bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinatorial control of
Pseudomonas aeruginosa
biofilm development by quorum-sensing and nutrient-sensing regulators
Authors: Chen Gong , Fanouraki Georgia , Anandhi Rangarajan Aathmaja , Winkelman Bradford T. , Winkelman Jared T. , Waters Christopher M. , Mukherjee Sampriti 
Published: August 2024

ABSTRACT

The human pathogen
Pseudomonas aeruginosa
, a leading cause of hospital-acquired infections, inhabits and forms sessile antibiotic-resistant communities called biofilms in a wide range of biotic and abiotic environments. In this study, we examined how two global sensory signaling pathways—the RhlR quorum-sensing system and the CbrA/CbrB nutritional adaptation system—intersect to control biofilm development. Previous work has shown that individually these two systems repress biofilm formation. Here, we used biofilm analyses, RNA-seq, and reporter assays to explore the combined effect of information flow through RhlR and CbrA on biofilm development. We find that the Δ
rhlR
Δ
cbrA
double mutant exhibits a biofilm morphology and an associated transcriptional response distinct from wildtype and the parent Δ
rhlR
and Δ
cbrA
mutants indicating codominance of each signaling pathway. The Δ
rhlR
Δ
cbrA
mutant gains suppressor mutations that allow biofilm expansion; these mutations map to the
crc
gene resulting in loss of function of the carbon catabolite repression protein Crc. Furthermore, the combined absence of RhlR and CbrA leads to a drastic reduction in the abundance of the Crc antagonist small RNA CrcZ. Thus, CrcZ acts as the molecular convergence point for quorum- and nutrient-sensing cues. We find that in the absence of antagonism by CrcZ, Crc promotes the expression of biofilm matrix components—Pel exopolysaccharide, and CupB and CupC fimbriae. Therefore, this study uncovers a regulatory link between nutritional adaption and quorum sensing with potential implications for anti-biofilm targeting strategies.

IMPORTANCE

Bacteria often form multicellular communities encased in an extracytoplasmic matrix called biofilms. Biofilm development is controlled by various environmental stimuli that are decoded and converted into appropriate cellular responses. To understand how information from two distinct stimuli is integrated, we used biofilm formation in the human pathogen
Pseudomonas aeruginosa
as a model and studied the intersection of two global sensory signaling pathways—quorum sensing and nutritional adaptation. Global transcriptomics on biofilm cells and reporter assays suggest parallel regulation of biofilms by each pathway that converges on the abundance of a small RNA antagonist of the carbon catabolite repression protein, Crc. We find a new role of Crc as it modulates the expression of biofilm matrix components in response to the environment. These results expand our understanding of the genetic regulatory strategies that allow
P. aeruginosa
to successfully develop biofilm communities.
Development and validation of a novel questionnaire to describe and assess sensations and triggers associated with refractory and unexplained chronic cough
Authors: Galgani Shannon , Sawyer Chelsea , King Jenny , Dockry Rachel , Wingfield-Digby James , Holt Kimberly , Mitchell Joanne , Sen Shilpi , Birchall Danielle , Solari Francesca , Smith Jacky , Yorke Janelle 
Published: August 2024

IntroductionRefractory or unexplained chronic cough (RUCC) is a common clinical problem with no effective diagnostic tools. The Sensations and Triggers Provoking Cough questionnaire (TOPIC) was developed to characterise cough in RUCC versus cough in other conditions.MethodsContent analysis of participant interviews discussing the sensations and triggers of chronic cough informed TOPIC development. Participants with chronic cough completed the draft-TOPIC (a subset repeating 5–7 days later), St George’s Respiratory Questionnaire (SGRQ), Cough Severity Diary (CSD) and Global Rating of Change Scale. The draft-TOPIC item list was reduced in hierarchical and Rasch analysis to refine the questionnaire to the TOPIC.Results49 items describing the triggers and sensations of cough were generated from participant interviews (RUCC n=14, chronic obstructive pulmonary disease (COPD) n=11, interstitial lung disease (ILD) n=10, asthma n=11, bronchiectasis n=3, cystic fibrosis n=7). 140 participants (median age 60.0 (19.0–88.0), female 56.4%; RUCC n=39, ILD n=38, asthma n=45, COPD n=6, bronchiectasis n=12) completed draft-TOPIC, where items with poor ‘fit’ for RUCC were removed to create TOPIC (8 trigger items, 7 sensation items). Median TOPIC score was significantly higher in RUCC (37.0) vs ILD (24.5, p=0.009) and asthma (7.0, p<0.001), but not bronchiectasis (20.0, p=0.318) or COPD (18.5, p=0.238), likely due to small sample sizes. The Rasch model demonstrated excellent fit in RUCC (χ2=22.04, p=0.85; PSI=0.88); as expected. When all participant groups were included, fit was no longer demonstrated (χ2=66.43, p=0.0001, PSI=0.89) due to the increased heterogeneity (CI=0.077). TOPIC correlated positively with SGRQ (r=0.47, p<0.001) and CSD (r=0.63, p<0.001). The test–retest reliability of TOPIC (intraclass correlation coefficient) was excellent (r=0.90, p<0.001).ConclusionsHigh TOPIC scores in the RUCC patients suggest their cough is characterised by specific sensations and triggers. Validation of TOPIC in cough clinics may demonstrate value as an aid to identify features of RUCC versus cough in other conditions.
Psychological well-being trajectories preceding incident mild cognitive impairment and dementia
Authors: Guo Jie , Wang Jiao , Dove Abigail , Bennett David A , Xu Weili 
Published: August 2024

BackgroundPoorer psychological well-being has been related to an increased dementia risk, but changes in psychological well-being along the dementia course are unclear. We explored psychological well-being trajectories before and after the diagnosis of mild cognitive impairment (MCI) and dementia.MethodsWithin the Rush Memory and Aging Project, 910 cognitively intact older adults were followed annually for up to 14 years to detect incident MCI and dementia. Psychological well-being and its six components (self-acceptance, autonomy, environmental mastery, purpose in life, positive relation with others, and personal growth) were annually measured based on Ryff’s Scales of Psychological Well-Being. Data were analysed using mixed-effect models with a backward timescale.ResultsCompared with participants who remained cognitively intact, those who developed incident MCI had a faster decline in psychological well-being (β −0.015, 95% CI −0.027 to –0.003), leading to lower well-being 2 years before MCI diagnosis (mean difference at year −2, −0.099, 95% CI −0.187 to –0.012). Considering different well-being components, those who developed MCI had lower levels of purpose in life and personal growth beginning 3 years (−0.126, 95% CI −0.251 to –0.001) and 6 years (−0.139, 95% CI −0.268 to –0.009) before MCI, respectively. The slope of psychological well-being decline was similar before and after MCI diagnosis for each component except for positive relation with others, which had an accelerated decline after MCI (β −0.042, 95% CI−0.075 to –0.009). Well-being trajectories remained similar for individuals with MCI regardless of whether they later developed dementia.ConclusionsPsychological well-being (specifically purpose in life and personal growth) became significantly lower before MCI diagnosis.
Estimating Exposure to Information on Social Networks
Authors: Nettasinghe Buddhika , Kadoma Kowe , Naaman Mor , Krishnamurthy Vikram 
Published: August 2024

Estimating exposure to information on a social network is a problem with important consequences for our society. The exposure estimation problem involves finding the fraction of people on the network who have been exposed to a piece of information (e.g., a URL of a news article on Facebook, a hashtag on Twitter). The exact value of exposure to a piece of information is determined by two features: the structure of the underlying social network and the set of people who shared the piece of information. Often, both features are not publicly available (i.e., access to the two features is limited only to the internal administrators of the platform) and are difficult to estimate from data. As a solution, we propose two methods to estimate the exposure to a piece of information in an unbiased manner: a vanilla method that is based on sampling the network uniformly and a method that non-uniformly samples the network motivated by the Friendship Paradox. We provide theoretical results that characterize the conditions (in terms of properties of the network and the piece of information) under which one method outperforms the other. Further, we outline extensions of the proposed methods to dynamic information cascades (where the exposure needs to be tracked in real time). We demonstrate the practical feasibility of the proposed methods via experiments on multiple synthetic and real-world datasets.
Synthesis, Studies of Shocked Pulse of 50 Scale on 100 Gy Irradiated Zinc Acetate Crystals for Photonic, NLO, Phase-Matching and Electronic Utilities
Authors: N Balamurugapandian , K Suganya , R Hariharasuthan , T Jayanalina , V Swarnalatha , K SenthilKannan , R Manikandan 
Published: August 2024

The Zinc Acetate - ZA is grown in 16–17 days as colorless crystal by slow evaporation manner; in the present work, the shocked pulses of range of 50 scaling of ZA-100 Gy irradiated sample is represented after the pulsed reference of shock waves as ZA-100Gy-50S in physical reference, the single crystalline XRD data of ZA-100Gy-50S is having 15.108, 9.254, 4.7999 of a, b, c values in Å and beta as 99.12° with P21/c as space group and monoclinic as the system; the UV-visible spectral cut-off wavelength for ZA-100Gy-50S is 224 nm; the band gap in eV as 5.53 from Tauc’s plot and is 5.5357 eV from UV-visible data. The Fluorescence wavelength gives the energy impact of 2.4047 eV. The NLO-SHG as 1.34 times than the standard KDP and the phase matching proviso of ZA-100Gy-50S is 93.8 mV The surface morphological impact of ZA-100Gy-50S crystal is with small cracks, no major flaws; the third-order NLO of ZA-100Gy-50S is of 13.92 × 10–6 esu by Z-Scan; the frequency doubling circuit and frequency tripling circuit are analyzed for the ZA-100Gy-50S and are 2.28 times, 3.23 times the input. The (111) based displaying of the display action with Red-Green-Blue filled polygonal effect.
Technology in Suicide Prevention: Fears and Functionality for Crisis Supporters
Authors: Hopkins Danielle , Mazzer Kelly , Rickwood Debra 
Published: August 2024

Background: Crisis supporters at Lifeline Australia consistently engage with distressed and often suicidal help‐seekers. The development of technological methods, such as machine learning (ML), in suicide prevention may complement their support work. Investigating attitudes towards the use of ML in crisis support is an important first step.Aims: The current study is aimed at investigating crisis supporters’ attitudes towards ML in crisis support/suicide prevention, beliefs about the effect of technology on the service and help‐seeking, and concerns/opinions about any future technology implementation.Methods: Two hundred fifty‐five crisis supporters aged 20–84 years were recruited through Lifeline Australia. Participants voluntarily completed an anonymous questionnaire, including measures of attitudes towards technology as well as open‐text options, which provided the data for a thematic analysis.Results: Crisis supporters were neutral to negative on an adapted measure of ML use in crisis support. Less than one‐third held the belief that technology would enhance Lifeline services, and over half of the participants felt help‐seekers would be less likely to contact Lifeline if technology was implemented. Thematic analysis of the open‐text questions revealed loss of human connection and mistrust of algorithms to be the most prominent barriers to future technological adoption by Lifeline crisis supporters.Limitations: Clearly defining terms of ML and technology was difficult to do in this hypothetical context, potentially impacting the attitudes expressed.Conclusions: Any new technology to support crisis supporters needs to be carefully codesigned with the workforce to ensure effective implementation and avoid any potential or perceived negative impacts on help‐seekers.
Ferroptosis‐Related Genes in IgA Nephropathy: Screening for Potential Targets of the Mechanism
Authors: Zhu Wenhui , Chen Yao , Xiao Jing , Cheng Chuchu , Ma Guijie , Wang Yang , Zhang Yonggang , Chen Ming 
Published: August 2024

Aims: Exploring key genes and potential molecular pathways of ferroptosis in immunoglobulin A nephropathy (IgAN).Methods: The IgAN datasets and ferroptosis‐related genes (FRGs) were obtained in the Gene Expression Omnibus (GEO) and FerrDb database. Differentially expressed genes (DEGs) were identified using R software and intersected with FRGs to obtain differentially expressed FRGs (DE‐FRGs). After that, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (PEA) and Gene Ontology (GO) functional annotation were performed on DE‐FRGs. In the Search Tool for the Retrieval of Interacting Genes (STRING) website, we construct a protein–protein interaction (PPI) network. The PPI network was further investigated with screening hub genes with Cytoscape software. The core genes were then subjected to gene set enrichment analysis (GSEA). Finally, the samples were analyzed for immune infiltration in R, and the correlation between hub genes and immune cells was analyzed.Results: A total of 347 DEGs were identified. CD44, CDO1, CYBB, IL1B, RRM2, AKR1C1, activated transcription factor‐3 (ATF3), CDKN1A, GDF15, JUN, MGST1, MIOX, MT1G, NR4A1, PDK4, TNFAIP3, and ZFP36 were determined as DE‐FRGs. JUN, IL1B, and ATF3 were then screened as hub genes. GSEA and immune infiltration analysis revealed that the hub genes were closely associated with immune inflammatory responses such as NOD‐like receptor signaling, IL‐17 signaling, and TNF signaling.Conclusions: Our results show that JUN and ATF3 are possibly critical genes in the process of IgAN ferroptosis and may be related with immune cell infiltration.
Invasive freshwater gastropods in South America: Physa acuta and its expansion to Austral Patagonia in Argentina
Authors: Gutiérrez Gregoric Diego Eduardo , Lucía Micaela de , Torres Santiago Hernán , Copa Jorge Luis Esteban , Darrigran Gustavo 
Published: August 2024

Physa acuta is a freshwater snail of North American origin that has spread to all continents. In South America it was detected for the first time in 1966 (Brazil) and is currently present in Argentina, Brazil, Peru, Chile, Colombia, Ecuador and Uruguay, occupying 13 of the 52 South American freshwater eco-regions. Its introduction would be related to the import and transportation of aquatic plants. Here we update the distribution of P. acuta in Argentina based on a review of scientific collections, published works and new collections. Our review expands the distribution of the species from 11/23 Argentine provinces (until 2010) to 19/23, and we report the first record for the province of Santa Cruz, this being the southernmost site of the species. This new discovery in the province of Santa Cruz (Austral Patagonia), with an established and reproducing population in an urban area, poses a potential threat to local biodiversity (where there are no records of other non-native mollusks) and to human and animal health. This is due to the finding of populations in southern Argentina that are naturally infested by Fasciola hepatica. The record of P. acuta in aquatic environments of southern Patagonia makes it necessary to generate monitoring and control plans with the objective of identifying the dispersion vectors and preventing the spread of the species in other water bodies in the region.
Effect of Ticagrelor Versus Clopidogrel After Off‐Pump Coronary Artery Bypass Grafting on Postoperative Atrial Fibrillation: A Cohort Study
Authors: Jiang Qin , Huang Keli , Yin Lixue , Kong Hong , Yang Zhenglin , Hu Shengshou 
Published: August 2024

Background

This study aimed to explore the effect of a P2Y
12
inhibitor regimen on the occurrence of postoperative atrial fibrillation (POAF) after off‐pump coronary artery bypass graft surgery in carriers with the cytochrome P450 family 2 subfamily C member19 loss‐of‐function allele.

Methods and Results

From May 2019 to November 2023, patients containing the cytochrome P450 family 2 subfamily C member19*2 or *3 allele undergoing elective first‐time off‐pump coronary artery bypass graft surgery including aspirin 100 mg/d and ticagrelor 180 mg/d (AT group; n=95) versus clopidogrel 75 mg/d (aspirin and clopidogrel group; n=95) were prospectively followed. The primary end point was the cumulative incidence of POAF in a week. The secondary end points were POAF burden, platelet aggregability, systemic immune‐inflammation index and heart rate variability. The incidence of POAF was 21.1% in the AT group versus 41.1% in the aspirin and clopidogrel group (hazard ratio, 0.46 [95% CI, 0.27–0.76];
P
=0.003). POAF burden, ADP‐induced platelet aggregation and systemic immune‐inflammation index was notably lower in the AT group than the aspirin and clopidogrel group. Heart rate variability data showed an increase in both high‐frequency and SD of normal‐to‐normal RR intervals in the AT group with a decreased low‐frequency/high‐frequency ratio, suggesting that the sympathetic/parasympathetic activation was balanced.

Conclusions
In patients carrying the cytochrome P450 family 2 subfamily C member19 loss‐of‐function allele, an AT regimen after off‐pump coronary artery bypass grafting was associated with a lower incidence of POAF, paralleled by lower atrial fibrillation burden, ADP‐induced platelet aggregation, lower systemic immune‐inflammation index reaction, and a balanced automatic nerve system compared with an aspirin and clopidogrel regimen. Inhibiting the systemic immune‐inflammation response and sustaining automatic nerve balance may underlie the therapeutic effect of POAF by a potent antiplatelet combination.
Inference on the Macroscopic Dynamics of Spiking Neurons
Authors: Baldy Nina , Breyton Martin , Woodman Marmaduke M. , Jirsa Viktor K. , Hashemi Meysam 
Published: August 2024

Abstract
The process of inference on networks of spiking neurons is essential to decipher the underlying mechanisms of brain computation and function. In this study, we conduct inference on parameters and dynamics of a mean-field approximation, simplifying the interactions of neurons. Estimating parameters of this class of generative model allows one to predict the system’s dynamics and responses under changing inputs and, indeed, changing parameters. We first assume a set of known state-space equations and address the problem of inferring the lumped parameters from observed time series. Crucially, we consider this problem in the setting of bistability, random fluctuations in system dynamics, and partial observations, in which some states are hidden. To identify the most efficient estimation or inversion scheme in this particular system identification, we benchmark against state-of-the-art optimization and Bayesian estimation algorithms, highlighting their strengths and weaknesses. Additionally, we explore how well the statistical relationships between parameters are maintained across different scales. We found that deep neural density estimators outperform other algorithms in the inversion scheme, despite potentially resulting in overestimated uncertainty and correlation between parameters. Nevertheless, this issue can be improved by incorporating time-delay embedding. We then eschew the mean-field approximation and employ deep neural ODEs on spiking neurons, illustrating prediction of system dynamics and vector fields from microscopic states. Overall, this study affords an opportunity to predict brain dynamics and responses to various perturbations or pharmacological interventions using deep neural networks.
Utilization of apple vision pro in ophthalmic surgery: A pilot study
Authors: Orione M. , Rubegni G. , Tartaro R. , Alberghina A. , Fallico M. , Orione C. , Russo A. , Tosi G. M. , Avitabile T. 
Published: August 2024

Purpose This paper explores the application of Apple Vision Pro in ophthalmic surgery, assessing its potential benefits in providing real-time imaging overlay, surgical guidance, and collaborative opportunities. Materials and method The device was worn by 10 ophthalmic surgeons during eyelid malposition surgery. All surgeons performed the entire surgery while wearing the visor. At the end of procedure, all operators had to rate Apple Vision Pro visor according to 10 specific item and system usability scale (SUS) questionnaire. Results The surgeons used the Apple Vision Pro during the entire procedure, and the results were positive, with high ratings for practicality, freedom of movement, integration into workflow, and learning. All surgeons rated the Apple Vision Pro above 85/100 in the SUS. Conclusion The incorporation of Apple Vision Pro in oculoplastic surgery offers several advantages, including improved visualization, enhanced precision, and streamlined communication among surgical teams. According to our preliminary results Apple Vision Pro could represents a valuable tool in ophthalmic surgery, with implications for enhancing surgical techniques and advancing XR research in the surgical field.
Dexamethasone intravitreal implant in the treatment of macular edema secondary to necrotizing retinitis
Authors: Copete Sergio , García-García Jose Gregorio , Júdez Enrique 
Published: August 2024

Purpose To describe our experience with the use of a sustained-release dexamethasone implant in three patients with recalcitrant macular edema that developed after necrotizing retinitis in the context of the previously treated virus. Case description Two immunocompetent patients presented with unilateral acute retinal necrosis (ARN) due to Varicella-Zoster (VZV). The other, an immunocompromised patient, presented with unilateral cytomegalovirus (CMV) necrotizing retinitis. The diagnoses were confirmed by anterior chamber polymerase chain reaction (PCR) and all were treated with oral valganciclovir and intravitreal ganciclovir (2 mg/0.1 ml). Infection was controlled but two of them required pars plana vitrectomy. Between 2 and 4 months after the resolution of signs of infection, resistant macular edema (RME) developed, and an intravitreal dexamethasone device was implanted after anterior chamber PCR had been negative. Functional and anatomical improvement was achieved, with the resolution of the edema accompanied by improvement in visual acuity in all patients. There was no evidence of reactivation at two years. No cataract or ocular hypertension was observed. One patient required two additional dexamethasone implants. Conclusion Dexamethasone intravitreal implant could be considered as an option for the treatment of macular edema developed after ARN. Care should be taken to avoid reactivation and patients need to be properly informed.