bluuebunny/crossref_metadata_2025_split huggingface dataset:
P1236 Oral microbiota dysbiosis in Inflammatory Bowel Disease patients
Authors: Rodrigues C , Gomes A , Mendes K , Correia M J , Pereira P , Lopes P C , Martins R , Veiga N , Rosa N , Soares C , Ministro P 
Published: January 2024

Abstract

Background
Recent data pointed that IBD is strictly related to gut microbiota although less is known about the connection between oral microbiota and IBD. It is also known that dysbiosis can lead to oral pathologies. Moreover, microbiome changes under therapeutic agents’ administration for IBD treatment have been described, including the identification of some bacteria as potential predictive markers for treatment effectiveness. The aim of our study was the quantification of salivary Firmicutes and Bacteroidetes in a cohort of IBD patients compared with a control group without IBD.

Methods
This was a collaborative transversal cohort study between an IBD consultation in a tertiary hospital and a faculty of dental medicine. Patients from IBD consultation were invited to participate and gave their informed consent. The exclusion criteria were the incapacity of mouth opening or give a written informed consent. Demographic and clinical data was collected. Oral health status was accessed to determine the periodontal diagnosis. Unstimulated saliva samples were collected before the oral examination for the quantification by quantitative real-time PCR. Statistical analysis was performed with SPSS 29.0 using Kruskal–Wallis H and Mann-Whitney U tests, and p values ≤ 0.05 were considered statistically significant.

Results
IBD patients presented an increased abundance of Firmicutes, both for UC (3.4 x10-5) and CD (4.9x10-5) as well as an increased abundance of Bacteroidetes for both UC (1.6 x10-5) and CD (1.4x10-5), when compared to the control group (figure 1).
No significant differences were found between different treatments groups or no treatment (table 1) in abundance of Firmicutes and Bacteroidetes, respectively, of UC (p = 0.292 and p = 0.912) and CD (p=0.413 and p=0.254) patients. Additionally, no significant differences were found for Firmicutes and Bacteroidetes abundances, respectively, regarding: CD versus UC (p=0.600 and p=0.971), active disease and remission (based on a composite criterion for inactive disease considering HBI &lt;5 for CD or a PMS ≤ 2 for UC, and FCP cut-off value of 150 mg/Kg), (p= 0.071 and p=0.242), smoking status (p=0.558 and p=0.488) and presence or absence of oral health (p=0.260 and p=0.556).

Conclusion
The oral microbiota characterization of IBD patients showed an elevated abundance of Firmicutes and Bacteroidetes when compared with healthy controls. These findings are valuable indicators of dysbiosis, emphasizing the intricate interplay between gut and oral microbiome in the context of inflammatory conditions. Future research is needed to clarify the oral-gut microbiome axis in IBD.
N01 “Just Live with it”- Exploring patients’ experience of using IBD-F scale in clinical practice – A mixed methods study using focus groups and cross-sectional questionnaires
Authors: Watson N , Chalmers D , Czuber-Dochan W 
Published: January 2024

Abstract

Background
Inflammatory bowel disease (IBD) related fatigue is one of the most common, yet debilitating symptoms reported by patients with IBD. The causes for the issue are not fully understood, and patients and clinicians alike struggle to communicate about this topic in consultations. In 2014, the IBD-F scale was created to assist this communication, and this study aimed to explore its role in the experiences of patients assessing and managing their IBD fatigue with Health Care Professionals (HCP’s).

Methods
A mixed methods study was conducted consisting of an online survey and 3 online patient focus groups. The survey was advertised through patient charities and explored individual fatigue assessment and management. 24 patients from across the UK were recruited to participate in the online focus groups, providing 243 minutes of discussion. This data was recorded, transcribed, and anonymised before being coded by two independent researchers.

Results
The online survey received 426 responses. 272 (64%) respondents reported fatigue levels between 7-10 on a scale of 0-10. When the medical assessment of their fatigue was explored, only 41(10%) respondents reported a medical assessment of the fatigue, 27 (6%) reported being offered support or advice, and 5 (1%) reported that the fatigue had been reassessed. 162 (38%) respondents said they would use the IBD-F on a regular basis and wanted this information to be shared with their medical teams, and 136 (32%) requested the results be attached to their clinical record.
The topics arising from the patient focus groups support the notion that fatigue is both overwhelming, and underserved. The main findings are collated into three main themes or “desires”, constructed to represent the patient’s call to HCP's; 1) The desire to “Give up”, 2) The desire to be heard, 3) The desire to change their situation. All groups reported a desire to improve clinical and public education around IBD fatigue and introduce communication tools like the IBD-F into clinical consultations and medical notes.

Conclusion
This mixed methods exploration highlights a significant, perceived gap in clinical provision for patients experiencing IBD related fatigue. IBD patients are reporting a sense of alienation and abandonment from HCP’s, but also a resounding desire to utilise their voices to educate their medical teams and a willingness to take advantage of additional resources to help improve education, communication and treatment of this symptom. Further research is needed to explore this phenomenon from the HCP’s perspective, and to explore the practical implications of the suggested changes to IBD fatigue education, assessment, and management within these clinical settings.
Figure 1:
N34 Transition of Inflammatory Bowel Disease patients from pediatric to adult Care: A single-center ten-years experience
Authors: Onidi F M , Mocci G , Elisei W , Corpino M , Orru' G , Marongiu A , Argiolas G , Runfola M , Locci G , Tamponi E , Zolfino T , Usai Satta P , Muscas A , Congia M , Savasta S 
Published: January 2024

Abstract

Background
Transition of adolescents with inflammatory bowel disease (IBD) to adult care is a challenge for patients, families, and healthcare providers. Considering that ~ 25% of IBD patients are diagnosed before the age of 16 years, and that these patients are at higher risk for poorer clinical disease outcomes. interest in the transition of care has been increasing considerably in the last decade.To assess the main clinical and epidemiological features of peadiatric IBD patients in a single pediatric center in Sardinia, Italy, at diagnosis and at the time of transition to the adult center

Methods
From January 2014 to June 2023 we performed a multicenter, observational, cross-sectional study that included pediatric patients with IBD enrolled in the only pediatric IBD reference center in Sardinia. Data were obtained from the patients’ medical records and from a questionnaire administered at the inclusion visit.

Results
Sixty-five IBD patients were enrolled (UC 40, CD 25, M 32, F 33). Median age at diagnosis was 13 years (IQR 2-18). After a median disease duration of 8 years (IQR: 1-25), no UC patients experienced proximal estension of proctitis or left-sided colitis, and no CD patients experienced new localizations of disease.
Fifteen patients developed extraintestinal manifestations. No significant difference was found in median diagnostic delay (DD) between UC [4 months (IQR: 1-84)] and CD patients [4,5 months (IQR: 1-48)].
At the transition visit, overall, twenty-nine patients (44,6%) were exposed to one biologic agent (vs 3% at baseline; p&lt;0.02); 0 patients (0%) were exposed to two biologic agents. 4,6% of patients (3/ 65) underwent surgery

Conclusion
Our results provide important insights into the clinical and epidemiological features of pediatric IBD population, and while waiting for a nation Italian registry, present eligible data on the IBD population in Sardinia
‘All These Unimportant Details’: John Ashbery at home
Authors: Norris Paul 
Published: January 2024

Abstract
John Ashbery is a domestic poet. He recognizes that the home contains and organizes a plurality of objects, but also a plurality of thoughts, experiences, and social roles. The domesticity of Ashbery’s poetry materializes many of the contradictory abstractions of modern life, and gives them a place, even if their relationship with each other remains obscure. His poetic homes are microcosms of America, macrocosms of the mind, and material languages. The suburban home is defined in opposition to everything chaotic, decentred, and unstable: rapidly advancing technology, the cyclical renewals of nature, a carnivorous economy, the expanse of air and sky. Paradoxically, the home depends on these opposing forces, even incorporating them into itself, because for Ashbery the domestic is the conscious frame within which things are understood. His image for this kind of domestic perception is the houseboat: homely, comfortable, anchored between nature and civilization, and always in flux.
Magmatic priming of a phreatic eruption sequence: the 2012 Te Maari eruptions at Mt Tongariro (New Zealand) imaged by magnetotellurics and seismicity
Authors: Heise Wiebke , Bannister Stephen , Williams Charles A , McGavin Peter , Caldwell T Grant , Bertrand Edward A , Usui Yoshiya , Kilgour Geoff 
Published: January 2024

SUMMARY
Magnetotelluric data from Mount Tongariro have been analysed using an unstructured tetrahedral finite-element inversion code that incorporates topography, which was not included in previous analysis of these data. Incorporating topography adds information, which stabilizes the resistivity inversion modelling, and for the first time allows details of the shallow hydrothermal system and its relationship with the underlying magmatic system to be resolved. Specifically, an electrically conductive zone between 4 and 12.5 km depth marks the underlying magmatic system, which is shown to directly connect via conductive pathways to the area where the most recent phreatic eruptions at Tongariro occurred in 2012. The resultant phreatic eruptions in 2012 August and November showed no new magmatic component to the eruption deposits. Nevertheless, by combining the magnetotelluric resistivity image with relocated seismicity, we can see that seismicity (a proxy for magma ascent) migrated from the top of the magmatic system into the hydrothermal system in the months preceding these eruptions. Magmatic interaction with the extant hydrothermal system likely caused the over pressurization for the phreatic eruption. This work highlights the utility of combining geophysical methods and petrological data to constrain phreatic eruption processes.
Improved beamforming schemes for estimation of multimode surface wave dispersion curves from seismic noise with reducing effect of the irregular array geometry and/or anisotropic source distribution
Authors: Qin Tongwei , Lu Laiyu 
Published: January 2024

SUMMARY
Dense array observation and seismic interferometry have revolutionized the imaging schemes of the earth structure. It is becoming possible to directly obtain the lateral variation of the earth's structure by applying array-based methods such as the cross-correlation beamforming (CBF) of the ambient noise to the subsets of the dense array, without tomography. CBF has been proven to extract the azimuth-averaged multimode surface wave dispersion curves. However, the resolution of the dispersion image generated by conventional CBF is low at high frequencies in the frequency–velocity (f-v) domain. Moreover, the irregular array geometry and uneven source distribution would bias the result of CBF, especially for the estimation of azimuth-dependent velocity. In this paper, two beamforming (BF) es are suggested to improve the resolution of multimode dispersion images in the f-v domain. First, the geometrical spreading of the wavefield is corrected to enhance the amplitude at high frequency (or large distance) and thereby improve the resolution of the dispersion image at high frequency. We call this scheme weighted correlation beamforming (WCBF). The azimuth-averaged velocity can be estimated with sufficient resolution using WCBF by stacking the BF output at each azimuth. We show that WCBF is the 2-D Fourier transform of the spatial wavefield from the viewpoint of the wavefield transform. Secondly, a modified beamforming scheme (MCBF) is suggested to reduce the effect of uneven source and/or irregular array geometry. The delay and summation in MCBF are performed only for plane waves incident from the stationary phase region. The azimuth-dependent velocity can therefore be estimated by MCBF with less dependence on the array geometry, as well as on the uneven source distribution. In terms of the estimation of azimuth-averaged phase velocity, we show the F-J method, another array-based method for extracting multimode surface waves from ambient noise using the Fourier–Bessel transform, is the azimuth-averaged version of WCBF. The reliability of WCBF and MCBF is verified based on the synthetic and field data using the array with different geometry. The dispersion image of multimode Rayleigh wave phase velocity at local and regional scales can be generated by WCBF or MCBF with high resolution. In particular, multimode dispersion curves at the local scale can be measured by MCBF with sufficient accuracy using quite short recordings from hours to days. This offers the possibility of a rapid assessment of the media properties.
ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches
Authors: Adams Trevor M , Zhao Peng , Kong Rui , Wells Lance 
Published: January 2024

Abstract
Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.
A purified diet affects intestinal epithelial proliferation and barrier functions through gut microbial alterations
Authors: Shiratori Hiroaki , Hattori Kisara M , Nakata Kazuaki , Okawa Takuma , Komiyama Seiga , Kinashi Yusuke , Kabumoto Yuma , Kaneko Yuria , Nagai Motoyoshi , Shindo Tomoko , Moritoki Nobuko , Kawamura Yuki I , Dohi Taeko , Takahashi Daisuke , Kimura Shunsuke , Hase Koji 
Published: January 2024

Abstract
The gut microbiota plays a crucial role in maintaining epithelial barrier function. Although multiple studies have demonstrated the significance of dietary factors on the gut microbiota and mucosal barrier function, the impact of a purified diet, which has long been used in various animal experiments, on intestinal homeostasis remains to be elucidated. Here, we compared the impact of two different types of diets, a crude diet and an AIN-93G-formula purified diet, on epithelial integrity and the gut microbiota. Purified diet-fed mice exhibited shorter villi and crypt lengths and slower epithelial turnover, particularly in the ileum. In addition, antimicrobial products, including REG3γ, were substantially decreased in purified diet-fed mice. Purified diet feeding also suppressed α1,2-fucosylation on the epithelial surface. Furthermore, the purified diet induced metabolic rewiring to fatty acid oxidation and ketogenesis. 16S ribosomal RNA gene sequencing of the ileal contents and mucus layer revealed distinct gut microbiota compositions between the purified and crude diet-fed mice. Purified diet feeding reduced the abundance of segmented filamentous bacteria (SFB), which potently upregulate REG3γ and fucosyltransferase 2 (Fut2) by stimulating group 3 innate lymphoid cells (ILC3s) to produce IL-22. These observations illustrate that the intake of a crude diet secures epithelial barrier function by facilitating SFB colonization, whereas a purified diet insufficiently establishes the epithelial barrier, at least partly owing to the loss of SFB. Our data suggest that the influence of purified diets on the epithelial barrier integrity should be considered in experiments using purified diets.
Civilizational Politics at the Commonwealth Games: Identity, Coloniality and LGBTIQ+ Inclusion
Authors: Vernon Patrick J 
Published: January 2024

Abstract
In 2022, the United Kingdom hosted the Commonwealth Games in Birmingham, with this games featuring a pride programme that promoted LGBTIQ+ inclusion around the Commonwealth. With British colonial norms and laws often providing the origins of homophobic and transphobic policies in Commonwealth member states, this paper sees LGBTIQ+ inclusivity narratives at the games as a significant object of study. Focusing on the theme of “welcoming,” the paper interrogates the various welcomes that were extended to different communities at the games; welcoming athletes from around the Commonwealth to Birmingham, welcoming queer people into the world of sport, and welcoming Commonwealth citizens into the LGBTIQ+ framework. Encapsulating these welcomes, it argues, was a liberal progress narrative that ignores ongoing British colonial violence, for example through the United Kingdom’s carceral border policy, or through culture war debates that demonize trans women. Contesting depictions of British democracy as the zenith of human development, this paper highlights the inconsistency of this with the UK Government’s politics of exclusion and the ways in which civilizationist agendas detract attention from the ongoing operation of coloniality. It also reflects on opportunities for resisting colonial violence in complex socio-political contexts.
Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea
Authors: Baquero Diana P , Bignon Eduardo A , Krupovic Mart 
Published: January 2024

Abstract
Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily-related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, “Thalassapleoviridae,” for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.
Climate acts as an environmental filter to plant pathogens
Authors: Caballol Maria , Redondo Miguel Ángel , Catalán Núria , Corcobado Tamara , Jung Thomas , Marçais Benoît , Milenković Ivan , Nemesio-Gorriz Miguel , Stenlid Jan , Oliva Jonàs 
Published: January 2024

Abstract
Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at &gt;250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.
The impact of source and consumption of news on mental distress among inflammatory bowel disease patients during the COVID-19 pandemic
Authors: Shaffer Seth R , Dolovich Casandra , El-Gabalawy Renée , Graff Lesley A , Singh Harminder , Jackson Gia L , Chochinov Sydney , Shaw Souradet , Bernstein Charles N 
Published: January 2024

Abstract

Background
We sought to understand the trends in media use, and how consumption and source affected mental health of persons with inflammatory bowel disease during the early parts of the pandemic. Dissemination of news during the coronavirus disease 2019 (COVID-19) pandemic was integral to educating the public but also could be harmful if constantly consumed, leading to worsening anxiety.

Methods
We performed a survey study in autumn 2020 during the second wave of COVID-19 in Manitoba. The survey included questions on consumption of COVID-19 news, along with validated measures of perceived stress, generalized anxiety, health anxiety, and depression. We used multivariable logistic regression analysis to assess trusted sources of news as a predictor of clinically significant mental health symptoms.

Results
Of the 2940 participants in the registry, 1384 (47.1%) persons responded. The most trusted sources of news were television (64.2%), internet (46.1%), newspaper (27.6%), friends/family (21.7%), social media (16.9%), and radio (16.6%). Those who trusted social media had higher odds of depression (aOR 1.52, 95%CI 1.04-2.22), and perceived stress (aOR 2.56, 95%CI 1.09-2.21). Persons who reported extreme difficulty limiting their time-consuming news about COVID-19 and who spent more than 1 h daily consuming information on COVID-19 both had increased odds of any clinically significant mental health symptoms.

Conclusions
It is unknown if consumption of COVID-19 news led to heightened mental health symptoms or if increasing anxieties and concerns led to consuming more news. Further research is needed to assess whether these elevated mental health symptoms led to worse disease outcomes.