bluuebunny/crossref_metadata_2025_split huggingface dataset:
N32 Implementation of chromoendoscopy in colorectal cancer screening in patients with Inflammatory Bowel Disease
Authors: Lavín Expósito C , Bouhmidi Assakali A , Jurado Monroy R M , Rodríguez Romero V , Vozmediano Sánchez P , Velasco del Burgo M , Alañon Barba M , Moraleda Cebrian F , Hidalgo Juárez M L , Pinilla Sánchez J , Bonillo Merino C , Cabanillas Navarro M L , Laguna Laguna M T , Salueña Salueña I , Sánchez Pardo A M , Barreto Suárez E , Sánchez Alonso M 
Published: January 2024

Abstract

Background
Patients with inflammatory bowel disease (IBD) have a higher risk of colorectal cancer (CRC), so we must implement the best available endoscopic technique to detect it early, decreasing the risk of CRC and death.
There is low adherence to CRC screening by chromoendoscopy with dye in patients with IBD, despite the fact that national and international clinical practice guidelines consider this technique of choice based on the available evidence.

Description Of The Initiative
The standardization of a screening procedure, based on the evidence of endoscopy, allows any member of the team, doctor or nurse, to detect the need for the indication, improving screening in terms of follow-up interval and technique.
Likewise, the inflammatory nurse will have to know the technique to be able to inform the patient and improve their adherence, preparation and resolve doubts.
The main aim is early detection of dysplasia and CRC.
The side aims are:
▪ To improve the implementation of chromoendoscopy as a technique for CRC screening.
▪ Improve patient adherence to colonoscopy.

Methods
The development of an endoscopic follow-up procedure according to risk factors in patients with ulcerative colitis and colonic Crohn's disease, in which chromoendoscopy is the technique of choice. The technique in our center is with 0.4% carmine indigo diffusion with catheter-diffuser, but it is possible to adapt other alternatives according to availability.
The procedure establishes the follow-up interval at 1, 3 or 5 years depending on the low, medium or high risk, respectively, depending on the activity, extent and duration of the disease, presence of stenosis and pseudopolyps, primary sclerosing cholangitis and/or family history of CRC.

Results
In our center, 100% of screenings are performed by chromoendoscopy with dye, by a single expert endoscopist, scheduled with a longer examination time than a conventional colonoscopy and with optimization of bowel preparation.

Conclusion
CRC screening of patients with IBD should preferably be performed with chromoendoscopy with dye, establishing follow-up intervals depending on known risk factors, both clinical, endoscopic and histological, and this indication should be standardized in a procedure that is known to all members of the team.
N46 Stress after an Ulcerative Colitis diagnosis: examining the role of psychological factors in Ulcerative Colitis using Interpretative Phenomenological Analysis
Authors: Black J , Norton C , Sweeney L , Czuber-Dochan W 
Published: January 2024

Abstract

Background
People with ulcerative colitis (UC) report higher levels of stress, anxiety, and depression than the general population. 89% of people with IBD in the UK surveyed in 2019 said they found coping hard. However, most relevant research relies on generic stress questionnaires which ignore confounders typical in UC, such as fatigue. This study aims to provide rich, detailed accounts of how individuals encounter stress after a UC diagnosis.

Methods
An hour-long, semi-structured interview was conducted in January 2022 with a 76-year-old man, reporting high levels of perceived stress and diagnosed with UC three months previously. He was asked about stressors, coping and support during UC diagnosis and beyond. Interpretative Phenomenological Analysis (IPA) examines the detailed, unique interpretation of a significant experience to an individual. IPA methodology follows four stages: exploratory notes; formulating Experiential Statements (ESs) summarising the meaning of the experience to the interviewee; connecting similar ESs and developing Personal Experiential Themes (PETs), the three to five most important elements of the participant’s experience.

Results
Four PETs were formulated:
My UC needs a positive, practical mental approach, not an emotional one
Mixed experience with healthcare services affected my anxiety and disease management
My UC symptoms and overall health affected my emotional well-being and coping
I believe there is an absence of evidence on UC’s causes, cure, or helpful lifestyle changes
The interviewee didn’t "dwell on these things" although he felt "it’s another thing and I’m going to have to deal with this long term". He "could email the nurse there if I had any problems and I did at one stage and got an instant reply" but at other times he felt "abandoned here because nobody is taking me seriously. I keep phoning these people up, they keep passing me to other people". He had developed "strategies to cope with being diagnosed" but was surprised "nobody seems to know why [UC onset] happens. There isn’t a cure for it. They don’t seem to know what causes these flare-ups etc. etc. and all we know is that it’s going to carry on."

Conclusion
Our interviewee described his symptoms and existing health and healthcare services as stressors, his family and clinicians’ support, his practical, unemotional approach to coping and the need to keep positive. IPA comprehensively captured the interviewee’s interpreted experiences after an UC diagnosis, charting nuanced relationships between stressors, support, and coping. Our study will analyse a further nine individuals’ experiences of stress in the year after an UC diagnosis to inform development of an intervention enhancing resilience to stress.
ECCO Grant Serotonin gets into your genes: the role of histone serotonylation in inflammatory response and visceral hypersensitivity in Crohn’s Disease
Authors: Ghiboub Mohammed , de Jonge Wouter J , Derikx Joep P M , van Heurn Ernst , van den Wijngaard Rene 
Published: January 2024

Abstract

Background and Aims
More than 70% of CD patients experience visceral hypersensitivity (VH) despite reaching remission. VH treatment is difficult because the mechanism of its complication is unknown. Serotonin is mainly produced in the gut and regulates several physiological processes, such as intestinal immunity and pain. Disturbances in serotonin levels are associated with CD severity and VH. Intriguingly, we have recently observed that serotonin can covalently bind to glutamine at position 5 on histone H3 tail, leading to histone serotonylation (H3Q5ser) in peripheral blood mononuclear cells (PBMCs). Another study has demonstrated that H3Q5ser can also occur in cultured neuronal cells. Our objective is to investigate the role of this newly discovered epigenetic signature (H3Q5ser) in immune cells and enteric neurons in CD and its potential impact on the transcriptional programs of the inflammatory response and VH.

Methods
To accomplish this goal, we will first determine the concentrations of serotonin in the mucosa and serum of active CD patients compared to healthy controls and establish how these levels relate to the enhancement of H3Q5ser in immune cells and enteric neurons. To study the functional role of H3Q5ser in cell activation, we will use site-directed or oligonucleotide- mediated mutagenesis to induce a point mutation in cultured enteric neuron cell lines and PBMCs to remove the binding site for serotonin on histone. Both wild-type and mutant cells will be incubated with or without serotonin and subjected to chromatin immunoprecipitation sequencing and RNA sequencing profiling to investigate the effect of H3Q5ser on the transcriptional programs associated with inflammation and VH.

Anticipated Impact
This project will provide a comprehensive understanding of the impact of the changes in serotonin concentrations on H3Q5ser-related gene expression in CD- associated VH and the inflammatory response. Our anticipated impact is subsequent studies that monitor H3Q5ser in VH in CD patients during treatment.
ECCO Grant Investigating regenerative pathways in salivary glands to mitigate oral manifestations of inflammatory bowel diseases
Authors: Monasterio G , Villablanca E 
Published: January 2024

Abstract

Background and Aims
Inflammatory bowel diseases (IBD) impact 4-16% of patients with extraintestinal manifestations in the upper gastrointestinal (GI) tract, including stomach and esophageal ulcers, dry mouth, taste alterations, halitosis, ulcers, and periodontitis. The underlying mechanisms remain unclear. This study hypothesizes that intestinal inflammation disrupts upper GI tract homeostasis by impairing salivary gland functions and aims to:
Aim 1: Elucidate cellular and molecular mechanisms of intestinal inflammation on upper GI tract mucosa and salivary glands.
Aim 2: Evaluate therapeutic potential of liver X receptor (LXR) activation in restoring salivary gland function in colitis-induced oral pathology.

Methods
I will use a novel mounting method for spatial proteogenomic analysis of upper GI tract mucosa to identify colitis-induced perturbations. Salivary glands will be studied separately, employing bulk and single-cell transcriptomic profiling to identify mechanisms driving colitis-induced atrophy, dysfunction, and candidate regenerative pathways. Additionally, salivary gland organoids will be used to study regeneration mechanisms in vitro, such as LXR activation, and the therapeutic potential of successful candidate pathways will be tested in vivo using pre-clinical models of colitis and salivary gland damage/repair (irradiation).

Anticipated Impact
This research will provide insights into mechanisms by which intestinal inflammation disrupts upper GI tract homeostasis through salivary gland impairment and assess the role of candidate pathways in salivary gland regeneration. In the short to medium term, findings may contribute to developing novel therapeutic strategies for managing colitis-induced oral pathology, benefiting the IBD community by improving patients' quality of life.
Impact of chronic obstructive pulmonary disease in patients with atrial fibrillation: an analysis from the GLORIA-AF registry
Authors: Romiti Giulio Francesco , Corica Bernadette , Mei Davide Antonio , Frost Frederick , Bisson Arnaud , Boriani Giuseppe , Bucci Tommaso , Olshansky Brian , Chao Tze-Fan , Huisman Menno V , Proietti Marco , Lip Gregory Y H 
Published: January 2024

Abstract

Aims
Chronic obstructive pulmonary disease (COPD) may influence management and prognosis of atrial fibrillation (AF), but this relationship has been scarcely explored in contemporary global cohorts. We aimed to investigate the association between AF and COPD, in relation to treatment patterns and major outcomes.

Methods and results
From the prospective, global GLORIA-AF registry, we analysed factors associated with COPD diagnosis, as well as treatment patterns and risk of major outcomes in relation to COPD. The primary outcome was the composite of all-cause death and major adverse cardiovascular events (MACEs). A total of 36 263 patients (mean age 70.1 ± 10.5 years, 45.2% females) were included; 2,261 (6.2%) had COPD. The prevalence of COPD was lower in Asia and higher in North America. Age, female sex, smoking, body mass index, and cardiovascular comorbidities were associated with the presence of COPD. Chronic obstructive pulmonary disease was associated with higher use of oral anticoagulant (OAC) [adjusted odds ratio (aOR) and 95% confidence interval (CI): 1.29 (1.13–1.47)] and higher OAC discontinuation [adjusted hazard ratio (aHR) and 95% CI: 1.12 (1.01–1.25)]. Chronic obstructive pulmonary disease was associated with less use of beta-blocker [aOR (95% CI): 0.79 (0.72–0.87)], amiodarone and propafenone, and higher use of digoxin and verapamil/diltiazem. Patients with COPD had a higher hazard of primary composite outcome [aHR (95% CI): 1.78 (1.58–2.00)]; no interaction was observed regarding beta-blocker use. Chronic obstructive pulmonary disease was also associated with all-cause death [aHR (95% CI): 2.01 (1.77–2.28)], MACEs [aHR (95% CI): 1.41 (1.18–1.68)], and major bleeding [aHR (95% CI): 1.48 (1.16–1.88)].

Conclusion
In AF patients, COPD was associated with differences in OAC treatment and use of other drugs; Patients with AF and COPD had worse outcomes, including higher mortality, MACE, and major bleeding.
Echinobase: a resource to support the echinoderm research community
Authors: Telmer Cheryl A , Karimi Kamran , Chess Macie M , Agalakov Sergei , Arshinoff Bradley I , Lotay Vaneet , Wang Dong Zhuo , Chu Stanley , Pells Troy J , Vize Peter D , Hinman Veronica F , Ettensohn Charles A 
Published: January 2024

Abstract
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein–protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.
Detectability analysis of very low frequency earthquakes: methods and application in Nankai using F-net and DONET broad-band seismometers
Authors: Takemura Shunsuke , Baba Satoru , Yabe Suguru , Yamashita Yusuke , Shiomi Katsuhiko , Matsuzawa Takanori 
Published: January 2024

SUMMARY
For a more quantitative discussion of slow earthquake activity, we evaluated the detectable limits of very low frequency earthquakes (VLFEs), which are seismic slow earthquakes observed in very low-frequency (&lt; 0.05 Hz) bands in the Nankai subduction zone. We performed numerical simulations using a local 3-D model and used the observed noise level of permanent broad-band seismometers. First, we investigated the effects of the source-time functions on the maximum amplitudes of the VLFE signals at a certain station. The maximum amplitudes of the VLFE signals were controlled by the VLFE moment rate. The detectable limit of VLFEs at each source location can be defined as the lowest moment rate of detectable VLFEs, which radiate signals larger than the noise levels of any component at ≥ 3 stations. For inland seismometers only, the detectable limits of VLFEs at deep (30–40 km) and shallow (≤ 10 km) depths were 1012–1012.3 and 1012.7 N·m s−1, respectively. Due to the geometrical spreading of VLFE signals and large noise levels in horizontal components, offshore seismometers improved the detectability of shallow VLFEs in regions where seismometers were densely deployed. Based on our detectability and published catalogues, shallow slow earthquakes are less active south-southwest off the Kii Peninsula, where geodetic studies expect mechanical coupling.
Development of a single-visit protocol for the management of pregnancy of unknown location following in vitro fertilization: a retrospective study
Authors: Dooley W M , de Braud L V , Wong M , Platts S , Ross J A , Jurkovic D 
Published: January 2024

Abstract

STUDY QUESTION
Can women with pregnancy of unknown location (PUL) following in vitro fertilization (IVF) be risk-stratified regarding the subsequent need for medical intervention, based on their demographic characteristics and the results of serum biochemistry at the initial visit?

SUMMARY ANSWER
The ratio of serum hCG to number of days from conception (hCG/C) or the initial serum hCG level at ≥5 weeks’ gestation could be used to estimate the risk of women presenting with PUL following IVF and needing medical intervention during their follow-up.

WHAT IS KNOWN ALREADY
In women with uncertain conception dates presenting with PUL, a single serum hCG measurement cannot be used to predict the final pregnancy outcomes, thus, serial levels are mandatory to establish a correct diagnosis. Serum progesterone levels can help to risk-stratify women at their initial visit but are not accurate in those taking progesterone supplementation, such as women pregnant following IVF.

STUDY DESIGN, SIZE, DURATION
This was a retrospective study carried out at two specialist early pregnancy assessment units between May 2008 and January 2021. A total of 224 women met the criteria for inclusion, but 14 women did not complete the follow-up and were excluded from the study.

PARTICIPANTS/MATERIALS, SETTING, METHODS
We selected women who had an IVF pregnancy and presented with PUL at ≥5 weeks’ gestation.

MAIN RESULTS AND THE ROLE OF CHANCE
A total of 30/210 (14.0%, 95% CI 9.9–19.8) women initially diagnosed with PUL required surgical intervention. The hCG/C was significantly higher in the group of women requiring an intervention compared to those who did not (P = 0.003), with an odds ratio of 3.65 (95% CI 1.49–8.89, P = 0.004). A hCG/C &lt;4.0 was associated with a 1.9% risk of intervention, which accounted for 25.7% of the study population. A similar result was obtained by substituting hCG/C &lt;4.0 with an initial hCG level &lt;100 IU/l, which was associated with 2.0% risk of intervention, and accounted for 23.8% of the study population (P &gt; 0.05)

LIMITATIONS, REASONS FOR CAUTION
A limitation of our study is that it is retrospective in nature, and as such, we were reliant on existing data.

WIDER IMPLICATIONS OF THE FINDINGS
A previous study in women with PUL after spontaneous conception found that a 2% intervention rate was considered low enough to eliminate the need for close follow-up and serial blood tests. Using the same 2% cut-off, a quarter of women with PUL after IVF could also avoid attending for further visits and investigations.

STUDY FUNDING/COMPETING INTEREST(S)
No external funding was required for this study. No conflicts of interest are required to be declared.

TRIAL REGISTRATION NUMBER
N/A.
Heparin-Binding Hemagglutinin of Mycobacterium tuberculosis Inhibits Autophagy via Toll-like Receptor 4 and Drives M2 Polarization in Macrophages
Authors: Zheng Qing , Li Zhi , Zhou Yu , Li Yuru , Gong Meiliang , Sun Heqiang , Deng Xinli , Ma Yueyun 
Published: January 2024

Abstract

Background
Tuberculosis (TB), predominantly caused by Mycobacterium tuberculosis (MTB) infection, remains a prominent global health challenge. Macrophages are the frontline defense against MTB, relying on autophagy for intracellular bacterial clearance. However, MTB can combat and evade autophagy, and it influences macrophage polarization, facilitating immune evasion and promoting infection. We previously found that heparin-binding hemagglutinin (HBHA) inhibits autophagy in A549 cells; however, its role in macrophage autophagy and polarization remains unclear.

Methods
Bacterial cultures, cell cultures, Western blotting, immunofluorescence, macrophage infection assays, siRNA knockdown, and enzyme-linked immunosorbent assay were used to investigate HBHA's impact on macrophages and its relevance in Mycobacterium infection.

Results
HBHA inhibited macrophage autophagy. Expression of recombinant HBHA in Mycobacterium smegmatis (rMS-HBHA) inhibited autophagy, promoting bacterial survival within macrophages. Conversely, HBHA knockout in the Mycobacterium bovis bacillus Calmette-Guérin (BCG) mutant (BCG-ΔHBHA) activated autophagy and reduced bacterial survival. Mechanistic investigations revealed that HBHA may inhibit macrophage autophagy through the Toll-like receptor 4–dependent PI3K-AKT-mTOR signaling pathway. Furthermore, HBHA induced macrophage M2 polarization.

Conclusions
Mycobacterium may exploit HBHA to suppress the antimicrobial immune response in macrophages, facilitating intracellular survival and immune evasion through autophagy inhibition and M2 polarization induction. Our findings may help identify novel therapeutic targets and develop more effective treatments against MTB infection.
Speaking Volumes: Introducing the UNGA Speech Corpus
Authors: Turco Linnea R 
Published: January 2024

Abstract
Many theoretical conclusions core to the study of international politics rely on having access to, and understanding, the rhetoric of international actors. One important development in advancing the empirical study of international relations (IR) theory, therefore, is the availability of machine-analyzable speech data. A collection of fine-grained textual representations of states’ speeches in the context of an important international organization, such as the United Nations General Assembly (UNGA), is needed to understand the ideas, preferences, and values that states put forth in their statements. An especially promising use for such a corpus of texts would be to measure states’ preferences based on their statements. In an effort to add to the burgeoning field of text-as-data in IR, I present the UNGA Speech Corpus, a collection of over 34,000 speeches delivered by states in the UNGA from 1993 to 2018. I use it to improve on recent work that links text to preferences in IR by combining a structural topic model with locally trained word embeddings to estimate the policy positions of states on specific topics. I then show how these “topic scores” can help scholars to improve their analyses of exigent international issues, such as global climate change governance.