bluuebunny/crossref_metadata_2025_split huggingface dataset:
beagle-agn I: simultaneous constraints on the properties of gas in star-forming and AGN narrow-line regions in galaxies
Authors: Vidal-García A , Plat A , Curtis-Lake E , Feltre A , Hirschmann M , Chevallard J , Charlot S 
Published: October 2023

ABSTRACT
We present the addition of nebular emission from the narrow-line regions (NLR) surrounding active galactic nuclei (AGNs) to beagle (BayEsian Analysis of GaLaxy sEds). Using a set of idealized spectra, we fit to a set of observables (emission-line ratios and fluxes) and test the retrieval of different physical parameters. We find that fitting to standard diagnostic-line ratios plus [O ii] λ3726, λ3729/[O iii] λ5007, H β/H α, [O i] λ6300/[O ii] λ3726, λ3729, and H α flux, degeneracies remain between dust-to-metal mass ratio ($\xi _\rm {d}^{\small NLR}$) and ionization parameter ($U_\rm {s}^{\small NLR}$) in the NLR gas, and between slope of the ionizing radiation ($\alpha _{\small PL}$, characterizing the emission from the accretion disc around the central black hole) and total accretion-disc luminosity ($L_\rm {acc}$). Since these degeneracies bias the retrieval of other parameters even at maximal signal-to-noise ratio (S/N), without additional observables, we suggest fixing $\alpha _{\small PL}$ and dust-to-metal mass ratios in both NLR and H ii regions. We explore the S/N in H β required for un-biased estimates of physical parameters, finding that S/N(H β) ∼ 10 is sufficient to identify an NLR contribution, but that higher S/N is required for un-biased parameter retrieval (∼20 for NLR-dominated systems, ∼30 for objects with approximately equal H β contributions from NLR and H ii regions). We also compare the predictions of our models for different line ratios to previously published models and data. By adding [He ii] λ4686-line measurements to a set of published line fluxes for a sample of 463 AGN NLR, we show that our models with $-4\lt \hbox{$\log U_{\small S}^{\small NLR}$}\lt -1.5$ can account for the full range of observed AGN properties in the local Universe.
Probing the roles of orientation and multiscale gas distributions in shaping the obscuration of active galactic nuclei through cosmic time
Authors: Alonso-Tetilla Alba V , Shankar Francesco , Fontanot Fabio , Menci Nicola , Valentini Milena , Buchner Johannes , Laloux Brivael , Lapi Andrea , Puglisi Annagrazia , Alexander David M , Allevato Viola , Andonie Carolina , Bonoli Silvia , Hirschmann Michaela , López Iván E , Raimundo Sandra I , Ramos Almeida Cristina 
Published: October 2023

ABSTRACT
The origin of obscuration in active galactic nuclei (AGNs) is still an open debate. In particular, it is unclear what drives the relative contributions to the line-of-sight column densities from galaxy-scale and torus-linked obscuration. The latter source is expected to play a significant role in Unification Models, while the former is thought to be relevant in both Unification and Evolutionary models. In this work, we make use of a combination of cosmological semi-analytic models and semi-empirical prescriptions for the properties of galaxies and AGN, to study AGN obscuration. We consider a detailed object-by-object modelling of AGN evolution, including different AGN light curves (LCs), gas density profiles, and also AGN feedback-induced gas cavities. Irrespective of our assumptions on specific AGN LC or galaxy gas fractions, we find that, on the strict assumption of an exponential profile for the gas component, galaxy-scale obscuration alone can hardly reproduce the fraction of log (NH/cm−2) ≥ 24 sources at least at z ≲ 3. This requires an additional torus component with a thickness that decreases with luminosity to match the data. The torus should be present in all evolutionary stages of a visible AGN to be effective, although galaxy-scale gas obscuration may be sufficient to reproduce the obscured fraction with 22 &lt; log (NH/cm−2) &lt; 24 (Compton-thin, CTN) if we assume extremely compact gas disc components. The claimed drop of CTN fractions with increasing luminosity does not appear to be a consequence of AGN feedback, but rather of gas reservoirs becoming more compact with decreasing stellar mass.
The global burden of antimicrobial resistance – urinary tract infections
Authors: Von Vietinghoff Sibylle , Shevchuk Olga , Dobrindt Ulrich , Engel Daniel Robert , Jorch Selina K , Kurts Christian , Miethke Thomas , Wagenlehner Florian 
Published: October 2023

ABSTRACT
Antimicrobial resistance (AMR) has emerged as a significant global healthcare problem. Antibiotic use has accelerated the physiologic process of AMR, particularly in Gram-negative pathogens. Urinary tract infections (UTIs) are predominantly of a Gram-negative nature. Uropathogens are evolutionarily highly adapted and selected strains with specific virulence factors, suggesting common mechanisms in how bacterial cells acquire virulence and AMR factors. The simultaneous increase in resistance and virulence is a complex and context-dependent phenomenon. Among known AMR mechanisms, the plenitude of different β-lactamases is especially prominent. The risk for AMR in UTIs varies in different patient populations. A history of antibiotic consumption and the physiology of urinary flow are major factors that shape AMR prevalence. The urinary tract is in close crosstalk with the microbiome of other compartments, including the gut and genital tracts. In addition, pharmacokinetic properties and the physiochemical composition of urinary compartments can contribute to the emergence of AMR. Alternatives to antibiotic treatment and a broader approach to address bacterial infections are needed. Among the various alternatives studied, antimicrobial peptides and bacteriophage treatment appear to be highly promising approaches. We herein summarize the present knowledge of clinical and microbiological AMR in UTIs and discuss innovative approaches, namely new risk prediction tools and the use of non-antibiotic approaches to defend against uropathogenic microbes.
Outcomes and Predictors of Rapid Antiretroviral Therapy Initiation for People With Newly Diagnosed HIV in an Integrated Health Care System
Authors: Dalal Avani , Clark Earl , Samiezade-Yazd Zahra , Lee-Rodriguez Christian , Lam Jennifer O , Luu Mitchell N 
Published: October 2023

Abstract

Background
Rapid antiretroviral therapy (ART) is the recommended treatment strategy for patients newly diagnosed with HIV, but the literature supporting this strategy has focused on short-term outcomes. We examined both long-term outcomes and predictors of rapid ART among patients newly diagnosed with HIV within an integrated health care system in Northern California.

Methods
This observational cohort study included adults newly diagnosed with HIV between January 2015 and December 2020 at Kaiser Permanente Northern California. Rapid ART was defined as ART initiation within 7 days of HIV diagnosis. We collected demographic and clinical data to determine short-term and long-term outcomes, including viral suppression, care retention, medication adherence, and cumulative viral burden. Logistic regression models were used to identify predictors of rapid ART initiation.

Results
We enrolled 1409 adults; 34.1% initiated rapid ART. The rapid ART group achieved viral suppression faster (48 vs 77 days; P &lt; .001) and experienced lower cumulative viral burden (log10 viremia copy-years, 3.63 vs 3.82; P &lt; .01) but had slightly reduced medication adherence (74.8% vs 75.2%; P &lt; .01). There was no improvement in long-term viral suppression and care retention in the rapid group during follow-up. Patients were more likely to initiate rapid ART after 2017 and were less likely if they required an interpreter.

Conclusions
Patients who received rapid ART had an improved cumulative HIV burden but no long-term improvement in care retention and viral suppression. Our findings suggest that rapid ART should be offered but additional interventions may be needed for patients newly diagnosed with HIV.
The history of dental health education: a case study of Britain
Authors: Towner Elizabeth M L 
Published: October 2023

Abstract
An understanding of the history of dental health education in any one country or area comes from an appreciation of the interplay of the particular social, political, economic, and technological forces over a period of time. Britain has been selected to illustrate this history because there is a particularly rich variety of primary and secondary source material which can be drawn upon in order to explore these various themes. Some of the primary sources include contemporary books, journals, and other literature, annual reports of local school medical officers and the Chief Medical Officer, government reports, and company records.
Oral health promotion in developing countries
Authors: Dickson Murray 
Published: October 2023

Abstract
Many people associate oral health promotion with health talks and posters, but to others it is more encompassing, as in the words of the World Health Organization: ‘health promotion is the process of enabling people to increase control over, and to improve, their health’ (Epp 1986). In the application of health promotion to oral health, one must come to consider an expanded sphere of determinants that influence oral disease in order to develop interventions that are effective, acceptable, and sustainable.
Evaluation and planning of oral health promotion programmes
Authors: Blinkhorn Anthony S 
Published: October 2023

Abstract
Oral health promotion has as its central theme the improvement and maintenance of the oral health of the general population. This, together with the necessity of updating the knowledge of all health and allied professionals about relevant aspects of preventive dentistry, constitutes the main everyday activities of those involved in oral health promotion and education.
In all dental health care systems health promotion is a minor budgetary item, but by the very nature of its public profile it is open to more scrutiny than many other branches of dentistry. Indeed, health promotion as a whole attracts more criticism than money, and investigations into its potential value are the source of much debate.
Blockade of Syk modulates neutrophil immune-responses via the mTOR/RUBCNL-dependent autophagy pathway to alleviate intestinal inflammation in ulcerative colitis
Authors: Zhu Fengqin , Jing Dehuai , Zhou Huihui , Hu Zongjing , Wang Yan , Jin Guiyuan , Yang Yonghong , Zhou Guangxi 
Published: October 2023

Abstract

Background
Ulcerative colitis (UC) is a progressive chronic inflammatory disorder. Neutrophils play a critical role in regulating intestinal mucosal homeostasis in UC. Spleen tyrosine kinase (Syk) is involved in several inflammatory diseases. Here, we evaluated the effects and underlying mechanisms of Syk on neutrophil immune-responses in UC.

Methods
Syk expression in the colonic tissues of patients with UC was determined using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), western blotting, and immunohistochemistry. Colonic biopsies from patients with UC were obtained for single-cell RNA-sequencing. Neutrophils isolated from peripheral blood were pre-treated with R788 (a Syk inhibitor) and gene differences were determined using RNA sequencing. Neutrophil functions were analyzed using qRT-PCR, flow cytometry, and Transwell assay. R788 was administered daily to mice with dextran sulfate sodium (DSS)-induced colitis to verify the effects of Syk on intestinal inflammation.

Results
Syk expression was increased in inflamed mucosa and neutrophils of patients with UC and positively correlated with disease activity. Pharmacological inhibition of Syk in neutrophils decreased the production of pro-inflammatory cytokines, chemokines, neutrophil extracellular traps, reactive oxygen species, and myeloperoxidase. Apoptosis and migration of neutrophils were suppressed by Syk blockade. Syk blockade ameliorated mucosal inflammation in DSS-induced murine colitis by inhibiting neutrophil-associated immune responses. Mechanistically, Syk regulated neutrophil immune-responses via the mammalian target of rapamycin kinase/rubicon-like autophagy enhancer-dependent autophagy pathway.

Conclusions
Our findings indicate that Syk facilitates specific neutrophil functional responses to mucosal inflammation in UC, and its inhibition ameliorates mucosal inflammation in DSS-induced murine colitis, suggesting its potential as a novel therapeutic target for UC treatment.
Emerging roles of activating transcription factor 2 in the development of breast cancer: a comprehensive review
Authors: Amarah Ahmed , Elsabagh Ahmed Adel , Ouda Amr , Karen Omar , Ferih Khaled , Elmakaty Ibrahim , Malki Mohammed Imad 
Published: October 2023

Abstract
Activating transcription factor 2 (ATF2) is a member of the leucine zipper family of DNA binding proteins that are responsible for regulating various genes that play an essential role in major biological and cellular functions. Since ATF2 plays a vital role in cellular proliferation and apoptosis, it is believed that it greatly affects the development of breast cancers. However, its exact role in breast cancer is incompletely understood. It remains a subject of debate, ambiguity, and continuous research. Several studies have suggested the role of ATF2 as an oncogene, promoting cellular proliferation and worsening the outcome of cancers. In contrast, other studies have postulated that ATF2 plays a tumor suppressive role in estrogen receptor-positive breast cancer. The ambiguity surrounding its role in breast cancer is the reason why there is an influx of recent studies and research in this area. In this narrative review, we investigate several studies that have been published about the role of ATF2 in breast cancer. We also explore studies that have examined the association between ATF2 and endocrine therapy resistance. ATF2 has been suggested to modulate estrogen receptor (ER) expression and activity, potentially affecting tamoxifen sensitivity in breast cancer cells. Therefore, the role of ATF2 in DNA repair mechanisms and drug resistance has been deeply explored in this review. Additionally, there are numerous ongoing clinical trials exploring the effect of targeting ATF2 pathways and mechanisms on the outcome of breast cancers, some of which we have discussed. The studies and clinical trials that are being conducted to understand the multifaceted role of ATF2 and its signaling pathways may provide valuable insight for developing efficient targeted therapeutic solutions to enhance the outcomes of breast cancer and overcome endocrine resistance. We suggest further research to elucidate the dual roles of ATF2 in breast cancer and potential therapeutic therapies for its treatment.
Masked inverse folding with sequence transfer for protein representation learning
Authors: Yang Kevin K , Zanichelli Niccolò , Yeh Hugh 
Published: October 2023

Abstract
Self-supervised pretraining on protein sequences has led to state-of-the art performance on protein function and fitness prediction. However, sequence-only methods ignore the rich information contained in experimental and predicted protein structures. Meanwhile, inverse folding methods reconstruct a protein’s amino-acid sequence given its structure, but do not take advantage of sequences that do not have known structures. In this study, we train a masked inverse folding protein masked language model parameterized as a structured graph neural network. During pretraining, this model learns to reconstruct corrupted sequences conditioned on the backbone structure. We then show that using the outputs from a pretrained sequence-only protein masked language model as input to the inverse folding model further improves pretraining perplexity. We evaluate both of these models on downstream protein engineering tasks and analyze the effect of using information from experimental or predicted structures on performance.
Attitudes towards technology supported rheumatoid arthritis care: investigating patient- and clinician-perceived opportunities and barriers
Authors: MacBrayne Amy , Curzon Paul , Soyel Hamit , Marsh William , Fenton Norman , Pitzalis Costantino , Humby Frances 
Published: October 2023

Abstract

Objectives
Globally, demand outstrips capacity in rheumatology services, making Mobile Health (mHealth) attractive, with the potential to improve access, empower patient self-management and save costs. Existing mHealth interventions have poor uptake by end users. This study was designed to understand existing challenges, opportunities and barriers for computer technology in the RA care pathway.

Methods
People with RA were recruited from Barts Health NHS Trust rheumatology clinics to complete paper questionnaires and clinicians were recruited from a variety of centres in the UK to complete an online questionnaire. Data collected included demographics, current technology use, challenges managing RA, RA medications and monitoring, clinic appointments, opportunities for technology and barriers to technology.

Results
A total of 109 patient and 41 clinician questionnaires were completed. A total of 83.5% of patients and 93.5% of clinicians use smartphones daily. However, only 25% had ever used an arthritis app and only 5% had persisted with one. Both groups identified managing pain, flares and RA medications as areas of existing need. Access to care, medication support and disease education were mutually agreeable opportunities; however, discrepancies existed between groups with clinicians prioritizing education over access, likely due to concerns of data overwhelm (80.6% considered this a barrier).

Conclusions
In spite of high technology use and willingness from both sides, our cohort did not utilize technology to support care, suggesting inadequacies in the existing software. The lack of an objective biomarker for RA disease activity, existing challenges in the healthcare system and the need for integration with existing technical systems were identified as the greatest barriers.

Trial registration
Registered on the Clinical Research Network registry (IRAS ID: 264690).
Self-reported diagnostic confidence predicts diagnostic accuracy in axial spondyloarthritis imaging
Authors: Ulas Sevtap Tugce , Radny Felix , Ziegeler Katharina , Eshed Iris , Greese Juliane , Deppe Dominik , Stelbrink Carsten , Biesen Robert , Haibel Hildrun , Rios Rodriguez Valeria , Rademacher Judith , Protopopov Mikhail , Proft Fabian , Poddubnyy Denis , Diekhoff Torsten 
Published: October 2023

Abstract

Objectives
Reporting diagnostic confidence (DC) in axial spondyloarthritis (axSpA) imaging is recommended by the ASAS guidelines. Our aim was to investigate whether self-reported DC predicts diagnostic accuracy in axSpA imaging using X-ray (XR), computed tomography (CT) and magnetic resonance imaging (MRI).

Methods
We performed a post hoc analysis including 163 patients with low back pain (89 axSpA and 56 non-axSpA). Nine blinded readers with different experience levels [inexperienced (&lt;1 year), semi-experienced (3–8 years) and experienced (&gt;12 years)] scored the sacroiliac joint images for compatibility with axSpA. DC was reported on a scale from 1 (not sure) to 10 (very sure). Mean DC scores and standard deviations were calculated for correct and incorrect responses using XR, CT, MRI, XR+MRI and CT+MRI. Differences in DC were assessed using the Mann–Whitney U test.

Results
DC scores were higher for correct axSpA diagnoses and differed significantly between correct and incorrect responses for all modalities (P &lt; 0.001), with a mean DC of 7.1 ± 2.1 and 6.3 ± 2.1 for XR, 8.3 ± 1.8 and 6.7 ± 2.0 for CT, 8.1 ± 1.9 and 6.2 ± 1.9 for MRI, 8.2 ± 1.8 and 6.7 ± 1.8 for XR+MRI and 8.4 ± 1.8 and 6.8 ± 1.8 for CT+MRI, respectively. This was also the case when looking at the results by experience group, except for XR in the inexperienced group.

Conclusion
Providing self-reported DC in radiological reports is useful information to predict diagnostic reliability in axSpA imaging.
An analysis of the risks that arise for discretionary trust settlements in the event of a divorce: to what extent does the Family Court’s asset division approach undermine discretionary trusts?
Authors: Chan Nicole 
Published: October 2023

Abstract
Following the House of Lords’ decision in White v White, the concept of ‘equality’ has made asset computation and division following divorce, particularly in ‘big-money’ cases, more extensive. This article examines whether discretionary trusts are vulnerable to interference by the Family Court during ancillary relief proceedings through considering three approaches. First, by varying the trust settlement under section 24(1)(c) of the Matrimonial Causes Act 1973 (‘MCA’). Second, through the ‘resource’ approach under section 25(2)(a) MCA. Third, by relying on the sham doctrine. It accordingly identifies practical considerations for trustees and settlors to ensure that their trust assets remain intact following divorce proceedings.
Validating and Optimizing a Method for Detecting Phytophthora Species by Baiting Leachate from Arrays of Container Nursery Plants
Authors: Swiecki Tedmund J. , Bernhardt Elizabeth A. , McClanahan Sean G. 
Published: October 2023

In 2014, Phytophthora root rot was identified as a serious problem in nursery plants grown for habitat restoration in California. To support efforts to produce restoration nursery stock free of Phytophthora species, we developed a standardized leachate baiting method that can be conducted by nursery staff. Each plant in an array of up to 42 container-grown nursery plants is irrigated six times at 15-min intervals with a standardized water volume. Irrigation leachate is collected in a specialized vessel containing a green (unripe) pear bait. Test sensitivity was assessed using arrays of Phytophthora-free plants containing varying numbers of plants from which Phytophthora had previously been baited. The percentage of tests with Phytophthora detections increased as the proportion of infested plants in the array increased. In tests of individual inoculated plants, Phytophthora detection from a given plant varied over time, especially for less susceptible hosts. This variability likely limits test sensitivity in arrays with few infested containers. Direct probability and Monte Carlo simulation models showed that testing two to three arrays per block and 20 to 40 plants per array provided the greatest increases in detection probability for blocks of 200 to 1,000 plants in which 1 to 5% of the plants were infected. Random sampling had lower detection success than sampling biased to increase the odds of selecting infected plants. Results of extensive testing at a case study nursery were consistent with model predictions. The leachate baiting method has wide applicability for detecting and identifying Phytophthora species in nursery stock. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .