bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zingiber officinale-derived exosome-like nanoparticles as antimicrobial agents via lipid-mediated inhibition
Authors: Zhu Chiying , Gao Bihu , Li Jiao 
Published: November 2024

Abstract
Microbial diseases represent a significant challenge to global health, highlighting the importance of developing novel alternative antibacterial agents. The widely used spice and traditional medicinal plant Zingiber officinale and its derivatives have been demonstrated to possess promising antibacterial properties. The aim of the present study was to assess the antibacterial efficacy of Zingiber officinale-derived exosome-like nanoparticles (ZODENs) against a model bacterium, Escherichia coli (E. coli). The ZODENs were isolated from the rhizome of Zingiber officinale and subjected to morphological, size distribution, and zeta potential characterization. The bacterial growth curve assays and colony formation assays demonstrated that the E. coli bacterial growth was remarkably inhibited following incubation with ZODENs. The ZODENs were observed to be internalized by the E. coli bacteria following incubation, and subsequently demonstrated remarkable bacterial killing effects. Furthermore, the ZODEN-derived lipids, rather than the remaining fractions, demonstrated the capacity to inhibit bacterial cells, indicating that the antibacterial activity of ZODENs was at least partially attributable to its lipid content. These findings have paved the way for the development of ZODEN-based novel antibacterial agents and will facilitate the future clinical translation of plant-derived nanomedicines.
The discontinuation of implantable cardioverter defibrillator shock therapies towards the end of life: consensus guideline from the British Heart Rhythm Society
Authors: Thomas Honey , Dutton Amy , Johnson Miriam J , Herbert Heather , Wallace Jane , Foley Paul 
Published: November 2024

Abstract
Implantable cardioverter defibrillators (ICDs) are implanted in increasing numbers of patients with the aim of treating ventricular arrhythmias in high-risk patients and reducing their risk of dying. Individuals are also living longer with these devices. As a result, a greater number of patients with an ICD will deteriorate either with worsening cardiac failure, another non-cardiac condition or general frailty and will have a limited prognosis. Frequently, they will be cared for by non-cardiac teams who may be less familiar with ICDs. Therefore, to ensure the person receives high-quality end-of-life care, they should have the opportunity to consider and discuss the option to deactivate the shock function of their ICD. If the ICD shock therapy is not discontinued, there is an increased risk that, as a person reaches the last days of life, the ICD may deliver multiple, painful shocks that are distressing. There is also a risk that the device may delay the person’s natural death, which the person would not have chosen if they had been given the opportunity to discuss discontinuation. The British Heart Rhythm Society has developed a practical guideline to support all healthcare professionals who are caring for patients who have an ICD. This includes descriptions of different device types, ethical and legal aspects, timing and nature of ICD discussions and practical advice regarding how the devices may be deactivated. It aims to promote awareness and timely discussion between professionals and patients and to encourage best practice.
HBM4EU chromates study: the Portuguese integrated and harmonized study on exposure to hexavalent chromium and related early effects
Authors: Viegas Susana , Martins Carla , Ribeiro Edna , Ladeira Carina , Pinhal Hermínia , Nogueira Ana , Santos Sílvia , Tavares Ana , Gomes Bruno Costa , Afonso Catarina Maia , Louro Henriqueta , João Silva Maria 
Published: November 2024

Abstract
In the scope of the European Union (EU) human biomonitoring initiative, a multicentric study on different occupational settings from several European countries was performed, to provide information on occupational exposure to hexavalent chromium [Cr(VI)], a known lung carcinogen. Biomonitoring approaches were used to obtain exposure data to support the implementation of new risk management measures and policy actions at the national and European levels. This work describes the Portuguese contribution to the study, which aimed to assess workers' exposure to Cr, by using exposure biomarkers (urinary chromium [U-Cr]), and industrial hygiene samples (air and hand wipes) and to link exposure to potential long-term health effects by using effect biomarkers. Exposure determinants influencing exposure were explored from the contextual information and human biomonitoring data. The ultimate goal of the study was to appraise the risk management measures contributing to minimize exposure and protect workers’ health. Several occupational settings and activities were considered, including plating, welding, and painting. A control group from the Portuguese general population was also included. Data on age, sex, and smoking habits from both groups were considered in the statistical analysis. Information on the risk management measures available for workers was collected and used to identify the ones that mainly contributed to reduce exposure. Environmental monitoring and human biomonitoring revealed that painters were the highest exposed group. The use of respiratory protection equipment showed an influence on total U-Cr levels for workers involved in painting activities. Concerning early health effects, the painters presented also a significantly higher level of DNA and chromosomal damage in peripheral blood cells, as compared to the control group, suggesting a plausible association between exposure to Cr(VI) and early genotoxic effects. The results showed that workers are exposed to Cr(VI) in those occupational settings. These findings point to the need to improve the prevention and risk management measures and the implementation and enforcement of new regulatory actions at the national level.
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome
Authors: Li Yinhu , Pan Guangze , Wang Shuai , Li Zhengtu , Yang Ru , Jiang Yiqi , Chen Yu , Li Shuai Cheng , Shen Bairong 
Published: November 2024

Abstract
The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.
AltGosling: automatic generation of text descriptions for accessible genomics data visualization
Authors: Smits Thomas C , L’Yi Sehi , Mar Andrew P , Gehlenborg Nils 
Published: November 2024

Abstract

Motivation
Biomedical visualizations are key to accessing biomedical knowledge and detecting new patterns in large datasets. Interactive visualizations are essential for biomedical data scientists and are omnipresent in data analysis software and data portals. Without appropriate descriptions, these visualizations are not accessible to all people with blindness and low vision, who often rely on screen reader accessibility technologies to access visual information on digital devices. Screen readers require descriptions to convey image content. However, many images lack informative descriptions due to unawareness and difficulty writing such descriptions. Describing complex and interactive visualizations, like genomics data visualizations, is even more challenging. Automatic generation of descriptions could be beneficial, yet current alt text generating models are limited to basic visualizations and cannot be used for genomics.

Results
We present AltGosling, an automated description generation tool focused on interactive data visualizations of genome-mapped data, created with the grammar-based genomics toolkit Gosling. The logic-based algorithm of AltGosling creates various descriptions including a tree-structured navigable panel. We co-designed AltGosling with a blind screen reader user (co-author). We show that AltGosling outperforms state-of-the-art large language models and common image-based neural networks for alt text generation of genomics data visualizations. As a first of its kind in genomic research, we lay the groundwork to increase accessibility in the field.

Availability and implementation
The source code, examples, and interactive demo are accessible under the MIT License at https://github.com/gosling-lang/altgosling. The package is available at https://www.npmjs.com/package/altgosling.
Predicting the subcellular location of prokaryotic proteins with DeepLocPro
Authors: Moreno Jaime , Nielsen Henrik , Winther Ole , Teufel Felix 
Published: November 2024

Abstract

Motivation
Protein subcellular location prediction is a widely explored task in bioinformatics because of its importance in proteomics research. We propose DeepLocPro, an extension to the popular method DeepLoc, tailored specifically to archaeal and bacterial organisms.

Results
DeepLocPro is a multiclass subcellular location prediction tool for prokaryotic proteins, trained on experimentally verified data curated from UniProt and PSORTdb. DeepLocPro compares favorably to the PSORTb 3.0 ensemble method, surpassing its performance across multiple metrics in our benchmark experiment.

Availability and implementation
The DeepLocPro prediction tool is available online at https://ku.biolib.com/deeplocpro and https://services.healthtech.dtu.dk/services/DeepLocPro-1.0/.
Practical application of PMA–qPCR assay for determination of viable cells of inter-species biofilm of Candida albicans–Staphylococcus aureus
Authors: Kendra Samuel , Czucz Varga Jarmila , Gaálová-Radochová Barbora , Bujdáková Helena 
Published: November 2024

Abstract
Determining the number of viable cells by calculating colony-forming units is time-consuming. The evaluation of mixed biofilms consisting of different species is particularly problematic. Therefore, the aim of this study was to optimize a molecular method—propidium monoazide quantitative polymerase chain reaction (PMA–qPCR)—for accurate and consistent differentiation between living and dead cells. In the practical experimental example, the number of genome copies representing living cells was determined in a mixed biofilm of Candida albicans–Staphylococcus aureus inhibited by photodynamic inactivation. Optimal conditions such as PMA concentration and the duration of light exposure, the optimization of DNA isolation from the mixed biofilm and standardization of PMA–qPCR parameters were tested prior to the main experiment. The genome copy number was calculated based on the known amount of genomic DNA in the qPCR and the genome size of the respective microorganism. The results showed that photodynamic inactivation in the presence of 1 mM methylene blue decreased the total genome copy number from 1.65 × 108 to 3.19 × 107, and from 4.39 × 107 to 1.91 × 107 for S. aureus and C. albicans (P &lt; 0.01), respectively. The main disadvantage is the overestimation of the number of living cells represented by genome copy numbers. Such cells are unable to reproduce and grow (no vitality) and are continuously dying. On the other hand, PMA–qPCR determines the copy numbers of all microbial species, including a mix of eukaryotic yeasts and prokaryotic bacteria in a biofilm in one step, which is a great advantage.
Immunomodulatory effects of HYCO-3, a dual action CO-releaser/Nrf2 activator
Authors: Stegnjaić Goran , Nikolovski Neda , Stanisavljević Suzana , Lazarević Milica , Momčilović Miljana , Foresti Roberta , Motterlini Roberto , Miljković Đorđe 
Published: November 2024

Abstract
HYCOs are hybrid molecules consisting of activators of the transcription factor Nrf2 conjugated to carbon monoxide (CO)-releasing moieties. These ‘dual action’ compounds (HYCOs) have been designed to mimic the activity of heme oxygenase-1 (HO-1), a stress inducible cytoprotective enzyme that degrades heme to CO which expression is regulated by Nrf2. HYCOs have recently shown efficacy in ameliorating experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. However, the mechanism(s) of action of HYCOs still remains to be fully investigated. Here, we assessed the effects of HYCO-3, a prototype of these hybrids, on myeloid-derived cells, microglial cells and T lymphocytes obtained from EAE-immunized mice. HYCO-3 exerted immunomodulatory effects on all the examined cell populations by inhibiting the generation of pro-inflammatory cytokines and nitric oxide, and downregulating antigen-presenting capacity of these cells. The observed effects support the view that HYCOs are promising candidates to be developed for the treatment of autoimmune and chronic inflammatory disorders.
‘Musing upon the king my brother’s wreck’: Shipwrecked Nostos in a Ulyssean Palimpsest in The Waste Land
Authors: Zhou Wei 
Published: November 2024

Abstract
In this article, I read the shipwrecked journeys in T. S. Eliot’s 1922 poem The Waste Land as belonging to a long-standing trope of travel by sea. By examining the connections between the scenes of shipwrecks in the poem and its intertexts, including works by Homer and Shakespeare, I reconstruct the characters’ homecoming journeys in a Ulyssean palimpsest of nostos (‘homecoming’) in these scenes. I argue that these scenes foreground the challenges of homecoming by sea while implying the hope for returns through mythical implications and dramatic effect. The article situates drowning and resurrection, the governing themes of the poem, in the critical lineage of nostos that encompasses deferred return and symbolic rebirth. Informed by the context of the Great War and Eliot’s New England heritage, the article challenges the work in modernist studies that tends to interpret Eliot’s depiction of these thwarted journeys as a rejection of homecoming.
The Risk of Venous Thromboembolism in Children With Inflammatory Bowel Disease
Authors: Harvey Philip R , McNulty David , Coupland Benjamin , Kemos Polychronis , Croft Nicholas M , Trudgill Nigel J 
Published: November 2024

Abstract

Background
Recent studies of children with inflammatory bowel disease (IBD) demonstrate an increased venous thromboembolism (VTE) risk. However, estimates of risk are variable and case numbers are limited. The aim of this study was to provide national estimates of the risk of VTE in children with IBD.

Methods
Hospital Episode Statistics was used to identify patients diagnosed with either IBD or VTE before reaching 18 years of age between 2001 and 2019. Populations and subgroups are described, and the risks of developing VTE in the general and IBD populations were calculated.

Results
Children with VTE following a diagnosis of IBD or in the previous 6 months (n = 85) and with VTE without IBD (n = 4160) were studied. The absolute risk in children with IBD was 9.42 (95% confidence interval [CI], 7.4-11.4) per 10 000 patient-years, compared with 0.18 (95% CI, 18-0.19) in children without IBD. Between 6 months prior to and 1 year following IBD diagnosis was the highest absolute risk period for VTE (18.0; 95% CI, 13.7-22.4). The relative risk of VTE in children with IBD vs children without IBD was greatest in younger patient groups: the relative risk for the age band 0 to 8 years was 96.5 (95% CI, 51.8-179.9) and for 9 to 11 years was 153.1 (95% CI, 81.2-288.8) vs 14.3 (95% CI, 10.3-20.0) for 15 to 17 years. Cerebral venous sinus thrombosis represented 17.6% of pediatric VTE events in IBD patients compared with 4.2% in children without IBD (P = .001).

Conclusions
This study confirms the increased risk of VTE in children with IBD compared with children without IBD. The time of greatest VTE risk was around diagnosis. Cerebral venous sinus thrombosis was significantly more common in children with IBD than other children.
Mycobacterium tuberculosis Antigen Rv1471 Induces Innate Immune Memory and Adaptive Immunity Against Infection
Authors: Huang Xuejiao , Wu Juan , Xu Jinchuan , Wang Huiling , Chen Zhenyan , Fan Xiao-Yong , Hu Zhidong 
Published: November 2024

Abstract
Mycobacterium tuberculosis (Mtb) contains approximately 4000 individual proteins. However, only about 100 have been evaluated as antigens in tuberculosis (TB) subunit vaccine development. In addition, no trained immunity-targeting subunit TB vaccine has been reported yet. This study tested Rv1471, a thioredoxin secreted by Mtb, as a candidate TB vaccine antigen due to its capacity to stimulate functional maturation of macrophages. Transcription analysis of Rv1471-trained macrophages indicated that innate immune memory was activated through pathways of Akt-mTOR-HIF-1α and aerobic glycolysis. Rv1471 also enhanced innate immune memory responses and protection against intracellular infections of different mycobacteria. In a murine model of TB, immunization with Rv1471 produced robust antigen-specific multifunctional T-cell immune responses and had substantial protective efficacy against Mtb challenge. Analysis of recall immunity showed that the Rv1471 triggered robust T-cell immunity after Mtb infection. These findings support the development of an innate immune memory–targeting subunit TB vaccine to increase vaccine efficacy.
Associations with sexual dysfunction among a Canadian cohort with inflammatory bowel disease
Authors: Weizman Adam V , Nguyen Derek M , Targownik Laura E , Mosko Jeff , Bollegala Natasha , Saibil Fred , Huang Vivian , Selk Amanda , Bernstein Michael 
Published: November 2024

Abstract

Background
Sexual dysfunction is common in individuals with inflammatory bowel disease (IBD). The aim of this study was to better characterize sexual dysfunction and associated factors among a Canadian cohort of IBD patients.

Methods
A cross-sectional survey study was conducted. The primary outcome was sexual dysfunction as measured by the Female Sexual Dysfunction Scale in females and the Male Sexual Dysfunction Scale in males. Analyses were stratified by sex and multiple linear regression was used to identify associations.

Results
In total, 351 respondents completed the survey. Both females and males were impacted by sexual dysfunction (IBD-FSDS 14.1 [± 13.8] and IBD-MSDS 7.2 [± 9.4, respectively]). Depression was common and strongly associated with sexual dysfunction (β coefficient 0.92 [0.13] for men and 0.84 [0.19] for women, P &lt;.001).

Conclusions
Sexual dysfunction was common and more impactful in women. Depression was strongly associated with sexual dysfunction. This underscores the need for multidisciplinary care in addressing sexual health among individuals living with IBD.
Best practices for the naming of species
Authors: Ruedas Luis A , Norris Ryan W , Timm Robert M 
Published: November 2024

Abstract
The process of describing a species has evolved considerably since the modern age of taxonomy was initiated with the publication of the 10th edition of Linnaeus’ Systema Naturæ in 1758. Nevertheless, the basic unit of the taxonomic framework remains the species group (species and subspecies). As a result, it is incumbent upon individuals undertaking species-group descriptions to strive for the highest standards, just as it is for reviewers and editors to hold authors to those same standards. The clear and mounting biodiversity crisis, the increasing proliferation of journals, the multiplication of journals publishing only in electronic format, the decline in the number of trained taxonomists, and the complex and at times misinterpreted wording of the rules governing taxonomy have resulted in a growing number of species names that are unavailable because one or more aspects required of a species-level taxonomic description are lacking. Here, we present best practices for the required elements of a taxonomic description and identify some of the common pitfalls leading to an inadequate description resulting in an unavailable name. We also suggest best practices that would enhance taxonomic descriptions and make them more informative.
Preparation for targeted sterile insect technique to control invasive Aedes aegypti (Diptera: Culicidae) in southern California: dose-dependent response, survivorship, and competitiveness
Authors: Birhanie Solomon Kibret , Thieme Castellon Jennifer , Macias Ale , Casas Rubi , Brown Michelle Q 
Published: November 2024

Abstract
Aedes aegypti is fast spreading across California, with over 300 cities within 22 central and southern counties being infested since its introduction in 2013. Due to its cryptic breeding habitats, control efforts have not been successful so far. This calls for innovative tools such as sterile insect technique (SIT) to reinforce the existing integrated pest management (IPM). Here, we assessed fitness, survivorship, and dose response of X-ray irradiated male Ae. aegypti in California. Locally acquired Ae. aegypti eggs were hatched and reared in temperature-controlled laboratory setting at the West Valley Mosquito and Vector Control District in Ontario, California. Freshly emerged adult male mosquitoes were manually separated using motor-operated aspirators and treated with X-ray radiation at different dosage (42–60 Gy). Dose response of irradiated males was analyzed and induced sterility determined. Survivorship of males treated with different X-ray doses was compared. Fecundity of females that mated with irradiated males at different X-ray doses was generally comparable. Overall, induced sterility increased with higher X-ray doses. Nulliparous females that mated with male Ae. aegypti treated with 55–60 Gy laid eggs with over 99% sterility. Non-irradiated male mosquitoes had higher survivorship (mean = 0.78; P = 0.0331) than irradiated mosquitoes (mean range = 0.50–0.65). The competitiveness index of irradiated males decreased with increasing X-ray treatment doses, 1.14 at 55 Gy and 0.49 at 60 Gy, and this difference was significant (P &lt; 0.01). Irradiated males showed high survivorship and competitiveness—key for the anticipated SIT application for the control of invasive Ae. aegypti in California.