bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft genomes of
Neisseria perflava
UMB0578,
Proteus mirabilis
UMB8339, and
Enterococcus faecalis
UMB7967 isolated from urine samples
Authors: Kula Alex , Khan Ali , Martinez Megan , Terry Jevan , Appleberry Helen , Wolfe Alan J. , Putonti Catherine
Published: August 2024

The urinary tract of females harbors a variety of microorganisms, both for those with and without symptoms. Here, we present the draft genome sequences of three isolates from urine samples
—Neisseria perflava
UMB0578,
Proteus mirabilis
UMB8339, and
Enterococcus faecalis
UMB7967.
Genome sequence of
Lactobacillus johnsonii
XZ17, isolated from a C57BL/6J mouse lung
Authors: Ravi Keerthikka , Oh Gina J. , Moore Bethany B. , Huffnagle Gary B. , Zhou Xiaofeng
Published: August 2024

Lactobacillus johnsonii
XZ17 was isolated from the lung homogenate of a healthy C57BL/6J mouse. XZ17 is diminished in the lungs of syngeneic bone marrow-transplanted recipient mice. Long-read sequencing of XZ17 yielded a single genome of 1,948,140 bp, with a GC content of 34.64%.
Draft genome sequences of 21
Bacillus
sp. isolates from raw bovine milk
Authors: Khullar Gauri , Cai Zhangbin , O'Brien Bridget , Suh Jinha , Ronholm Jennifer
Published: August 2024

Members of the
Bacillus
genus are commonly used as probiotics in livestock production. We isolated several
Bacillus
strains from healthy dairy cattle. The role of these strains in mammary health is of interest. Here, we present 21 draft genome assemblies and annotations of
Bacillus
sp. isolated from fresh raw milk.
Complete genome sequences of
Geobacillus stearothermophilus
strains EF60045 and SJEF4-2 from Korean hot springs
Authors: Sung Jae-Yoon , Ganbat Dariimaa , Kim Seong Bo , Lee Sang-Jae , Lee Dong-Woo
Published: August 2024

We report the complete genomes of
Geobacillus stearothermophilus
strains EF60045 and SJEF4-2 from Korean hot springs, with 3,769 and 3,625 thermophilic genes, respectively.
G. stearothermophilus
EF60045 shows four methylation patterns.
G. stearothermophilus
SJEF4-2 harbors three plasmids. These findings enhance understanding of
Geobacillus
strains, aiding in their development as microbial platform hosts.
Genome sequence of Xenia2 a DV cluster phage that infects
Gordonia rubripertincta
Authors: Agaiby Carol , Ahmed Maha , Argueta Aidan , Arrowood Kyle , Barrier Keelynn P. , Church Meghan W. , Connell Cheryl R. , Dao Ken D. , Dao Kathleen Huyen T. , Davenport Makenzie R. , Edmondson Megan D. , Estabrook Makenzie I. , Gondhi Santoshi , Gonzalez Patricia , Leduc Francine , Ma Trang , Mansoor Adam , Mansoor Sara , Mattley Lillian , Meyer Cyrus , Nguyen Loc , Niaz Emaan , Parker Jenna M. , Ross Delaney C. , Scott Devin M. , Semryck Brianna , Takla Kyrillos , Tiramdas Aishwarya , Upputuru Sai Kaushik , Pollenz Richard S.
Published: August 2024

Xenia2 is a DV cluster actinobacteriophage that infects
Gordonia rubripertincta
NRRL B-16540. The genome is 68,135bp, has a GC content of 57.9% and 98 predicted protein-coding genes, 33 of which have a predicted function. Xenia2 has a lysis cassette with an endolysin (lysin A) and four different holin-like transmembrane proteins.
Genome characterization of BI2 subcluster
Streptomyces scabiei
bacteriophages GoblinVoyage and Doxi13
Authors: Jin Hanna , Chana Nihal K. , Tang Annie L. , Kaur Paramjit , Lamichhane Brishti , Leung Sze Ching , Scheiderer Diane , Sivaprakasam Vighnesh V. , Marcelino Dannah T. , Hull Gregory J. , Kamara Toma M. ,   2023 UMBC Phage Hunters,   STEM BUILD at UMBC Cohort 7, Guimaro Maria C. , Caruso Steven M.
Published: August 2024

We present the bacteriophages GoblinVoyage and Doxi13, siphoviruses isolated on
Streptomyces scabiei
RL-34. They belong to the BI2 cluster and have genomes consisting of 60.9% GC content with identical 3’ end sticky overhangs. The genome lengths of GoblinVoyage and Doxi13 are 43,540 bp and 43,696 bp, respectively.
Genomic characterization of
Enterobacter
sp.
PGRG2
and
Achromobacter insolitus PGRG5
: bacterial strains isolated from soil present near electronics manufacture industry for heavy metal remediation
Authors: Garg Ritika , Dang Shweta , Gauba Pammi
Published: August 2024

This article reports the whole-genome sequence of PGRG5 and the draft genome sequence of PGRG2. These strains were isolated from electronic waste contaminated soil. According to microbial identification, strain PGRG2 was identified as
Enterobacter
sp. (unclassified) with a size of ~4.4 Mbp and PGRG5 as
Achromobacter insolitus
with a size of ~6.2 Mbp.
Complete genome sequence of
Pseudomonas aeruginosa
Y010, a taro rhizosphere strain producing potent antimicrobial agents
Authors: Wen Yongqi , Cao Huiluo , Mo Zhifeng , Fang Hanshu , Xu Zeling
Published: August 2024

Pseudomonas aeruginosa
Y010, isolated from the taro rhizosphere, exhibits great antagonistic abilities against
Dickeya
strains that cause soft-rot and blackleg diseases of plants by producing potent antimicrobial agents. The complete genome of Y010 was sequenced and annotated, which is 6,415,628 bp in length with 66.39% GC content.
Characterization and comparative genomic analysis of a marine
Bacillus
phage reveal a novel viral genus
Authors: Jin Min , Yu Meishun , Feng Xuejin , Li Yinfang , Zhang Menghui
Published: August 2024

Bacillus pumilus
exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from
B. pumilus
derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the
Peduoviridae
family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel
Bacillus
phage belonging to a new genus under the
Peduoviridae
family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of
Bacillus
phage diversity and
Bacillus
-phage interactions, as well as provide essential knowledge for the industrial application of
B. pumilus
.

IMPORTANCE

Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered “dark matter” because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions.
Bacillus pumilus
shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting
B. pumilus
is apparent. In this study, we isolated and characterized a
B. pumilus
phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of
B. pumilus
.
Oropharyngeal microbiome profiling and its association with age and heart failure in the elderly population from the northernmost province of China
Authors: Liu Jian , He Xiao-Yu , Yang Ke-Laier , Zhao Yue , Dai En-Yu , Chen Wen-Jia , Raj Aditya Kumar , Li Di , Zhuang Min , Yin Xin-Hua , Ling Hong
Published: August 2024

Respiratory tract infections are the most common triggers for heart failure in elderly people. The healthy respiratory commensal microbiota can prevent invasion by infectious pathogens and decrease the risk of respiratory tract infections. However, upper respiratory tract (URT) microbiome in the elderly is not well understood. To comprehend the profiles of URT microbiota in the elderly, and the link between the microbiome and heart failure, we investigated the oropharyngeal (OP) microbiome of these populations in Heilongjiang Province, located in the North-East of China, a high-latitude and cold area with a high prevalence of respiratory tract infection and heart failure. Taxonomy-based analysis showed that six dominant phyla were represented in the OP microbial profiles. Compared with young adults, the OP in the elderly exhibited a significantly different microbial community, mainly characterized by highly prevalent
Streptococcus
,
unidentified_Saccharibacteria
,
Veillonella
,
unidentified_Pre votellaceae
, and
Neisseria
. While
unidentified_Prevotellaceae
dominated in the young OP microbiome. There was competition for niche dominance between
Streptococcus
and member of Prevotellaceae in the OP. Correlation analysis revealed that the abundance of
unidentified_Saccharibacteria
was positive, while
Streptococcus
was negatively correlated to age among healthy elderly. The bacterial structure and abundance in the elderly with heart failure were much like healthy controls. Certain changes in microbial diversity indicated the potential OP microbial disorder in heart failure patients. These results presented here identify the respiratory tract core microbiota in high latitude and cold regions, and reveal the robustness of OP microbiome in the aged, supplying the basis for microbiome-targeted interventions.

IMPORTANCE

To date, we still lack available data on the oropharyngeal (OP) microbial communities in healthy populations, especially the elderly, in high latitude and cold regions. A better understanding of the significantly changed respiratory tract microbiota in aging can provide greater insight into characteristics of longevity and age-related diseases. In addition, determining the relationship between heart failure and OP microbiome may provide novel prevention and therapeutic strategies. Here, we compared OP microbiome in different age groups and elderly people with or without heart failure in northeastern China. We found that OP microbial communities are strongly linked to healthy aging. And the disease status of heart failure was not a powerful factor affecting OP microbiome. The findings may provide basic data to reveal respiratory bacterial signatures of individuals in a cold geographic region.
Interplay between gut microbiota and tryptophan metabolism in type 2 diabetic mice treated with metformin
Authors: Xie Yvhao , Li Xinxin , Meng Qingshi , Li Jinjun , Wang Xin , Zhu Liying , Wang Weiwei , Li Xiaoqiong
Published: August 2024

Tryptophan (TRP) metabolites have been identified as potent biomarkers for complications of type 2 diabetes mellitus (T2DM). However, it remains unclear whether the therapeutic effect of metformin in T2DM is related to the modulation of TRP metabolic pathway. This study aims to investigate whether metformin affects TRP metabolism in T2DM mice through the gut microbiota. A liquid chromatography-tandem mass spectrometry method was established to determine 16 TRP metabolites in the serum, colon content, urine, and feces of T2DM mice, and the correlations between metabolites and the T2DM mice gut microbiota were performed. The method demonstrated acceptable linearity (
R
2
> 0.996), with the limit of quantification ranging from 0.29 to 69.444 nmol/L for 16 analytes, and the limit of detection ranging from 0.087 to 20.833 nmol/L. In T2DM mice, metformin treatment effectively restored levels of indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), and the ILA/IPA ratio, along with several aryl hydrocarbon receptor ligands in the serum, with a notable impact in the colon but not in the urine. This restoration was accompanied by a shift in the relative abundance of
Dubosiella
,
Turicibacter
,
RF39
,
Clostridia_UCG-014
,
and Alistipes
. Spearman’s correlation analysis revealed positive correlations between
Turicibacter
and
Alistipes
with IPA and indole-3-acetic acid. Conversely, these genera displayed negative correlations with ILA and kynurenine. In addition, our study revealed the presence of endogenous indole pathway in germ-free mice, and the impact of metformin on endogenous TRP metabolism in T2DM mice cannot be disregarded. Further research is needed to investigate the regulation of TRP metabolism by metformin.

IMPORTANCE

This study provides valuable insights into the interrelationship between metformin administration, changes in the tryptophan (TRP) metabolome, and gut microbiota in type 2 diabetes mellitus (T2DM) mice. Indole-3-lactic acid (ILA)/indole-3-propionic acid (IPA) emerges as a potential biomarker for the development of T2DM and prediction of therapeutic response. While the indole metabolic pathway has long been associated exclusively with the gut microbiome, recent research has demonstrated the ability of host interleukin-4-induced-1 to metabolize TRP. The detection of indole derivatives in the serum of germ-free mice suggests the existence of inherent endogenous indole metabolic pathways. These findings deepen our understanding of metformin's efficacy in correcting TRP metabolic disorders and provide valuable directions for further investigation. Moreover, this knowledge may pave the way for the development of targeted treatment strategies for T2DM, focusing on the gut microbiome and restoration of associated TRP metabolism.
Inhibition of SARS-CoV-2 infection by
Porphyromonas gingivalis
and the oral microbiome
Authors: Bontempo Alexander , Chirino Alexandra , Heidari Alireza , Lugo Alexandra , Shindo Satoru , Pastore Maria R. , Madonia Riccardo , Antonson Sibel A. , Godoy Cristina , Nichols Frank C. , Potempa Jan , Davey Mary Ellen , Kawai Toshihisa , Cayabyab Mark J.
Published: August 2024

The COVID-19 pandemic persists despite the availability of vaccines, and it is, therefore, crucial to develop new therapeutic and preventive approaches. In this study, we investigated the potential role of oral microbiome in SARS-CoV-2 infection. Using an
in vitro
SARS-CoV-2 pseudovirus infection assay, we found a potent inhibitory effect exerted by
Porphyromonas gingivalis
on SARS-CoV-2 infection mediated by known
P. gingivalis
compounds such as phosphoglycerol dihydroceramide (PGDHC) and gingipains as well as by unknown bacterial factors. We found that the gingipain-mediated inhibition of infection is likely due to cytotoxicity, whereas PGDHC inhibited virus infection by an unknown mechanism. Unidentified factors present in
P. gingivalis
supernatant inhibited SARS-CoV-2 likely via the fusion step of the virus life cycle. We addressed the role of other oral bacteria and found certain periodontal pathogens capable of inhibiting SARS-CoV-2 pseudovirus infection by inducing cytotoxicity on target cells. In the human oral cavity, we observed that the modulatory activity of oral microbial communities varied among individuals, in that some saliva-based cultures were capable of inhibiting while others were enhancing infection. These findings contribute to our understanding of the complex relationship between the oral microbiome and viral infections, offering potential avenues for innovative therapeutic strategies in combating COVID-19.

IMPORTANCE

The oral microbiome is important in health and disease, and in this study, we addressed the potential role of the oral microbiome in COVID-19 infection. Our
in vitro
studies suggest that certain bacteria of the oral microbiome such as
P. gingivalis
produce compounds that could potentially inhibit SARS-CoV-2 infection. These findings elucidating the interactions between the oral microbiome and SARS-CoV-2 infection will be important in our understanding of COVID-19 pathogenesis and the development of innovative therapeutic and preventive strategies against COVID-19 infection.
Core microbes in
Cordyceps militaris
sclerotia and their nitrogen metabolism-related ecological functions
Authors: Luo Li , Dai Fei , Xu Zhongshun , Guan Jingqiang , Fei Gangxiang , Qu Jiaojiao , Yao Min , Xue Yuan , Zhou Yeming , Zou Xiao
Published: August 2024

Cordyceps militaris
infects insects and forms sclerotia within the insect remains, establishing insect–microbe complexes. Here,
C
.
militaris
sclerotia samples from a single location in China over a 5-year period were subjected to high-throughput DNA sequencing, and the core microbes (which were stably enriched in the sclerotia over the 5 years) were identified. Next, seven bacterial strains were isolated from the
C. militaris
sclerotia, their biochemical characteristics were assessed, and they were co-cultured with
C. militaris
to study their effects on
C. militaris
metabolite production and biomass. Furthermore, the effects of NH
4
, NO
3
, and peptone media on
C. militaris
were compared. The results showed that
Rhodococcus
,
Phyllobacterium
,
Pseudomonas
,
Achromobacter
,
Ensifer
,
Stenotrophomonas
,
Sphingobacterium
,
Variovorax
, and
Acinetobacter
were the core microbes. Although co-culture of
C. militaris
with the seven bacterial strains isolated from the sclerotia did not directly increase the cordycepin level, they all had NO
3
reduction ability, and four had urea decomposition ability. Meanwhile,
C. militaris
in NH
4
medium had an increased cordycepin level compared to
C. militaris
in the other two media. From this, we inferred that bacteria in the sclerotia can convert NO
3
to NH
4
, and then cordycepin is produced using NH
4
, which was confirmed by RNA-seq and real-time fluorescence quantitative PCR. Thus, bacteria in the sclerotia may indirectly affect the
C. militaris
metabolite production by regulating nitrogen metabolism. In summary, there are stable core microbes in the
C. militaris
sclerotia, and they may directly and indirectly affect the growth and metabolite production of
C. militaris
.

IMPORTANCE

The model
Cordyceps
species
Cordyceps militaris
is rich in therapeutic compounds. It has recently been demonstrated that symbiotic microbes in sclerotia affect
Cordyceps’
growth, development, and secondary metabolite production. In this study, core microbes were identified based on
C. militaris
sclerotia samples obtained from the same site over 5 years. Additionally, bacterial strains isolated from
C. militaris
sclerotia were found to affect metabolite production and nitrogen utilization, based on functional tests. Moreover, based on the bacterial nitrogen metabolism capacity in the sclerotia and its influence on
C. militaris
metabolite production, we deduced that bacteria in the sclerotia can indirectly affect
C. militaris
metabolite production by regulating nitrogen metabolism. This is the first report on how bacteria in the sclerotia affect
C. militaris
metabolite production from the perspective of the nitrogen cycle. The results increase our understanding of microbial functions in
C. militaris
sclerotia.
Mutation of
Pseudomonas aeruginosa lasI/rhlI
diminishes its cytotoxicity, oxidative stress, inflammation, and apoptosis on THP-1 macrophages
Authors: Ren Yanying , You Xiaojuan , Zhu Rui , Li Dengzhou , Wang Chunxia , He Zhiqiang , Hu Yue , Li Yifan , Liu Xinwei , Li Yongwei
Published: August 2024

The management of
Pseudomonas aeruginosa
(
P. aeruginosa
) infections presents a substantial challenge to clinics and public health, emphasizing the urgent need for innovative strategies to address this issue. Quorum sensing (QS) is an intercellular communication mechanism that coordinates bacterial activities involved in various virulence mechanisms, such as acquiring host nutrients, facilitating biofilm formation, enhancing motility, secreting virulence factors, and evading host immune responses, all of which play a crucial role in the colonization and infection of
P. aeruginosa
. The LasI/R and RhlI/R sub-systems dominate in the QS system of
P. aeruginosa
. Macrophages play a pivotal role in the host’s innate immune response to
P. aeruginosa
invasion, particularly through phagocytosis as the initial host defense mechanism. This study investigated the effects of
P. aeruginosa
’s QS system on THP-1 macrophages. Mutants of PAO1 with
lasI/rhlI
deletion, as well as their corresponding complemented strains, were obtained, and significant downregulation of QS-related genes was observed in the mutants. Furthermore, the
ΔlasI
and
ΔlasIΔrhlI
mutants exhibited significantly attenuated virulence in terms of biofilm formation, extracellular polymeric substances synthesis, bacterial adhesion, motility, and virulence factors production. When infected with
ΔlasI
and
ΔlasIΔrhlI
mutants, THP-1 macrophages exhibited enhanced scavenging ability against the mutants and demonstrated resistance to cytotoxicity, oxidative stress, inflammatory response, and apoptosis induced by the culture supernatants of these mutant strains. These findings offer novel insights into the mechanisms underlying how the
lasI/rhlI
mutation attenuates cytotoxicity, oxidative stress, inflammation, and apoptosis in macrophages induced by
P. aeruginosa
.

IMPORTANCE

P. aeruginosa
is classified as one of the ESKAPE pathogens and poses a global public health concern. The QS system of this versatile pathogen contributes to a broad spectrum of virulence, thereby constraining therapeutic options for serious infections. This study illustrated that the
lasI/rhlI
mutation of the QS system plays a prominent role in attenuating the virulence of
P. aeruginosa
by affecting bacterial adhesion, biofilm formation, extracellular polymeric substances synthesis, bacterial motility, and virulence factors’ production. Notably, THP-1 macrophages infected with mutant strains exhibited increased phagocytic activity in eliminating intracellular bacteria and enhanced resistance to cytotoxicity, oxidative stress, inflammation, and apoptosis. These findings suggest that targeted intervention toward the QS system is anticipated to diminish the pathogenicity of
P. aeruginosa
to THP-1 macrophages.
Using a landscape fingerprint to identify changes in fault-slip behavior
Authors: Ross Emily O. , Reber Jacqueline E. , Titus Sarah J. , García Antonio F.
Published: August 2024

The Gabilan mesa tilts gently southwest away from the San Andreas fault in central California (western United States). Rather than attributing its existence to plate convergence, we argue that this large landform developed in response to a change in slip behavior along the San Andreas fault. Our interpretation is based on results from physical experiments. When we isolate a change in slip behavior (i.e., creeping to locked) as the only variable influencing deformation, a half-dome feature forms alongside the slip transition and mimics the shape and location of the Gabilan mesa adjacent to the San Andreas fault. We show other examples of half-dome features along the North Anatolian (Turkey), Philippine, and Chaman (Afghanistan-Pakistan) faults, suggesting that these domed landforms may provide indications of slip behavior transitions on poorly monitored faults.
Predicting extubation failure in preterm infants using lung ultrasound: a diagnostic accuracy study
Authors: Sett Arun , Foo Gillian , Ngeow Alvin , Thomas Niranjan , Kee Penny P L , Zayegh Amir , Hodgson Kate A , Donath Susan M , Tingay David G , Davis Peter G , Manley Brett J , Rogerson Sheryle R
Published: August 2024

Objective

To determine the accuracy of pre-extubation lung ultrasound (LUS) to predict reintubation in preterm infants born <32 weeks’ gestation.

Design

Prospective diagnostic accuracy study.

Setting

Two neonatal intensive care units.

Methods

Anterior and lateral LUS was performed pre-extubation. The primary outcome was the accuracy of LUS scores (range 0–24) to predict reintubation within 72 hours. Secondary outcomes were accuracy in predicting (1) reintubation within 7 days, (2) reintubation stratified by postnatal age and (3) accuracy of lateral imaging only (range 0–12). Pre-specified subgroup analyses were performed in extremely preterm infants born <28 weeks’ gestation. Cut-off scores, sensitivities and specificities were calculated using receiver operating characteristic analysis and reported as area under the curves (AUCs).

Results

One hundred preterm infants with a mean (SD) gestational age of 27.4 (2.2) weeks and birth weight of 1059 (354) g were studied. Thirteen were subsequently reintubated. The AUC (95% CI) of the pre-extubation LUS score for predicting reintubation was 0.63 (0.45–0.80). Accuracy was greater in extremely preterm infants: AUC 0.70 (0.52–0.87) and excellent in infants who were <72 hours of age at the time of extubation: AUC 0.90 (0.77–1.00). Accuracy was poor in infants who were >7 days of age. Lateral imaging alone demonstrated similar accuracy to scanning anterior and lateral regions.

Conclusions

In contrast to previous studies, LUS was not a strong predictor of reintubation in preterm infants. Accuracy is increased in extremely preterm infants. Future research should focus on infants at highest risk of extubation failure and consider simpler imaging protocols.

Trial registration number

Australian New Zealand Clinical Trials Registry: ACTRN12621001356853.
Qualitative exploration of patients’ experiences with Intrabeam TARGeted Intraoperative radioTherapy (TARGIT-IORT) and External-Beam RadioTherapy Treatment (EBRT) for breast cancer
Authors: Bagga Sandeep Kumar , Swiderska Natalie , Hooker Charlotte , Royle Jennifer , Ennis-O'Connor Marie , Freeney Siobhan , Watson Dympna , Woolcock Robin , Lodge George , Laws Siobhan , Vaidya Jayant S
Published: August 2024

Objective

To gather a deep qualitative understanding of the perceived benefits and impacts of External-Beam RadioTherapy (EBRT) and TARGeted Intraoperative radioTherapy (TARGIT-IORT) using Intrabeam to assess how the treatments affected patient/care partner experiences during their cancer treatment and beyond.

Design and participants

A patient-led working group was established to guide study design and to help validate findings. Patients with experience of receiving EBRT or TARGIT-IORT were purposively sampled by Hampshire Hospitals NHS Foundation Trust. These patients had been offered both regimens as per their clinical features and eligibility. Semistructured interviews were conducted with 29 patients and care partners with lived experience of either EBRT (n=12, 5-day FAST-Forward regimen and n=3, 3-week regimen) or TARGIT-IORT (n=14). Thematic analysis was then carried out by two coders generating 11 themes related to EBRT or TARGIT-IORT.

Setting

Semistructured interviews were conducted virtually via Zoom during February and March 2023.

Results

A number of procedural grievances were noted among EBRT patients. EBRT was perceived as being disruptive to normal routines (work, home and travel) and caused discomfort from side effects. TARGIT-IORT was perceived by patients and care partners as the safer option and efficient with minimal if any disruptions to quality of life. The need for timely accessible information to reduce anxieties was noted in both cohorts.

Conclusions

This qualitative study found that patients perceived EBRT as being greatly disruptive to their lives. In contrast, the one-off feature of TARGIT-IORT given while they are asleep during surgery gives them the feeling of stamping out the cancer without conscious awareness. These insights can help healthcare staff and policy-makers further justify the incorporation of the treatment favoured by these patient perceptions (TARGIT-IORT) more widely in routine practice. Further research is planned to explore TARGIT-IORT in more diverse populations and in the 35 countries where it is an established treatment option.
Behavioural attitudes of three-wheeled taxi drivers towards mitigation of on-road air pollution in urban cities in Sri Lanka: a qualitative study from South Asia
Authors: Adikaram W D C Niroshini , Arambepola Carukshi
Published: August 2024

Objectives

In recent years, urban areas across South Asia have experienced alarming levels of air pollution, primarily attributed to the rapid growth of motorised transportation. Three-wheeled taxis, commonly known as ‘tuk-tuks’, constitute a significant portion of the public transport system in Sri Lankan cities, making it crucial to understand the behavioural attitudes of their drivers in addressing on-road air pollution as they are key stakeholders in urban mobility and environmental sustainability. Therefore, this research aimed to contribute valuable insights into the behavioural attitudes of three-wheeled taxi drivers towards mitigation of on-road air pollution.

Methods

We recruited 67 three-wheeled taxi drivers to participate in semi-structured focus group interviews and in-depth interviews through purposive sampling. The sample size was determined on the basis of data saturation. We collected data from on-site note-taking, audio recording and transcribing the interviews, and subjected them to content thematic analysis manually.

Result

Behavioural attitudes for mitigation were mainly based on efforts to minimise on-road air pollution, perception of minimising on-road air pollution, knowledge, socio-demographic and legislative factors related to behaviour.

Conclusion

Behavioural attitudes on mitigation were multi-faceted. To minimise the hazards as well as mitigate air pollution, educating and supporting them financially and by inducing a behavioural change are recommended to safeguard their health.
The need for thoracic magnetic resonance imaging before vertebral augmentation surgery in patients with lumbar vertebral fractures
Authors: Zhang Yuye , Tang Wenxiang , Niu Yanping , Zhao Xushen , Hua Jun , Zhou Xiaozhong , Lin Fanguo
Published: August 2024

Background

Osteoporotic vertebral compression fractures (OVCFs) of the lumbar region may be accompanied by thoracic fractures. Treating only the lumbar fractures can lead to worsening of the thoracic fractures or unresolved postoperative symptoms. This study aims to investigate the need to perform thoracic MRI before vertebral augmentation (including percutaneous vertebroplasty and percutaneous kyphoplasty) in patients with lumbar OVCF.

Methods

This study retrospectively analyzed patients with lumbar OVCF who were scheduled for surgical treatment. All patients underwent thoracic and lumbar MRI before surgery. We evaluated the proportion of thoracic fractures accompanying lumbar fractures at each segment and identified the common locations of these accompanying fractures. Univariate and multivariate analyses were conducted to determine the risk factors and optimal thresholds for predicting accompanying thoracic fractures.

Results

The study recruited 700 patients, of whom 96 (13.71%) had new thoracic fractures along with lumbar fractures. The most common thoracic segments affected were T10 (22.50%), T9 (19.17%), T8 (26.67%), and T7 (20.83%). Univariate analysis showed significant differences in age and cause of injury between the thoracic fracture group and the control group. The bone density of the thoracic fracture group was significantly lower than that of the control group. Multivariate logistic regression analysis indicated that lifting heavy objects, sprains, and low bone density are risk factors for thoracic fractures in patients with lumbar OVCF.

Conclusion

It is crucial to perform thoracic MRI before surgery in patients with lumbar OVCF. This helps to avoid missing thoracic fractures, prevent the worsening of injuries, and ensure better postoperative outcomes.
Yukawa–Casimir wormholes in the framework of f(R) gravity
Authors: Venkatesha V. , Chalavadi Chaitra Chooda , Malik Adnan
Published: August 2024

In this article, we explore the Yukawa modification of the Casimir wormhole within the framework of f(R) gravity. To accomplish this, we adopt an approach proposed by Garattini (Eur Phys J C 81:824, 2021), wherein the original Casimir source is modified by a Yukawa term in three distinct scenarios. We utilize these Yukawa Casimir energy densities to assess the feasibility of traversable wormholes. The resulting shape function satisfies the criteria for traversability under the specified parameter values. Furthermore, we scrutinize the energy conditions and the violation of the null energy conditions suggests the presence of exotic matter within the Yukawa Casimir wormholes. Additionally, we analyze the embedding procedures for the wormhole geometry.
Nonlinear chiral forms in the Sen formulation
Authors: Janaun Sujiphat , Phonchantuek Anajak , Vanichchapongjaroen Pichet
Published: August 2024

The Sen formulation for chiral (2p)-form in $$4p+2$$

4
p
+
2

dimensions describes a system with two separate sectors, one is physical while the other is unphysical. Each contains a chiral form and a metric. In this paper, we focus on the cases where the self-duality condition for the unphysical sector is linear while for the physical sector can be nonlinear. We show the decoupling at the Hamiltonian and Lagrangian levels. The decoupling at the Hamiltonian level follows the idea in the literature. Then by an appropriate field redefinition of the corresponding first-order Lagrangian, the separation at the Lagrangian level follows. We derive the diffeomorphism of the theory in the case where the chiral form in the physical sector has nonlinear self-dual field strength and couples to external $$(2p+1)$$

(
2
p
+
1
)

-form field. Explicit forms of Sen theories are also discussed. The Lagrangian for the quadratic theory is separated into two Henneaux–Teitelboim Lagrangians. We also discuss the method of generating explicit nonlinear theories with $$p=1$$

p
=
1

. Finally, we also show that the M5-brane action in the Sen formulation is separated into a Henneaux–Teitelboim action in unphysical sector and a gauge-fixed PST in physical sector.
Extreme and Dragon-King Events in a Discrete Neuron Model
Authors: Joseph Dianavinnarasi , Kumarasamy Suresh , Karthikeyan Anitha , Rajagopal Karthikeyan
Published: August 2024

This study investigates the behavior of the Izhikevich discrete neuron model across various parameter configurations. Bifurcation diagrams and Lyapunov exponents are utilized to examine the impact of these parameters on the behavior of the system. The study specifically identifies important parameter ranges in which the attractor undergoes a sudden expansion, displaying characteristics of extreme events. Within the system, two distinct categories of extreme events can be identified: rare occurrences of small probability events located in the tail of the probability distribution and Dragon-King (DK) events, which possess a high probability amplitude. DK events are verified through the use of the DK test. The research concludes by examining the practical ramifications of these findings. The significance of forecasting and controlling extreme events in intricate systems is underscored, along with the cruciality of identifying their happening.
Infectious disease models with generalized nonlinear vaccination rate and temporary immunity
Authors: Ma Zhihui , Wang Shufan , Lin Xuanru
Published: August 2024

This paper incorporates generalized nonlinear vaccination rate and temporary immunity into the infectious disease models and presents the corresponding system. The qualitative results show that the disease-free equilibrium point and the endemic equilibrium point are globally asymptotically stable under some certain conditions. The local sensitivity analysis reveals that the importance of the critical parameters to the effective reproduction number [Formula: see text] in the order from high to low is [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text], respectively. The global sensitivity analysis shows that the parameters which impact on the effective reproduction number [Formula: see text] are [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] in the descending order. Based on the dynamical behavior and the sensitivity analysis of the considered system, the controlling measures are presented to prevent and control the infectious diseases: (1) increasing the nonlinear vaccination rate of the susceptible subpopulation, (2) controlling the number of immigrants to infectious areas, (3) increasing vaccination coverage of immigrants and newborns and (4) improving the effectiveness of vaccines and reducing the rate of immune loss.
Platinum-group elements and Nb–Ta geochemistry of the Deccan basalts from Kumbharli and other Ghat sections and the Koyna Seismic Zone, Maharashtra (India): crustal contamination and implications for sulfide saturation of the magma
Authors: Banerjee Ratul , Mondal Sisir K.
Published: August 2024

The Deccan basalts from the Kumbharli, Nadlapur, Bijaynagar, Hazarmacchi and Surli Ghat sections (surface samples) and the Koyna borehole-7 (KBH-7, subsurface samples) from Maharashtra (western India) demonstrate a two-stage crystallization process. Olivine and chromite were crystallized earlier in a shallow crustal magma chamber while clinopyroxene and plagioclase phenocrysts were crystallized in the subvolcanic conduits forming the crystal mush and carried to the surface by the evolved Fe–Ti-rich ascending basaltic magma. The high modal abundance of plagioclase at the top and clinopyroxene at the bottom part of the Kumbharli Ghat section is responsible for an increase in Sr and a decrease in Sc content towards the upper flows. The surface and subsurface basalt samples contain Pd = 5–31 ppb, Pt = 4–15 ppb, Ir = 1–4 ppb, Ru = 1–3 ppb and Rh = 3–5 ppb. Negative relations of Pd/Ir, Pd/Ru and Pd/Rh with MgO from both sets of samples indicate partitioning of Ir, Ru and Rh to early fractionated cumulus chromite (or olivine). Magnetite is a late crystallizing phase from the evolved Fe–Ti-rich basaltic magma. With an increasing modal abundance of magnetite, there is an increase in FeO
total
, TiO
2
and V with Pd indicating the fractionation of Pd by magnetite. The geochemical characters show that the surface basalt samples are less contaminated compared with the subsurface KBH-7 basalts. High Nb (6.8–13.6 ppm) and low Ta (0.2–0.37 ppm) content and elevated Nb/Ta ratios of the surface samples from the ghat sections indicate the possible interaction of the basaltic magma with the carbonate metasomatized subcontinental lithospheric mantle. On the other hand, a high degree of partial melting with limited crustal contamination can also elevate the Nb/Ta ratios of the basalts from the ghat sections. Deccan basalts from the study areas do not bear the signature of sulfide supersaturation and subsequent immiscible sulfide segregation. This is evidenced by their high chalcophile element concentrations (Ni = 79–103 ppm, Cu = 121–259 ppm) and ratios like Cu/Zr ( ≥ 1) and Ni/MgO (13.7–21.8) with low Cu/Pd (2140–29 938) compared with other Ni–Cu sulfide mineralized continental flood basalts. The lack of crustal sulfur in the various contaminants is perhaps the main reason for this sulfide-undersaturated character of the Deccan basalts of the current study.
Generative AI for Self-Adaptive Systems: State of the Art and Research Roadmap
Authors: Li Jialong , Zhang Mingyue , Li Nianyu , Weyns Danny , Jin Zhi , Tei Kenji
Published: August 2024

Self-adaptive systems (SASs) are designed to handle changes and uncertainties through a feedback loop with four core functionalities: monitoring, analyzing, planning, and execution. Recently, generative artificial intelligence (GenAI), especially the area of large language models, has shown impressive performance in data comprehension and logical reasoning. These capabilities are highly aligned with the functionalities required in SASs, suggesting a strong potential to employ GenAI to enhance SASs. However, the specific benefits and challenges of employing GenAI in SASs remain unclear. Yet, providing a comprehensive understanding of these benefits and challenges is complex due to several reasons: limited publications in the SAS field, the technological and application diversity within SASs, and the rapid evolution of GenAI technologies. To that end, this article aims to provide researchers and practitioners a comprehensive snapshot that outlines the potential benefits and challenges of employing GenAI’s within SAS. Specifically, we gather, filter, and analyze literature from four distinct research fields and organize them into two main categories to potential benefits: (i) enhancements to the autonomy of SASs centered around the specific functions of the MAPE-K feedback loop, and (ii) improvements in the interaction between humans and SASs within human-on-the-loop settings. From our study, we outline a research roadmap that highlights the challenges of integrating GenAI into SASs. The roadmap starts with outlining key research challenges that need to be tackled to exploit the potential for applying GenAI in the field of SAS. The roadmap concludes with a practical reflection, elaborating on current shortcomings of GenAI and proposing possible mitigation strategies.

†
Performance Modeling of Distributed Data Processing in Microservice Applications
Authors: Gao Yicheng , Casale Giuliano , Singhal Rekha
Published: August 2024

Microservice applications are increasingly adopted in distributed data processing systems, such as in mobile edge computing and data mesh architectures. However, existing performance models of such systems fall short in providing comprehensive insights into the intricate interplay between data placement and data processing. To address these issues, this article proposes a novel class of performance models that enables joint analysis of data storage access workflows, caching, and queueing contention. Our proposed models introduce a notion of access path for data items to model hierarchical data locality constraints. We develop analytical solutions to efficiently approximate the performance metrics of these models under different data caching policies, finding in particular conditions under which the underlying Markov chain admits a product-form solution. Extensive trace-driven simulations based on real-world datasets indicate that service and data placement policies based on our proposed models can respectively improve by up to 35% and 37% the average response time in edge and data mesh case studies.
Exploiting the Extended Neighborhood of Hexagonal Qubit Architecture for Mapping Quantum Circuits
Authors: Kole Abhoy , Datta Kamalika , Sengupta Indranil , Drechsler Rolf
Published: August 2024

In this work mapping of quantum circuits to regular hexagonal grid with coupling degree of six has been investigated. Architectures involving superconducting qubits impose restrictions on 2-qubit gate operations to be carried out only between physically coupled qubits, also referred to as nearest-neighbor (NN) constraint. The noise introduced by the 2-qubit gates and the execution time greatly affect the computational reliability. Existing mapping techniques suffer either from the adopted approach to reduce gate overhead or from their inability to take advantage of such architectural regularity. We outlined three different qubit mapping approaches using Remote-CNOT templates, Swap gates and combination of both. We show the benefits of assigning the Cartesian coordinate system in hexagonal grid for runtime elevation and devised approaches for reduction in gate overheads. While the template-based approach gives a strict upper bound of additional gate overheads for a particular qubit mapping, the combined approach provides better result employing a larger lookahead window. Experiments on benchmark quantum circuits confirm that the proposed Swap-based method provides an average

\(25\%\)

improvement in gate overheads over a recent work and the combined approach contributes further

\(15\%\)

average improvement on the result at the expense of a little higher runtime.
The Hidden Threat: Analysis of Linux Rootkit Techniques and Limitations of Current Detection Tools
Authors: Stühn Jakob , Hilgert Jan-Niclas , Lambertz Martin
Published: August 2024

This article addresses the significant threat posed by rootkits as part of the diverse malware landscape of today. Rootkits enable an attacker to regain access to an already comprised system at root-level making their prompt identification and removal crucial. However, rootkits implement advanced stealth features, enabling them to evade detection by conventional measures during analysis. Consequently, analysts generally rely on customized tools to detect the presence of a rootkit. However, our research highlights significant deficits in the tools available for the detection of rootkits on the Linux operating system, which is frequently encountered in investigations of server environments. Recognizing the need for improved awareness and capabilities among investigators, we conducted an in-depth analysis of 21 distinct Linux rootkits allowing us to dive into their techniques and features. Furthermore, we critically assessed the effectiveness of standard detection tools, revealing their limitations. Based on these insights, we propose best practices for investigators to effectively identify and detect signs of rootkit infections. Additionally, we provide a repository of indicators of compromise we extracted during our analyses to facilitate the detection of the analyzed rootkits on compromised systems along with a utility to detect rootkits via hidden files on a live system.
Sense of Embodiment Supports Motor Learning and Adaptation in Tele-Robotics
Authors: Falcone Sara , Lieftink Robin , Brouwer Anne-Marie , Dresscher Douwe , Heylen Dirk , Erp Jan Van
Published: August 2024

In this article, we transition from the theoretical and experimental groundwork of manipulating and measuring Sense of Embodiment (SoE) to addressing a fundamental question: What is the purpose of optimizing the SoE in a teleoperation system? This exploration centers on investigating the potential positive effects of SoE on motor adaptation, the acceleration of motor learning, and the potential enhancement of task performance. The article delves into this investigation by focusing on two critical research questions: (1) what is the effect of SoE on task performance in a perceptual-motor task? (2) What is the effect of SoE on the asymptote of the learning curve in a perceptual-motor task? Drawing insights from the existing literature, the hypothesis emerges that enhancing SoE yields positive effects not only on task performance (H1) but also on the overall embodiment experience (H2). An additional layer of exploration is introduced through an exploratory research question: Are these results consistent across diverse scenarios and tasks? The study design encompasses two distinct user studies, each set in different applications and featuring various avatars, yet all anchored in similar tasks, specifically a modified peg-in-hole task: (1) in the first experiment, participants operated a robotic arm with a human-like hand as end-effector, and they were required to perform a classic peg-in-hole task; (2) in user study 2, the task is transformed into a variation that we called “peg-on-button,” wherein participants use a robotic arm with a gripper as the end-effector to press a lit button. In both studies, a consistent pattern emerges: a setup that fosters embodiment has a positive impact on motor learning and adaptation, resulting in improved task performance. A supportive setup also reduces the perception of the surrogate as a mere mediator between the operator and the remote environment, especially when contrasted with a setup that suppresses embodiment. The positive effects on motor learning and task performance advocate for the incorporation of embodiment-supportive designs in teleoperational setups. However, the nuanced relationship between SoE and long-term task performance prompts a call for further exploration and consideration of various factors influencing teleoperation outcomes across diverse scenarios and tasks.