuum expectation value (VEV) of the modulus $$\tau $$
τ
. This provides the requisite large value of the CKM CP-violating phase while the strong CP phase $${\bar{\theta }}$$

θ

¯

remains zero or is tiny. Within the considered framework we discuss phenomenologically viable quark mass matrices with three types of texture zeros, which are realized by assigning both the left-handed and right-handed quark fields to $$A_4$$

A
4

singlets $$\textbf{1}$$
1
, $${\mathbf{1'}}$$

1
′

and $$\mathbf{1''}$$

1

′
′

with appropriate weights. The VEV of $$\tau $$
τ
is restricted to reproduce the observed CKM parameters. We discuss cases in which the modulus VEV is close to the fixed points i, $$\omega $$
ω
and $$i\infty $$

i
∞

. In particular, we focus on the VEV of $$\tau $$
τ
, which gives the absolute minima of the supergravity-motivated modular- and CP-invariant potentials for the modulus $$\tau $$
τ
, so called, modulus stabilisation. We present a successful model, which is consistent with the modulus stabilisation close to $$\tau =\omega $$

τ
=
ω

.
Network analysis of the relationship between different heart rate variability metrics during sleep
Authors: Mateos-Salgado Erik Leonardo , Pineda-Sánchez José Esael , Ayala-Guerrero Fructuoso , Gutiérrez-Chávez Carlos Alberto 
Published: September 2024

AbstractHeart rate variability (HRV) refers to the physiological phenomenon of variation in heartbeat duration, which can be characterized using various metrics. Considering a complex systems approach, in this study we used network modeling to quantitatively evaluate the relationship between different HRV metrics during sleep. Polysomnography recordings were performed on 24 healthy participants and their cardiac activity was sampled from the N2, N3, and REM sleep stages. Fifty-eight HRV metrics were calculated, and the relationship between each was assessed using mutual information (MI). One network was created for each sleep stage; HRV metrics constituted its nodes, and MI values were used to establish its edges. Repeated measures ANOVA was applied to each metric to assess variation between sleep stages. It was found that all three networks had characteristics of complex networks. Several communities of shared similar metrics were found across the three sleep stages. Of these, one community had the same metrics in stages N2 and N3, but in REM sleep was divided into three communities. REM sleep exhibited significant differences compared to the other sleep stages in several metrics. These preliminary findings allow us to suggest the application of this method in other HRV research contexts, which will determine its scope and limitations.
Investigating the Perception of Facial Anonymization Techniques in 360° Videos
Authors: Wöhler Leslie , Ikehata Satoshi , Aizawa Kiyoharu 
Published: September 2024

In this work, we investigate facial anonymization techniques in 360° videos and assess their influence on the perceived realism, anonymization effect, and presence of participants. In comparison to traditional footage, 360° videos can convey engaging, immersive experiences that accurately represent the atmosphere of real-world locations. As the entire environment is captured simultaneously, it is necessary to anonymize the faces of bystanders in recordings of public spaces. Since this alters the video content, the perceived realism and immersion could be reduced. To understand these effects, we compare non-anonymized and anonymized 360° videos using blurring, black boxes, and face-swapping shown either on a regular screen or in a head-mounted display (HMD).
Our results indicate significant differences in the perception of the anonymization techniques. We find that face-swapping is the most realistic and least disruptive; however, participants raised concerns regarding the effectiveness of the anonymization. Furthermore, we observe that presence is affected by facial anonymization in HMD condition. Overall, the results underscore the need for facial anonymization techniques that balance both photo-realism and a sense of privacy.
The Book Review Column
Authors: Tran Nicholas 
Published: September 2024

Graph Theory in America: The First Hundred Years (Princeton University Press, 2023) by Robin Wilson, John J. Watkins, and David J. Parks chronicles the first hundred years of graph theory in North America, starting with the arrival of James Joseph Sylvester at Johns Hopkins University in 1876 and ending with the proof of the four color theorem by Kenneth Appel and Wolfgang Haken in 1976.
Computability and Complexity: Foundations and Tools for Pursuing Scientific Applications (Springer, 2024) by decorated author Rod Downey is a new undergraduate textbook that covers advanced topics such as parameterized complexity, generic case complexity, and smoothed analysis.
How to Think about Algorithms, 2nd ed. (Cambridge University Press, 2024) by Jeff Edmonds aims to teach students to think like a designer of algorithms. This new edition includes a short chapter on machine learning algorithms and more than 150 new exercises. A review of the first edition of this book appeared in this column in 2009.
Differential Privacy (The MIT Press, 2025) by Simson L. Garfinkel, a senior data scientist at the US Department of Homeland Security, explains the algorithmic technology used by Google, Apple, and the US Census Bureau to protect the privacy of individuals in large datasets.
The Effect of Vitamin D Supplementation on Glycemic Control and Cardiovascular Risk Factors in Type 2 Diabetes: An Updated Systematic Review and Meta‐Analysis of Clinical Trials
Authors: Afraie Maryam , Bahrami Pourya , Kohnepoushi Parisa , Khateri Sorour , Majidi Lobat , Saed Lotfollah , Zamani Kamran , Baharm Hedyeh Mohammadi , Moradi Yousef , Moradpour Farhad 
Published: September 2024

Background and Aims: The purpose of this meta‐analysis was to investigate the effect of vitamin D supplementation on hemoglobin A1C (HbA1C), fasting blood sugar (FBS), low‐density lipoprotein (LDL), high‐density lipoprotein (HDL), systolic blood pressure (SBP), and the total vitamin D level in patients with Type 2 diabetes (T2DM).Methods: A systematic search was conducted in databases such as PubMed (Medline), Scopus, Embase, Web of Science, Cochrane Library, and ClinicalTrials.gov using relevant keywords from January 1990 to January 2024. After screening and extracting data, a qualitative evaluation of articles was performed using the Cochrane risk‐of‐bias tool for randomized trials (RoB 2).Results: The findings revealed that vitamin D supplementation significantly decreased the mean HbA1C (SMD: −0.15; 95% CI: −0.29, −0.20; Isquare: 79.76%; p value < 0.001) and mean FBS (SMD: −0.28; 95% CI: −0.40, −0.15; Isquare: 70.13%; p value < 0.001), lowered SBP (SMD: −0.06; 95% CI: −0.16, −0.05; Isquare: 39.63%; p value = 0.23), and reduced LDL (SMD: −0.11; 95% CI: −0.28, −0.05; Isquare: 73.66%; p value < 0.001). Furthermore, vitamin D supplementation increased the average HDL (SMD: 0.13; 95% CI: 0.04, 0.29; Isquare: 79.33%; p value < 0.001) and vitamin D levels (SMD: 1.78; 95% CI: 1.53, 2.04; Isquare: 91.92%; p value < 0.001) in patients with T2DM. Subgroup analyses showed that weight gain, BMI, and duration of the disease could reduce the effect of vitamin D supplementation on diabetes control in affected patients.Conclusion: The results also indicated that taking vitamin D supplements in the amount of 50,000 IU had a significant effect on reducing the indicators related to diabetes control. Based on the combined evidence, the findings of this meta‐analysis suggest that vitamin D supplementation can significantly improve glycemic control and reduce the risk of complications associated with T2DM, especially cardiovascular diseases (CVDs).
Integrated Germline and Somatic Features Reveal Divergent Immune Pathways Driving Response to Immune Checkpoint Blockade
Authors: Sears Timothy J. , Pagadala Meghana S. , Castro Andrea , Lee Ko-han , Kong JungHo , Tanaka Kairi , Lippman Scott M. , Zanetti Maurizio , Carter Hannah 
Published: September 2024

Abstract
Immune checkpoint blockade (ICB) has revolutionized cancer treatment; however, the mechanisms determining patient response remain poorly understood. Here, we used machine learning to predict ICB response from germline and somatic biomarkers and interpreted the learned model to uncover putative mechanisms driving superior outcomes. Patients with higher infiltration of T-follicular helper cells had responses even in the presence of defects in the MHC class-I (MHC-I). Further investigation uncovered different ICB responses in tumors when responses were reliant on MHC-I versus MHC-II neoantigens. Despite similar response rates, MHC II–reliant responses were associated with significantly longer durable clinical benefits (discovery: median overall survival of 63.6 vs. 34.5 months; P = 0.0074; validation: median overall survival of 37.5 vs. 33.1 months; P = 0.040). Characteristics of the tumor immune microenvironment reflected MHC neoantigen reliance, and analysis of immune checkpoints revealed LAG3 as a potential target in MHC II–reliant but not MHC I–reliant responses. This study highlights the value of interpretable machine learning models in elucidating the biological basis of therapy responses.