bluuebunny/crossref_metadata_2025_split huggingface dataset:
A207 CLONAL PATTERNS BETWEEN POUCH NEOPLASIA AND PRIOR COLORECTAL NEOPLASIA IN INFLAMMATORY BOWEL DISEASE PATIENTS: AN EXPLORATORY COHORT STUDY
Authors: Van Lierop L , te Groen M , Derikx L , Ylstra B , Hoentjen F , Nagtegaal I , Doubrava-Simmer F 
Published: March 2023

Abstract

Background
Inflammatory bowel disease (IBD) patients with an ileo-anal pouch anastomosis (IPAA) bear an increased risk of pouch neoplasia, with prior colorectal neoplasia as the strongest predictor. It is unknown if pouch neoplasia develops independently or is derived from prior colorectal neoplasia.

Purpose
We aimed to assess potential clonality between prior colorectal neoplasia and pouch neoplasia in IPAA patients with IBD.

Method
In this explorative study we used the Dutch Nationwide Pathology Databank to identify IBD patients with both pouch neoplasia and colorectal neoplasia prior to colectomy. Clonality was assessed on colonic tissue of the lesion with shallow whole genome sequencing based copy number aberration (CNA) analysis and validated with immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).

Result(s)
We included 13 patients who fulfilled the inclusion criteria. Three patients showed matching clonality CNA profiles between prior colorectal neoplasia and pouch neoplasia, validated with matching IHC and FISH for p19 and HER2. Patients with matching clonal samples also showed on retrospective review concordant histology of the neoplastic lesion pre- and post IPAA, positive resection margins, metastasized disease or a short interval (&lt;2 years) between colorectal and pouch neoplasia diagnoses.

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Conclusion(s)
Three patients showed matching clonality patterns of neoplastic lesions, confirmed by clinical and histological data. Most pouch neoplasia in our cohort were molecularly different from their prior colorectal neoplasia. CNA provides a feasible method for clonality assessment in patients with colorectal neoplasia and subsequent pouch neoplasia.

Disclosure of Interest
None Declared
A220 ONTARIO POPULATION TRENDS IN INTESTINAL AND EXTRA-INTESTINAL CANCERS OVER 25 YEARS AMONG PERSONS WITH INFLAMMATORY BOWEL DISEASES AND MATCHED CONTROLS
Authors: Murthy S K , Kaplan G G , Coward S , Kuenzig E , Benchimol E I , Zubieta A , Otley A , Bitton A , Bernstein C N , Targownik L , Jones J , Begum J , Pugliese M , Singh H 
Published: March 2023

Abstract
NOT PUBLISHED AT AUTHOR’S REQUEST

Please acknowledge all funding agencies by checking the applicable boxes below
CCC, CIHR

Disclosure of Interest
S. Murthy: None Declared, G. Kaplan Grant / Research support from: Ferring, Janssen, AbbVie, GlaxoSmith Kline, Merck, and Shire, Consultant of: AbbVie, Janssen, Pfizer, Amgen, Takeda, Gilead, Speakers bureau of: AbbVie, Janssen, Pfizer, Amgen, and Takeda, S. Coward: None Declared, E. Kuenzig: None Declared, E. Benchimol Consultant of: Hoffman La-Roche Limited, Peabody & Arnold LLP, McKesson Canada, Dairy Farmers of Ontario for matters unrelated to medications used to treat inflammatory bowel disease., A. Zubieta: None Declared, A. Otley: None Declared, A. Bitton: None Declared, C. Bernstein Grant / Research support from: Abbvie Canada, Janssen Canada, Pfizer Canada, Bristol Myers Squibb Canada, Takeda Canada; Amgen Canada, Sandoz Canada , Consultant of: Abbvie Canada, Amgen Canada, Bristol Myers Squibb Canada, JAMP Pharmaceuticals, Janssen Canada, Pfizer Canada, Sandoz Canada, Takeda, Speakers bureau of: Abbvie Canada, Janssen Canada, Pfizer Canada and Takeda Canada, L. Targownik Grant / Research support from: Janssen Canada, Consultant of: AbbVie Canada, Takeda Canada, Merck Canada, Pfizer Canada, Janssen Canada, Roche Canada, and Sandoz Canada, J. Jones Consultant of: Janssen, Abbvie, Pfizer, Takeda, Speakers bureau of: Janssen, Abbvie, Pfizer, Takeda, J. Begum: None Declared, M. Pugliese: None Declared, H. Singh Consultant of: Pendopharm, Amgen Canada, Bristol Myers Squibb Canada, Roche Canada, Sandoz Canada, Takeda Canada, and Guardant Health, Inc.,
A267 IDENTIFYING ENTEROBACTERIACEAE VIRULENCE GENES ASSOCIATED WITH ACTIVE DISEASE IN ULCERATIVE COLITIS PATIENTS USING CULTURE-DEPENDENT AND -INDEPENDENT APPROACHES
Authors: Tertigas D , Rinawi F , Griffiths A , Surette M 
Published: March 2023

Abstract

Background
The prevalence of inflammatory bowel disease (IBD) in Canada is among the highest in the world and is estimated to affect 1 in 100 Canadians by 2030. Ulcerative colitis (UC) is a type of IBD characterized by mucosal inflammation of the large intestine. UC is believed to arise through a complex interplay of the host immune responses and changes in the gut microbiota in a genetically susceptible individual. Therapies targeting the gut microbiota, such as antibiotics and fecal microbiota transplantation (FMT), have been effective in treating UC, suggesting infectious triggers should be explored.

Purpose
Some data suggests the development of UC can be driven by pathogenic bacteria of the family Enterobacteriaceae, which can carry virulence genes important for colonizing the gut (e.g. fimH) and disrupting the intestinal epithelium (e.g. hylA). However, many studies have focused on a single species (e.g. Escherichia coli) and thereby underestimate the importance of these virulence genes that are shared across the Enterobacteriaceae family. I aim to investigate whether specific virulence genes contribute to disease activity in some patients with UC and to show that these virulence genes are carried by strains of many Enterobacteriaceae species.

Method
UC patient stool samples were collected throughout enrolment in randomized control trials of FMT for adult UC and microbiome studies in early-onset pediatric UC. The stool samples were cultured on MacConkey agar to enrich for Enterobacteriaceae. Samples from before and after treatment were sent for targetted cultured-enriched metagenomic sequencing and strains were isolated from baseline samples only for whole genome sequencing. The taxonomy of each genome and taxonomic composition of each metagenome were annotated along with virulence genes and antimicrobial resistance genes. Phenotypic assays of cultured isolates were used to capture diversity and virulence activity.

Result(s)
Approximately 7500 colonies from UC patient stool samples were isolated and phenotyped. Based on the initial screens, 130 isolates were selected to comprise our Enterobacteriaceae strain collection. Across all patient samples, we detected 19 different species of the Enterobacteriaceae family across six genera from the genomic and metagenomic data. We identified virulence genes found across multiple species from the Enterobacteriaceae family within genomes and metagenomes, and by performing phenotypic assays of the cultured isolates.

Conclusion(s)
Further exploration of the distribution of these virulence genes in UC patients during active disease or remission and healthy controls can provide insight into the pathogenesis of UC. Identifying infectious agents in even a subset of UC patients will allow for more targeted diagnosis and treatment approaches.

Disclosure of Interest
None Declared
A290 PHENOTYPE AND OUTCOME OF PATIENTS HOSPITALIZED FOR ACUTE PANCREATITIS IN A TERTIARY PEDIATRIC CENTER
Authors: Li T , Blain S , Korman C , David A , Mohamed M , Elhaoua D , Alvarez F , Deslandres C , Dirks M , Halac U , Grzywacz K , Lallier M , Jantchou P 
Published: March 2023

Abstract

Background
A recent meta-analysis of 48 studies, showed an equal prevalence of AP (16%) among the following etiologies; systemic disease, alcohol, medication, genetics, gallstones and infection in North American hospitalized and ambulatory pediatric patients. However, data on the epidemiology of severe pediatric acute pancreatitis (AP) in Canada are lacking.

Purpose
We aim to evaluate the clinical presentation, etiologies, comorbidities and outcome of pediatric patients with AP admitted to a tertiary hospital in Quebec, Canada.

Method
A retrospective observational cohort study (January 2014-December 2021) was performed at the CHU Sainte-Justine. Descriptive analyses were performed with SAS statistical softwar

Result(s)
Among the 214 patients included (110 (51%) males), 58 (27.1%) were already hospitalized at time of AP diagnosis (AP as secondary diagnosis) while 156 (72.9%) were admitted from the emergency room mainly with a presentation of abdominal pain (AP as primary diagnosis). Thirty-two patients (15.0%) were transferred to the ICU due to hemodynamic instability or respiratory failure. Comorbidities included cancer (38 patients (17.7%)), obesity (17 (7.9%)) and inflammatory bowel disease (15 (7.0%)). The three most commonly identified etiologies were medication (19.6%), biliary disease (16.3%) and infection (14,9%). Despite extensive investigations, 26.2% of cases were idiopathic. The main complications were, ascites (48 patients (22.4%)), necrotic pancreatitis (10 (4.6%)) and pancreatic pseudocyst (10 (4.6%)). The median duration of hospitalization for AP as a primary diagnosis was 4 days (interquartile range (IQR) 2-7) as compared to 22 (11-37) for AP as a secondary diagnosis.

Conclusion(s)
Approximately one third of hospitalized patients had an underlying condition requiring treatments that could cause AP, which explains the high prevalence of drug-induced AP in this report. The longest hospitalizations were associated with AP as secondary diagnosis. Ongoing work will identify factors associated with disease severity and outcome in particular in primary AP.

Please acknowledge all funding agencies by checking the applicable boxes below
None

Disclosure of Interest
None Declared
Evaluating deployment strategies for spotted lanternfly (Lycorma delicatula Hemiptera: Fulgoridae) traps
Authors: Nixon Laura J , Barnes Caitlin , Deecher Elizabeth , Madalinska Katarzyna , Nielsen Anne , Urban Julie , Leskey Tracy C 
Published: March 2023

Abstract
The spotted lanternfly, Lycorma delicatula (White) (Hemiptera: Fulgoridae), is an invasive planthopper that was first detected in the United States in Berks County, PA, in 2014, and has since spread to 13 states in the Eastern United States. This phloem-feeding pest has a broad host range, including economically important crops such as grapevine, Vitis spp. Monitoring presence and relative abundance of L. delicatula is essential to develop pest management tools. Here, we compared deployment strategies to optimize use of L. delicatula monitoring traps. Standard circle traps, sticky bands, and circle traps with replaceable bag tops were deployed at sites with either high or low populations present. Trap deployment at different heights and on different host tree species and trap sampling intervals were evaluated for standard circle traps only. Circle traps captured significantly more L. delicatula adults at low-density sites compared with other trap types in 2021, and no differences were detected at high-density sights. Traps deployed 1 m from the ground captured significantly more adults than those deployed at 0.5 m; no differences were detected for nymphs. While no significant differences in captures were found among intervals, weekly or biweekly sampling prevented specimen degradation. Although traps deployed on Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae) captured significantly or numerically more L. delicatula at most sites, traps deployed on other hosts also yielded consistent captures. We were also able to alter the construction of circle trap skirts to allow for deployment on different sized tree trunks.
Frequent and efficient harvesting as an economically viable strategy to regulate coffee berry borer on commercial farms in Hawaii
Authors: Aristizábal Luis F , Johnson Melissa A , Shriner Suzanne , Wall Marisa 
Published: March 2023

Abstract
Coffee is the second most economically important agricultural crop in Hawaii, valued at around $175M for green and roasted coffee in the 2021–2022 season. With the introduction of coffee berry borer (CBB, Hypothenemus hampei Ferrari) to Hawaii in 2010, growers have faced a significant challenge in producing the specialty coffee that the region is known for. This tiny beetle infests the coffee seed and reduces the yield and quality of coffee products. While field sanitation, frequent harvesting and strip-picking are known to be essential for controlling CBB, the associated costs and benefits of these cultural control practices have not been estimated for Hawaii. In the present study, we examined two CBB management strategies across 10 commercial coffee farms on Hawaii Island: (i) conventional management including frequent sprays of pesticides and few rounds of sanitation and harvesting, and (ii) cultural control-focused management consisting of few sprays of pesticides and frequent sanitation and harvesting. Cultural management resulted in significantly lower mean CBB infestation (4.6% vs. 9.0%), total defects (5.5% vs. 9.1%), and CBB damage to processed coffee (1.6% vs. 5.7%) compared to conventional management. Additionally, yields were higher (mean increase of 3,024 lbs of cherry/acre) and harvested more efficiently (4.8 vs. 7.9 raisins/tree) on culturally managed vs. conventional farms. Lastly, the cost of chemical controls was 55% lower and the net benefit of frequent harvesting was 48% higher on cultural vs. conventional farms. Our findings demonstrate that frequent and efficient harvesting is an effective and economically viable alternative to frequent pesticide applications.
Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense
Authors: Kahlon Parvinderdeep S , Förner Andrea , Muser Michael , Oubounyt Mhaned , Gigl Michael , Hammerl Richard , Baumbach Jan , Hückelhoven Ralph , Dawid Corinna , Stam Remco 
Published: March 2023

Abstract
Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.
MR elastography identifies regions of extracellular matrix reorganization associated with shorter survival in glioblastoma patients
Authors: Svensson Siri Fløgstad , Halldórsson Skarphéðinn , Latysheva Anna , Fuster-Garcia Elies , Hjørnevik Trine , Fraser-Green Jorunn , Birkeland Bugge Robin Anthony , Grinband Jack , Holm Sverre , Sinkus Ralph , Vik-Mo Einar Osland , Emblem Kyrre Eeg 
Published: March 2023

AbstractBackgroundBiomechanical tissue properties of glioblastoma tumors are heterogeneous, but the molecular mechanisms involved and the biological implications are poorly understood. Here, we combine magnetic resonance elastography (MRE) measurement of tissue stiffness with RNA sequencing of tissue biopsies to explore the molecular characteristics of the stiffness signal.MethodsMRE was performed preoperatively in 13 patients with glioblastoma. Navigated biopsies were harvested during surgery and classified as “stiff” or “soft” according to MRE stiffness measurements (|G*|norm). Twenty-two biopsies from eight patients were analyzed by RNA sequencing.ResultsThe mean whole-tumor stiffness was lower than normal-appearing white matter. The surgeon’s stiffness evaluation did not correlate with the MRE measurements, which suggests that these measures assess different physiological properties. Pathway analysis of the differentially expressed genes between “stiff” and “soft” biopsies showed that genes involved in extracellular matrix reorganization and cellular adhesion were overexpressed in “stiff” biopsies. Supervised dimensionality reduction identified a gene expression signal separating “stiff” and “soft” biopsies. Using the NIH Genomic Data Portal, 265 glioblastoma patients were divided into those with (n = 63) and without (n = 202) this gene expression signal. The median survival time of patients with tumors expressing the gene signal associated with “stiff” biopsies was 100 days shorter than that of patients not expressing it (360 versus 460 days, hazard ratio: 1.45, P &lt; .05).ConclusionMRE imaging of glioblastoma can provide noninvasive information on intratumoral heterogeneity. Regions of increased stiffness were associated with extracellular matrix reorganization. An expression signal associated with “stiff” biopsies correlated with shorter survival of glioblastoma patients.
Autoimmunity in Long Covid and POTS
Authors: El-Rhermoul Fatema-Zahra , Fedorowski Artur , Eardley Philip , Taraborrelli Patricia , Panagopoulos Dimitrios , Sutton Richard , Lim Phang Boon , Dani Melanie 
Published: March 2023

Abstract
Orthostatic intolerance and other autonomic dysfunction syndromes are emerging as distinct symptom clusters in Long Covid. Often accompanying these are common, multi-system constitutional features such as fatigue, malaise and skin rashes which can signify generalized immune dysregulation. At the same time, multiple autoantibodies are identified in both Covid-related autonomic disorders and non-Covid autonomic disorders, implying a possible underlying autoimmune pathology. The lack of specificity of these findings precludes direct interpretations of cause and association, but their prevalence with its supporting evidence is compelling.
Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development
Authors: Field Sterling , Jang Geng-Jen , Dean Caroline , Strader Lucia C , Rhee Seung Y 
Published: March 2023

Abstract
This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.
Antagonistic regulation of target genes by the SISTER OF TM3–JOINTLESS2 complex in tomato inflorescence branching
Authors: Wang Xiaotian , Liu Zhiqiang , Bai Jingwei , Sun Shuai , Song Jia , Li Ren , Cui Xia 
Published: March 2023

Abstract
Inflorescence branch number is a yield-related trait controlled by cell fate determination in meristems. Two MADS-box transcription factors (TFs)—SISTER OF TM3 (STM3) and JOINTLESS 2 (J2)—have opposing regulatory roles in inflorescence branching. However, the mechanisms underlying their regulatory functions in inflorescence determinacy remain unclear. Here, we characterized the functions of these TFs in tomato (Solanum lycopersicum) floral meristem and inflorescence meristem (IM) through chromatin immunoprecipitation and sequencing analysis of their genome-wide occupancy. STM3 and J2 activate or repress the transcription of a set of common putative target genes, respectively, through recognition and binding to CArG box motifs. FRUITFULL1 (FUL1) is a shared putative target of STM3 and J2 and these TFs antagonistically regulate FUL1 in inflorescence branching. Moreover, STM3 physically interacts with J2 to mediate its cytosolic redistribution and restricts J2 repressor activity by reducing its binding to target genes. Conversely, J2 limits STM3 regulation of target genes by transcriptional repression of the STM3 promoter and reducing STM3-binding activity. Our study thus reveals an antagonistic regulatory relationship in which STM3 and J2 control tomato IM determinacy and branch number.
Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico
Authors: Yan Xiaokang , Williams Michael R , Barboza Castillo Ameriks D , Kireev Dmitri , Hathaway Nathaniel A 
Published: March 2023

Abstract
Gene regulation plays essential roles in all multicellular organisms, allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are conserved from yeast to human. Posttranslational modification of chromatin is a critical component of gene regulation. Specifically, tri-methylation of the nucleosome component histone 3 at lysine 9 (H3K9me3) is a key feature of this pathway along with the hallmark heterochromatin protein 1 (HP1). Histone methyltransferases are recruited by HP1 to deposit H3K9me3 marks which nucleate and recruit more HP1 in a process that spreads from the targeting site to signal for gene repression. One of the enzymes recruited is SETDB1, a methyltransferase which putatively catalyzes posttranslational methylation marks on H3K9. To better understand the contribution of SETDB1 in heterochromatin formation, we downregulated SETDB1 through knockdown by a dCas9-KRAB system and examined heterochromatin formation in a chromatin in vivo assay (CiA-Oct4). We studied the contribution of SETDB1 to heterochromatin formation kinetics in a developmentally crucial locus, Oct4. Our data demonstrate that SETDB1 reduction led to a delay in both gene silencing and in H3K9me3 accumulation. Importantly, SETDB1 knockdown to a ∼50% level did not stop heterochromatin formation completely. Particle-based Monte Carlo simulations in 3D space with explicit representation of key molecular processes enabled the elucidation of how SETDB1 downregulation affects the individual molecular processes underlying heterochromatin formation.