bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for proactive and retroactive temporal pattern analysis in simultaneous masking
Authors: Laback Bernhard , Tabuchi Hisaaki , Kohlrausch Armin
Published: June 2024

Amplitude modulation (AM) of a masker reduces its masking on a simultaneously presented unmodulated pure-tone target, which likely involves dip listening. This study tested the idea that dip-listening efficiency may depend on stimulus context, i.e., the match in AM peakedness (AMP) between the masker and a precursor or postcursor stimulus, assuming a form of temporal pattern analysis process. Masked thresholds were measured in normal-hearing listeners using Schroeder-phase harmonic complexes as maskers and precursors or postcursors. Experiment 1 showed threshold elevation (i.e., interference) when a flat cursor preceded or followed a peaked masker, suggesting proactive and retroactive temporal pattern analysis. Threshold decline (facilitation) was observed when the masker AMP was matched to the precursor, irrespective of stimulus AMP, suggesting only proactive processing. Subsequent experiments showed that both interference and facilitation (1) remained robust when a temporal gap was inserted between masker and cursor, (2) disappeared when an F0-difference was introduced between masker and precursor, and (3) decreased when the presentation level was reduced. These results suggest an important role of envelope regularity in dip listening, especially when masker and cursor are F0-matched and, therefore, form one perceptual stream. The reported effects seem to represent a time-domain variant of comodulation masking release.
Teaching old dogs new tricks: genetic engineering methanogens
Authors: Myers Tyler , Dykstra Christy M.
Published: June 2024

Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.
Streptococcus dysgalactiae
subsp.
equisimilis
infection and its intersection with
Streptococcus pyogenes
Authors: Xie Ouli , Davies Mark R. , Tong Steven Y. C.
Published: June 2024

Streptococcus dysgalactiae
subsp.
equisimilis
(SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen,
Streptococcus pyogenes
. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and
S. pyogenes
, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with
S. pyogenes
. In doing so, we highlight the importance of understanding the overlap of SDSE and
S. pyogenes
to inform surveillance and disease control strategies.
Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences
Authors: Tsurumaki Megumi , Sato Asako , Saito Motofumi , Kanai Akio
Published: June 2024

The Candidate Phyla Radiation (CPR) represents an extensive bacterial clade comprising primarily uncultured lineages and is distinguished from other bacteria by a significant prevalence of insertion sequences (ISs) within their rRNA genes. However, our understanding of the taxonomic distribution and characteristics of these ISs remains limited. In this study, we used a comprehensive approach to systematically determine the nature of the rRNA ISs in CPR bacteria. The analysis of hundreds of rRNA gene sequences across 65 CPR phyla revealed that ISs are present in 48% of 16S rRNA genes and 82% of 23S rRNA genes, indicating a broad distribution across the CPR clade, with exceptions in the 16S and 23S rRNA genes of
Candidatus
(
Ca
.) Saccharibacteria and the 16S rRNA genes of
Ca
. Peregrinibacteria. Over half the ISs display a group-I-intron-like structure, whereas specific 16S rRNA gene ISs display features reminiscent of group II introns. The ISs frequently encode proteins with homing endonuclease (HE) domains, centered around the LAGLIDADG motif. The LAGLIDADG HE (LHE) proteins encoded by the rRNA ISs of CPR bacteria predominantly have a single-domain structure, deviating from the usual single- or double-domain configuration observed in typical prokaryotic LHEs. Experimental analysis of one LHE protein, I-ShaI from
Ca
. Shapirobacteria, confirmed that its endonuclease activity targets the DNA sequence of its insertion site, and chemical cross-linking experiments demonstrated its capacity to form homodimers. These results provide robust evidence supporting the hypothesis that the explosive proliferation of rRNA ISs in CPR bacteria was facilitated by mechanisms involving LHEs.

IMPORTANCE

Insertion sequences (ISs) in rRNA genes are relatively limited and infrequent in most bacterial phyla. With a comprehensive bioinformatic analysis, we show that in CPR bacteria, these ISs occur in 48% of 16S rRNA genes and 82% of 23S rRNA genes. We also report the systematic and biochemical characterization of the LAGLIDADG homing endonucleases (LHEs) encoded by these ISs in the first such analysis of the CPR bacteria. This study significantly extends our understanding of the phylogenetic positions of rRNA ISs within CPR bacteria and the biochemical features of their LHEs.
Identification of a copper-responsive small molecule inhibitor of uropathogenic
Escherichia coli
Authors: Hanson Braden S. , Hailemariam Amanuel , Yang Yongjian , Mohamed Faras , Donati George L. , Baker Dwight , Sacchettini James , Cai James J. , Subashchandrabose Sargurunathan
Published: June 2024

Urinary tract infections (UTIs) are a major global health problem and are caused predominantly by uropathogenic
Escherichia coli
(UPEC). UTIs are a leading cause of prescription antimicrobial use. Incessant increase in antimicrobial resistance in UPEC and other uropathogens poses a serious threat to the current treatment practices. Copper is an effector of nutritional immunity that impedes the growth of pathogens during infection. We hypothesized that copper would augment the toxicity of select small molecules against bacterial pathogens. We conducted a small molecule screening campaign with a library of 51,098 molecules to detect hits that inhibit a UPEC Δ
tolC
mutant in a copper-dependent manner. A molecule, denoted as
E. coli
inhibitor or ECIN, was identified as a copper-responsive inhibitor of wild-type UPEC strains. Our gene expression and metal content analysis results demonstrate that ECIN works in concert with copper to exacerbate Cu toxicity in UPEC. ECIN has a broad spectrum of activity against pathogens of medical and veterinary significance including
Acinetobacter baumannii, Pseudomonas aeruginosa
, and methicillin-resistant
Staphylococcus aureus
. Subinhibitory levels of ECIN eliminate UPEC biofilm formation. Transcriptome analysis of UPEC treated with ECIN reveals induction of multiple stress response systems. Furthermore, we demonstrate that L-cysteine rescues the growth of UPEC exposed to ECIN. In summary, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC.

IMPORTANCE

Urinary tract infection (UTI) is a ubiquitous infectious condition affecting millions of people annually. Uropathogenic
Escherichia coli
(UPEC) is the predominant etiological agent of UTI. However, UTIs are becoming increasingly difficult to resolve with antimicrobials due to increased antimicrobial resistance in UPEC and other uropathogens. Here, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC. In addition to
E. coli
, this small molecule also inhibits pathogens of medical and veterinary significance including
Acinetobacter baumannii, Pseudomonas aeruginosa,
and methicillin-resistant
Staphylococcus aureus
.
Performance of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of invasive pulmonary filamentous fungi infections in non-neutropenic patients
Authors: Wang Hansheng , Yu Dan , Chen Xiao , Zhou Yanhui , Qian Xin , Liu Dan , Wang Lei , Tang Yijun , Wang Meifang
Published: June 2024

The diagnosis of invasive pulmonary fungal disease depends on histopathology and mycological culture; there are few studies on touch imprints of bronchoscopic biopsies or lung tissue biopsies for the diagnosis of pulmonary filamentous fungi infections. The purpose of the present study was to explore the detection accuracy of rapid on-site evaluation of touch imprints of bronchoscopic biopsies or lung tissue biopsies for the filamentous fungi, and it aims to provide a basis for initiating antifungal therapy before obtaining microbiological evidence. We retrospectively analyzed the diagnosis and treatment of 44 non-neutropenic patients with invasive pulmonary filamentous fungi confirmed by glactomannan assay, histopathology, and culture from February 2017 to December 2023. The diagnostic positive rate and sensitivity of rapid on-site evaluation for these filamentous fungi identification, including diagnostic turnaround time, were calculated. Compared with the final diagnosis, the sensitivity of rapid on-site evaluation was 81.8%, and the sensitivity of histopathology, culture of bronchoalveolar lavage fluid, and glactomannan assay of bronchoalveolar lavage fluid was 86.4%, 52.3%, and 68.2%, respectively. The average turnaround time of detecting filamentous fungi by rapid on-site evaluation was 0.17 ± 0.03 hours, which was significantly faster than histopathology, glactomannan assay, and mycological culture. A total of 29 (76.3%) patients received earlier antifungal therapy based on ROSE diagnosis and demonstrated clinical improvement. Rapid on-site evaluation showed good sensitivity and accuracy that can be comparable to histopathology in identification of pulmonary filamentous fungi. Importantly, it contributed to the triage of biopsies for further microbial culture or molecular detection based on the preliminary diagnosis, and the decision on early antifungal therapy before microbiological evidence is available.
Microbial diversity, genomics, and phage–host interactions of cyanobacterial harmful algal blooms
Authors: Krausfeldt Lauren E. , Shmakova Elizaveta , Lee Hyo Won , Mazzei Viviana , Loftin Keith A. , Smith Robert P. , Karwacki Emily , Fortman P. Eric , Rosen Barry H. , Urakawa Hidetoshi , Dadlani Manoj , Colwell Rita R. , Lopez Jose V.
Published: June 2024

The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom “hotspots” near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of “-omics” to reveal important biological processes that could support the effective management and prediction of cyanoHABs.

IMPORTANCE

Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.
Effectiveness of nirsevimab immunoprophylaxis against respiratory syncytial virus-related outcomes in hospital and primary care settings: a retrospective cohort study in infants in Catalonia (Spain)
Authors: Coma Ermengol , Martinez-Marcos Montserrat , Hermosilla Eduardo , Mendioroz Jacobo , Reñé Anna , Fina Francesc , Perramon-Malavez Aida , Prats Clara , Cereza Gloria , Ciruela Pilar , Pineda Valentí , Antón Andrés , Ricós-Furió Gemma , Soriano-Arandes Antoni , Cabezas Carmen
Published: June 2024

Background

In Catalonia, infants under 6 months old were eligible to receive nirsevimab, a novel monoclonal antibody against respiratory syncytial virus (RSV). We aimed to analyse nirsevimab’s effectiveness across primary and hospital care outcomes.

Methods

Retrospective cohort study from 1 October 2023 to 31 January 2024, including all infants born between April and September 2023. We established two cohorts based on nirsevimab administration (immunised and non-immunised). We followed individuals until the earliest moment of an outcome—RSV infection, primary care attended bronchiolitis and pneumonia, hospital emergency visits due to bronchiolitis, hospital admission or intensive care unit (ICU) admission due to RSV bronchiolitis—death or the end of the study. We used the Kaplan-Meier estimator and fitted Cox regression models using a calendar time scale to estimate HRs and their 95% CIs.

Results

Among 26 525 infants, a dose of nirsevimab led to an adjusted HR for hospital admission due to RSV bronchiolitis of 0.124 (95% CI: 0.086 to 0.179) and an adjusted HR for ICU admission of 0.099 (95% CI: 0.041 to 0.237). Additionally, the adjusted HRs observed for emergency visits were 0.446 (95% CI: 0.385 to 0.516) and 0.393 (95% CI: 0.203 to 0.758) for viral pneumonia, 0.519 (95% CI: 0.467 to 0.576) for bronchiolitis attended in primary care and 0.311 (95% CI: 0.200 to 0.483) for RSV infection.

Conclusion

We demonstrated nirsevimab’s effectiveness with reductions of 87.6% and 90.1% in hospital and ICU admissions, respectively. These findings offer crucial guidance for public health authorities in implementing RSV immunisation campaigns.
Identifying neonatal transport research priorities: a modified Delphi consensus
Authors: Mistry Aarti , Leslie Andrew , Ojha Shalini , Sharkey Don
Published: June 2024

Objectives

With increasing advances in neonatal transport, a focused research strategy is required to increase the evidence base towards providing optimal care. We aimed to identify the most important neonatal transport research questions as prioritised by parents and healthcare professionals (HCPs).

Design

Key stakeholders participated in a modified three-stage Delphi consensus process. Research questions were identified and submitted through two survey stages before the final priority setting workshop.

Participants

Parents of babies who received neonatal care, neonatal HCPs and stakeholders.

Outcome

Identify the top 10 research priorities for neonatal transport.

Results

Overall, 269 survey responses from HCPs/stakeholders (n=161) and parents (n=108) were analysed from two survey rounds. Consensus was reached on 22 of 43 research priorities for the final priority setting workshop. The agreed top research priorities covered the domains of: (1) Pain assessment and management, (2) Long-term neurological outcomes, (3) Impact of transfer on birth-related brain injury, (4) Investigating risk of transport, (5) Safety restraints for infants, (6) Optimal temperature management, (7) Respiratory management and outcomes, (8) Benchmarking of important of transport measures, (9) Understanding transport environmental exposures, (10) Mental health and burden of transfer on families.

Conclusion

We have identified the top research questions for neonatal transport through an extensive process actively engaging parents, HCPs and key stakeholders. Targeted funding and research resources, directed towards addressing these prioritised research areas, will inform evidence-based practices and international frameworks specific to neonatal transport, helping minimise research waste and ultimately improve outcomes for these high-risk infants and their families.
Relevance of meeting general outpatients’ information needs to their perceptions of healthcare quality in a hospital in Ghana: a Healthcare Quality Survey using modified SERVQUAL analysis
Authors: Asare Anita Ago , Otchi Elom , Manu Adom
Published: June 2024

Background

Patients determine quality of healthcare by their perception of the gap between the healthcare they experience/receive and that which they expect. This can be influenced by the ability of healthcare staff to adequately communicate information about the healthcare provided. This study assessed the level of relevance of meeting patients’ information needs with respect to their assessment of healthcare quality in a private hospital’s general outpatient department in Ghana.

Design

Study design was cross-sectional using exit self-administered questionnaires among 390 outpatients. Healthcare quality was measured using a modified form of the Service Quality model gap analysis (gap between experience and expectations). A negative gap signifies unmet patient expectations. Microsoft Excel and Stata V.15.0 were used for analysis using t-test and multiple linear regression. A p value ≤0.05 denotes statistical significance.

Findings

The mean percentage of patients’ expectations of quality of healthcare was 87.6% (SE 0.031), while patient experience was 86.0% (SE 0.029), with a significant negative gap of −0.08 (p<0.002). Their highest expectation of the quality of healthcare was for their information needs to be met, with a mean score of 4.44 (SE 0.03). Two of the four items under the information needs dimension that showed no statistically significant gaps were ‘saying all their problems’ (gap=0.00; p<0.9) and ‘explanation of treatment/medications’ (gap=0.01; p<0.6). Those with statistically significant negative gaps were ‘explanation of investigations and procedures’ (gap=−0.18; p<0.0001) and ‘explanation of the diagnoses’ (gap=−0.11; p<0.02), signifying unmet expectations.

Conclusions

The outpatient’s greatest need for quality healthcare in this study was for their information needs to be met. Providing information on patient diagnoses and investigations are the areas least likely to be adequately communicated to patients.
Predicting and preventing heart failure
Authors: Taylor Clare J , Beezer Janine , Fuat Ahmet , Halliday Brian P , Ludman Andrew J , Pellicori Pierpaolo , Savage Henry Oluwasefunmi , Cleland John G F
Published: June 2024

Current guidelines for the treatment of heart failure do not focus on its prevention despite the steady global rise in prevalence. A new framework is needed to help clinicians routinely and efficiently identify patients at high risk of heart failure based on family history and risk factors, including obesity, hypertension, and diabetes mellitus. At present, guidelines recommend lifestyle changes, healthy diet, physical activity, antihypertensive treatment, cholesterol-lowering agents, and sodium-glucose co-transporter two inhibitor treatment to address risk factors for heart failure. However, in recent years, outcomes for patients with a diagnosis of heart failure have stagnated, highlighting the need for earlier implementation of better prevention strategies. Updated guidelines must include a roadmap that specifies who should intervene and at what point in the care cycle, to give patients the best possible chance at avoiding or delaying heart failure. A combination of public awareness campaigns, education for healthcare professionals, and improved screening methods is needed to aid the prediction and, crucially, prevention of heart failure.
Diagnosis and initial management of heart failure
Authors: Pellicori Pierpaolo , Ahmed Fozia Z , Beezer Janine , Fuat Ahmet , Halliday Brian P , Ludman Andrew J , Savage Henry Oluwasefunmi , Taylor Clare , Cleland John GF
Published: June 2024

Timely diagnosis of heart failure leads to anticipated introduction of effective treatments, improved quality of life, and better outcomes. However, for many patients, diagnosis of heart failure is still made too late for a variety of reasons, including the heterogeneity and lack of specificity of its signs and symptoms, the absence of universally accepted diagnostic criteria and limited access to specialist care. Implementing and potentially expanding the use of natriuretic peptide testing for individuals at high risk can aid identification of preclinical cardiac dysfunction amenable to treatment, delay progression of disease or refute a heart failure diagnosis in equivocal cases. In addition, greater public awareness of the signs and symptoms of heart failure and how it differs from other cardiovascular diseases may lead affected individuals to seek prompt medical attention. Improving early diagnosis and treatment relies on bringing heart failure to the fore in both the public arena and the clinic.
Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes
Authors: Cha Junha , Kim Da Hee , Kim Gamin , Cho Jae-Won , Sung Euijeong , Baek Seungbyn , Hong Min Hee , Kim Chang Gon , Sim Nam Suk , Hong Hyun Jun , Lee Jung Eun , Hemberg Martin , Park Seyeon , Yoon Sun Ock , Ha Sang-Jun , Koh Yoon Woo , Kim Hye Ryun , Lee Insuk
Published: June 2024

Background

Oropharyngeal squamous cell carcinoma (OPSCC) induced by human papillomavirus (HPV-positive) is associated with better clinical outcomes than HPV-negative OPSCC. However, the clinical benefits of immunotherapy in patients with HPV-positive OPSCC remain unclear.

Methods

To identify the cellular and molecular factors that limited the benefits associated with HPV in OPSCC immunotherapy, we performed single-cell RNA (n=20) and T-cell receptor sequencing (n=10) analyses of tonsil or base of tongue tumor biopsies prior to immunotherapy. Primary findings from our single-cell analysis were confirmed through immunofluorescence experiments, and secondary validation analysis were performed via publicly available transcriptomics data sets.

Results

We found significantly higher transcriptional diversity of malignant cells among non-responders to immunotherapy, regardless of HPV infection status. We also observed a significantly larger proportion of CD4+follicular helper T cells (Tfh) in HPV-positive tumors, potentially due to enhanced Tfh differentiation. Most importantly, CD8+resident memory T cells (Trm) with elevatedKLRB1(encoding CD161) expression showed an association with dampened antitumor activity in patients with HPV-positive OPSCC, which may explain their heterogeneous clinical outcomes. Notably, all HPV-positive patients, whose Trm presented elevatedKLRB1levels, showed low expression ofCLEC2D(encoding the CD161 ligand) in B cells, which may reduce tertiary lymphoid structure activity. Immunofluorescence of HPV-positive tumors treated with immune checkpoint blockade showed an inverse correlation between the density of CD161+Trm and changes in tumor size.

Conclusions

We found that CD161+Trm counteracts clinical benefits associated with HPV in OPSCC immunotherapy. This suggests that targeted inhibition of CD161 in Trm could enhance the efficacy of immunotherapy in HPV-positive oropharyngeal cancers.

Trial registration number

NCT03737968.
Emotionally intelligent themes in medical leaders’ decision-making during COVID-19
Authors: White Bobbie Ann Adair , Dayag Heather Valenova , Barry Erin S , Quinn Joann Farrell
Published: June 2024

Background

The COVID-19 pandemic presented unprecedented challenges for leaders in healthcare requiring decision-making and crisis response that can often be tricky without the right level of trust. Trust is fostered and facilitated with emotional intelligence (EI); thus, a critical examination of medical leaders’ reflections was essential to understand how leaders perceived their leadership responses during the initial response to COVID-19. This exploratory study used an EI lens to investigate leaders’ perceptions of their decision-making during COVID-19.

Methods

A purposeful sample of seven leaders in medicine who experienced leading during COVID were invited to participate in semi-structured interviews.

Results

Four themes around leadership response during the uncertain times of the COVID-19 were identified. The themes included communication, interprofessional collaboration including decision-making and strategic planning, internal and external awareness, and finally, trust and psychological safety.

Conclusions

Incorporating EI competencies into crisis leadership education for healthcare professionals could enhance medical leaders’ preparedness to adapt, collaborate and communicate effectively in a crisis.
Species communities can accurately predict the occurrence of an imperilled fish
Authors: Brownscombe Jacob W. , Bzonek Paul , Drake D. Andrew R.
Published: June 2024

Species distribution information is essential for conservation. However, sampling the full range of a species’ potential distribution is rarely feasible, necessitating the development of models to predict distributions, as well as relevant environmental and biotic drivers. We applied a novel approach to model the distribution of a species at risk in Canada, silver shiner (SS; Notropis photogenis) in tributaries of Lake Ontario using the fish community as a predictor of SS occurrence. Associative rule learning (ARL) identified simple species combinations that provided strong insight into SS distribution, which may be particularly useful for identifying new occupied locations, including making sampling decisions in real time. The species with the most positive or negative associations with SS identified by ARL were included in a random forests model, which predicted SS distribution with high accuracy in test data from the study tributary system and in a neighbouring system where SS is exceedingly rare. Predicting species distributions based on biotic associations presents opportunities for discovering new populations, identifying critical habitat, and evaluating the suitability of sites for re-introduction potential.
Monitoring estuarine fish communities: environmental DNA (eDNA) metabarcoding as a complement to beach seining
Authors: Saunders Mark D. , Steeves Royce , MacIntyre Leah P. , Knysh Kyle M. , Coffin Michael R.S. , Boudreau Monica , Pater Christina C. , van den Heuvel Michael R. , Courtenay Simon C.
Published: June 2024

Environmental deoxyribonucleic acid (eDNA) metabarcoding offers advantages over physical capture for identifying and quantifying animals in monitoring programs. In this study, the fish community was sampled at three stations (inner, middle, and outer estuary) in three estuaries in August 2020, and four estuaries in June and August 2021 (Prince Edward Island, Canada) using both beach seining and eDNA metabarcoding. Two 12S primer sets, 12S-160 and 12S-248F, with different amplicon lengths, yielded similar results. eDNA metabarcoding consistently detected species captured by 186 co-located beach seines and revealed additional species. It also detected monthly (June–August), interannual (2020–2021), and spatial shifts in the fish community, distinguishing stations separated by as little as 0.4 km. Positive correlations existed between eDNA metabarcoding species reads and beach seining captures. These findings suggest eDNA metabarcoding complements physical capture methods for characterizing nearshore fish communities in Prince Edward Island’s estuaries. While eDNA techniques lack certain population parameter information provided by physical methods, such as size, sex, and age structure, they offer a more comprehensive diversity assessment and presence–abundance insights, especially in inaccessible environments.
An improved calculation of the $$D_{(s)}^*D_{(s)}V$$ and $$B_{(s)}^*B_{(s)}V$$ couplings from light-cone sum rules
Authors: Jin Su-Ping , Jiang Hua-Yu
Published: June 2024

We present an improved calculation of the $$D_{(s)}^*D_{(s)}V$$

D

(
s
)

∗

D

(
s
)

V

and $$B_{(s)}^*B_{(s)}V$$

B

(
s
)

∗

B

(
s
)

V

coupling constants, where V denotes $$\rho $$
ρ
, $$K^*$$

K
∗

, $$\omega $$
ω
, and $$\phi $$
ϕ
mesons. These couplings govern the long-distance quantum chromodynamics (QCD) in interactions between heavy pseudo-scalar/vector mesons and light vector mesons. Our analysis is conducted within the framework of QCD light-cone sum rules (LCSRs) by utilizing the light-cone distribution amplitudes (LCDAs) of light vector mesons. By systematically incorporating the subleading power corrections and higher-twist contributions at the leading order (LO) and including the next-to-leading order (NLO) corrections at leading power, we achieve enhanced accuracy in the light-cone operator product expansion (OPE) for the underlying correlation function. In assessing the reliability of the established LCSRs, we consider uncertainties arising from the choice of the quark–hadron duality region in the double dispersion relation. Building upon these improvements, we accomplish an optimized computation and analysis for the strong coupling constants $$g_{H^*HV}$$

g

H
∗

H
V

which are used to extract the effective coupling $$\lambda $$
λ
in the heavy meson chiral perturbation theory (HM$$\chi $$
χ
PT). Furthermore, we investigate the SU(3) flavor symmetry-breaking effects in detail and compare our sum rule calculations with previous studies in an exploratory way.
Hidden BPS states of electroweak monopoles and a new bound estimate
Authors: Gunawan A. , Ramadhan H. S. , Prasetyo I.
Published: June 2024

Using the BPS Lagrangian method, we obtain a distinct set of Bogomolny equations for the Cho–Maison monopoles from the bosonic sector of a regularized electroweak theory. In the limit of $$n\rightarrow \infty $$

n
→
∞

of the permittivity regulator, $$\epsilon \left( \rho ^n\right) $$

ϵ

ρ
n

, the mass of the monopole can be estimated as $$M_W\sim 3.56$$

M
W

∼
3.56

TeV. This value is within the latest theoretical window, 2.98–3.75 TeV. We also discuss some possible regularization mechanisms of the electroweak monopole in the Yang–Mills sector and the existence of its BPS state.
Towards a realistic setup for a dynamical measurement of deviations from Newton’s $$1/r^2$$ law: the impact of air viscosity
Authors: Baeza-Ballesteros J. , Donini A. , Molina-Terriza G. , Monrabal F. , Simón A.
Published: June 2024

A novel experimental setup to measure deviations from the $$1/r^2$$

1
/

r
2

distance dependence of Newtonian gravity was proposed in Donini and Marimón (Eur Phys J C 76:696, 2016). The underlying theoretical idea was to study the orbits of a microscopically-sized planetary system composed of a “Satellite”, with mass $$m_{\textrm{S}} \sim {\mathcal {O}}(10^{-9})$$

m
S

∼
O

(

10

-
9

)

g, and a “Planet”, with mass $$M_{\textrm{P}} \sim {\mathcal {O}} (10^{-5}) $$

M
P

∼
O

(

10

-
5

)

 g at an initial distance of hundreds of microns. The detection of precession of the orbit in this system would be an unambiguous indication of a central potential with terms that scale with the distance differently from 1/r. This is a huge advantage with respect to the measurement of the absolute strength of the attraction between two bodies, as most electrically-induced background potentials do indeed scale as 1/r. Detection of orbit precession is unaffected by these effects, allowing for better sensitivities. In Baeza-Ballesteros et al. (Eur Phys J C 82:154, 2022), the impact of other subleading backgrounds that may induce orbit precession, such as, e.g., the electrical Casimir force or general relativity, was studied in detail. It was found that the proposed setup could test Yukawa-like corrections, $$\alpha \times \exp (-r/\lambda ),$$

α
×
exp
(
-
r
/
λ
)
,

to the 1/r potential with couplings as low as $$\alpha \sim 10^{-2}$$

α
∼

10

-
2

for distances as small as $$\lambda \sim 10$$

λ
∼
10

$$\upmu $$
μ
m, improving by roughly an order of magnitude present bounds. In this paper, we start to move from a theoretical study of the proposal to a more realistic implementation of the experimental setup. As a first step, we study the impact of air viscosity on the proposed setup and see how the setup should be modified in order to preserve the theoretical sensitivity achieved in Donini and Marimón (2016) and Baeza-Ballesteros et al. (2022).
Simple representations of BPS algebras: the case of $$Y(\widehat{\mathfrak {gl}}_2)$$
Authors: Galakhov Dmitry , Morozov Alexei , Tselousov Nikita
Published: June 2024

BPS algebras are the symmetries of a wide class of brane-inspired models. They are closely related to Yangians – the peculiar and somewhat sophisticated limit of DIM algebras. Still they possess some simple and explicit representations. We explain here that for $$Y(\widehat{\mathfrak {gl}}_r)$$

Y
(

gl
^

r

)

these representations are related to Uglov polynomials, whose families are also labeled by natural r. They arise in the limit $$\hbar {\longrightarrow } 0$$

ħ
⟶
0

from Macdonald polynomials, and generalize the well-known Jack polynomials ($$\beta $$
β
-deformation of Schur functions), associated with $$r=1.$$

r
=
1
.

For $$r=2$$

r
=
2

they approximate Macdonald polynomials with the accuracy $$O(\hbar ^2),$$

O
(

ħ
2

)
,

so that they are eigenfunctions of two immediately available commuting operators, arising from the $$\hbar $$
ħ
-expansion of the first Macdonald Hamiltonian. These operators have a clear structure, which is easily generalizable, – what provides a technically simple way to build an explicit representation of Yangian $$Y(\widehat{\mathfrak {gl}}_2),$$

Y
(

gl
^

2

)
,

where $$U^{(2)}$$

U

(
2
)

are associated with the states $$|\lambda {\rangle },$$

|
λ
⟩
,

parametrized by chess-colored Young diagrams. An interesting feature of this representation is that the odd time-variables $$p_{2n+1}$$

p

2
n
+
1

can be expressed through mutually commuting operators from Yangian, however even time-variables $$p_{2n}$$

p

2
n

are inexpressible. Implications to higher r become now straightforward, yet we describe them only in a sketchy way.
Sengupta transformations and Carrollian relativistic theory
Authors: Banerjee Rabin , Bhattacharya Soumya , Majhi Bibhas Ranjan
Published: June 2024

A detailed and systematic formulation of Carrollian relativity is provided. Based on the transformations, first provided by Sengupta (Nuovo Cim, 54:512, 1966), we construct a mapping between Lorentz relativistic and Carrollian relativistic vectors. Using this map the Carroll theory is built from the standard Maxwell action. We show that we get self-consistent equations of motion from the action, both in electric and magnetic limits. We introduce Carroll electric and magnetic fields. A new set of maps is derived that connects Carroll electric and magnetic fields with the usual Maxwell ones and yields Carroll equations in terms of fields. Consistency of results with the potential formulation is shown. Carroll version of symmetries like duality, gauge, shift, Noether and boost are treated in details and their implications elaborated. Especially, boost symmetry provides a link to the various maps used in this paper.
Limit Law for Zagreb and Wiener Indices of Random Exponential Recursive Trees
Authors: Al-Saedi Ali Q. M. , Nabiyyi Ramin Imany , Javanian Mehri
Published: June 2024

The Wiener index is the sum of distances of all pairs of nodes in a graph; and the Zagreb index is defined as the sum of squares of the degrees of nodes in a rooted tree. In this note, we calculate the first two moments of the Wiener and Zagreb indices of random exponential recursive trees (random ERTs) from two systems of recurrence relations. Then, by an application of the contraction method, we characterize the limit law for a scaled Zagreb index of ERTs. Via the martingale convergence theorem, we also show the almost sure convergence and quadratic mean convergence of an appropriately scaled Wiener index that is indicative of the distance of two randomly chosen nodes.
Local and Global Dynamics of a Ratio-Dependent Holling–Tanner Predator–Prey Model with Strong Allee Effect
Authors: Lou Weiping , Yu Pei , Zhang Jia-Fang , Arancibia-Ibarra Claudio
Published: June 2024

In this paper, the impact of the strong Allee effect and ratio-dependent Holling–Tanner functional response on the dynamical behaviors of a predator–prey system is investigated. First, the positivity and boundedness of solutions of the system are proved. Then, stability and bifurcation analysis on equilibria is provided, with explicit conditions obtained for Hopf bifurcation. Moreover, global dynamics of the system is discussed. In particular, the degenerate singular point at the origin is proved to be globally asymptotically stable under various conditions. Further, a detailed bifurcation analysis is presented to show that the system undergoes a codimension-[Formula: see text] Hopf bifurcation and a codimension-[Formula: see text] cusp Bogdanov–Takens bifurcation. Simulations are given to illustrate the theoretical predictions. The results obtained in this paper indicate that the strong Allee effect and proportional dependence coefficient have significant impact on the fundamental change of predator–prey dynamics and the species persistence.
Gaussian Process Regression Based Silver Price Forecasts
Authors: Jin Bingzi , Xu Xiaojie
Published: June 2024

A significant number of market participants have placed a high level of importance on price estimates for the primary metal commodities for a considerable amount of time. To tackle the problem, we investigate the daily reported price of silver in our study. The sample that is being analyzed spans a period of 13 years, starting on April 20, 2011, and ending on April 19, 2024. The price series which is being investigated has important implications for the commercial world. Specifically, when it comes to this unique circumstance, Gaussian process regression models are developed utilizing cross-validation strategies and Bayesian optimization procedures. The forecasting of prices is therefore accomplished via the use of the methods that are developed as a result of the situation. For the out-of-sample evaluation period that extends from October 5, 2021 to April 19, 2024, our empirical forecasting approach yields price estimates deemed reasonably accurate. The relative root mean square error reached for the silver price is 0.2257%, with the corresponding root mean square error of 0.0515, mean absolute error of 0.0389, and correlation coefficient of 99.967%. Due to the availability of models that forecast prices, investors and governments are supplied with the information they need to make educated judgments on the silver market by providing them with the knowledge they require. The framework of the Gaussian process regression with Bayesian optimizations demonstrates its good potential for modeling and forecasting sophisticated commodity price series for market participants.
A Quasi-Static Model Accounting for Friction-Induced Hysteresis in Tendon-Actuated Superelastic Notched Tube Instruments
Authors: Beckers Wim-Alexander , Borghesan Gianni , Poorten Emmanuel Vander
Published: June 2024

Superelastic notched tube instruments are being increasingly employed in surgical robotics. Due to their superelastic material properties, they can achieve small bending radii even for large bending angles, which makes them very interesting for minimally invasive interventions, typically dealing with confined spaces. Several works have aimed to model the behavior of such tubes in regard to the actuation force. The most extensive considers the superelastic material properties as well as the friction between the instrument and the tendon. However, no model is able to capture both the hysteresis behavior of the superelastic material as well as the hysteresis behavior induced by the friction. This text proposed a quasi-static method for modeling the behavior of nitinol notched tube instruments accounting for both material- and friction-induced hysteresis. The model is validated on four samples and compared to state of the art models. Results show an average notch position root mean square error of 1.06 mm (5.5%) and 0.46 mm (2.4%) for the method with measured parameters and optimized parameters, respectively.
Autonomous Soft-Tissue Needle Steering Using Reinforcement Learning Guided by Human Input
Authors: Ou Yafei , Tavakoli Mahdi
Published: June 2024

Soft-tissue needle steering, where a deformable needle is inserted into the tissue to guide its tip to a desired position, is a common minimally invasive surgery (MIS) procedure. The diverse types of needles and complex tissue dynamics limit the use of existing approaches that utilize models of the needle and the tissue for automating the task. In this work, we employ a data-driven approach using deep reinforcement learning (DRL) to achieve autonomous needle steering by viewing it as a multi-goal reinforcement learning problem. Human interventions are incorporated during training to accelerate learning and reduce catastrophic failures. Generative adversarial imitation learning (GAIL) is combined with regular DRL by utilizing a hindsight relabeling scheme for human interventions to encourage the agent to imitate human behavior. To emulate the sim-to-real process, an agent is first trained in a simplistic simulation environment for needle steering and then transferred to a sophisticated one considered as the real world with fine-tuning (sim-to-sim). Experimental results show that with human interventions, the proposed method outperforms the other compared DRL approaches and can achieve good performance with only 2,000 training steps in the complex simulation environment, achieving an average return comparable to that of a 55,000-step agent trained from scratch.
The Impact of Nature Realism on the Restorative Quality of Virtual Reality Forest Bathing
Authors: Masters Rachel , Nicoly Jalynn , Gaddy Vidya , Interrante Victoria , Ortega Francisco
Published: June 2024

Virtual reality (VR) forest bathing for stress relief and mental health has recently become a popular research topic. As people spend more of their lives indoors and have less access to the restorative benefit of nature, having a VR nature supplement has the potential to improve quality of life. However, the optimal design of VR nature environments is an active area of investigation with many research questions to be explored. One major issue with VR is the difficulty of rendering high-fidelity assets in real time without causing cybersickness, or VR motion sickness, within the headset. Due to this limitation, we investigate if the realism of VR nature is critical for the restorative effects by comparing a low-realism nature environment to a high-realism nature environment. We only found a significant difference in the perceived restorativeness of the two environments, but after observing trends in our data toward the stress reduction potential of the high-realism environment, we suggest exploring more varieties of high and low-realism environments in future work to investigate the full potential of VR and how people respond.