output.yaml

input_text: |-
  Title: Oral intake of titanium dioxide nanoparticles affect the course and prognosis of ulcerative colitis in mice: involvement of the ROS-TXNIP-NLRP3 inflammasome pathway.
  Abstract: Titanium dioxide (TiO2), no matter in nanoscale or micron sizes, has been widely used in food industry as additives for decades. Given the potential impact of TiO2 on the gastrointestinal epithelial and parenchymal cells, including goblet cells, the public consumers may suffer the risk of diseases caused by its widespread dissemination in food products. We therefore set out to investigate the impact of TiO2 NPs on the course and prognosis of ulcerative colitis by oral gavaging TiO2 NPs at the doses levels of 0, 30, 100, and 300 mg/kg during the induction (7 days, from day 1 to day 7) and recovery (10 days, from day 8 to day 17) phases of colitis in mice.The ulcerative colitis (UC) disease model was established by administrating of 2.5% dextran sulfate sodium (DSS) solution. Our results show that TiO2 NPs significantly enhanced the severity of DSS-induced colitis, decreased the body weight, increased the disease activity index (DAI) and colonic mucosa damage index (CMDI) scores, shortened the colonic length, increased the inflammatory infiltration in the colon. The most significant changes occurred in the low dose (30 mg/kg) group of TiO2 NPs exposure during the development phase of UC and the high dose (300 mg/kg) group of TiO2 NPs during UC self-healing phase. Increased reactive oxygen species (ROS) level and upregulation of anti-oxidant enzymes including total superoxide dismutase (T-SOD), glutathione peroxidase (GSH-PX) and catalase (CAT), demonstrate that the TiO2 NP exposure has triggered oxidative stress in mice. Moreover, the upregulation of caspase-1 mRNA and increased expression of thioredoxin interacting protein (TXNIP) further demonstrate the involvement of the ROS-TXNIP-NLR family pyrin domain containing 3 (NLRP3) inflammasome pathway in aggravating the development of UC.Oral intake of TiO2 NPs could affect the course of acute colitis in exacerbating the development of UC, prolonging the UC course and inhibiting UC recovery.© 2023. The Author(s).
  Keywords: Inflammatory bowel disease; Oral intake; ROS-TXNIP-NLRP3 inflammasome pathway; Titanium dioxide nanoparticles; Ulcerative colitis
raw_completion_output: |-
  genes:
  - caspase-1
  - NLRP3
  - TXNIP
  exposures:
  - titanium dioxide nanoparticles
  gene_exposures_relationships:
  - caspase-1: upregulation
  - NLRP3: involvement in inflammasome pathway
  - TXNIP: increased expression
prompt: |+
  From the text below, extract the following entities in the following format:

  genes: <semicolon-separated list of genes>
  exposures: <a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change>
  gene_exposures_relationships: <semicolon-separated list of gene to molecular activity relationships>


  Text:
  Title: Oral intake of titanium dioxide nanoparticles affect the course and prognosis of ulcerative colitis in mice: involvement of the ROS-TXNIP-NLRP3 inflammasome pathway.
  Abstract: Titanium dioxide (TiO2), no matter in nanoscale or micron sizes, has been widely used in food industry as additives for decades. Given the potential impact of TiO2 on the gastrointestinal epithelial and parenchymal cells, including goblet cells, the public consumers may suffer the risk of diseases caused by its widespread dissemination in food products. We therefore set out to investigate the impact of TiO2 NPs on the course and prognosis of ulcerative colitis by oral gavaging TiO2 NPs at the doses levels of 0, 30, 100, and 300 mg/kg during the induction (7 days, from day 1 to day 7) and recovery (10 days, from day 8 to day 17) phases of colitis in mice.The ulcerative colitis (UC) disease model was established by administrating of 2.5% dextran sulfate sodium (DSS) solution. Our results show that TiO2 NPs significantly enhanced the severity of DSS-induced colitis, decreased the body weight, increased the disease activity index (DAI) and colonic mucosa damage index (CMDI) scores, shortened the colonic length, increased the inflammatory infiltration in the colon. The most significant changes occurred in the low dose (30 mg/kg) group of TiO2 NPs exposure during the development phase of UC and the high dose (300 mg/kg) group of TiO2 NPs during UC self-healing phase. Increased reactive oxygen species (ROS) level and upregulation of anti-oxidant enzymes including total superoxide dismutase (T-SOD), glutathione peroxidase (GSH-PX) and catalase (CAT), demonstrate that the TiO2 NP exposure has triggered oxidative stress in mice. Moreover, the upregulation of caspase-1 mRNA and increased expression of thioredoxin interacting protein (TXNIP) further demonstrate the involvement of the ROS-TXNIP-NLR family pyrin domain containing 3 (NLRP3) inflammasome pathway in aggravating the development of UC.Oral intake of TiO2 NPs could affect the course of acute colitis in exacerbating the development of UC, prolonging the UC course and inhibiting UC recovery.© 2023. The Author(s).
  Keywords: Inflammatory bowel disease; Oral intake; ROS-TXNIP-NLRP3 inflammasome pathway; Titanium dioxide nanoparticles; Ulcerative colitis

  ===

...
input_text: |-
  Title: Infliximab Rescue Therapy in Pediatric Severe Colitis.
  Abstract: Clinical remission has been achieved with infliximab in patients with refractory ulcerative colitis (UC). However, there is conflicting data regarding its effectiveness as rescue therapy in adult acute severe colitis. Furthermore, pediatric inflammatory bowel disease (IBD) is associated with more severe disease that may be less amenable to attempted rescue. We reviewed our experience and outcomes with pediatric severe colitis after attempted inpatient rescue with infliximab.A single-institution, retrospective review was conducted of pediatric patients with UC or indeterminate colitis who received inpatient rescue infliximab therapy from 1/2000 to 1/2019. Rescue infliximab therapy was considered if a child failed non-biologic therapy or progressed to fulminant or toxic colitis. Primary outcome was failed therapy resulting in colectomy. A p-value of <0.05 determined significance.Thirty patients met inclusion criteria. The median age at administration of rescue infliximab treatment was 14 years [IQR 13,17]. Rescue therapy with infliximab was successful in 33% (n = 10), while 67% (n = 20) underwent colectomy. Children on maintenance steroids were less likely to be successfully rescued with infliximab and require colectomy (p = 0.03). Children requiring colectomy had a longer hospital stay (p = 0.03), more abdominal radiographs (p = 0.01), and were on a longer duration of antibiotics (p = <0.01) compared to children who were successfully rescued with infliximab. There was no difference in baseline vital signs or laboratory abnormalities between the two groups.In severe acute ulcerative or indeterminate colitis cases where infliximab has not been previously used, rescue infliximab can be used to avoid colectomy but has a high failure rate.IV.Retrospective study.Copyright © 2023 Elsevier Inc. All rights reserved.
  Keywords: Infliximab; Pediatric colitis; Severe colitis
raw_completion_output: |-
  genes: N/A
  exposures: Infliximab
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - Infliximab
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Stakeholder-identified barriers and enablers to ultrasound implementation in inflammatory bowel disease services in the UK: a qualitative interview study.
  Abstract: The study sought to explore and better understand the perceptions and experiences of stakeholders in relation to the use of ultrasound for the assessment of inflammatory bowel disease (IBD) in adults in the UK.A qualitative semistructured interview study, using template analysis and normalisation process theory, was undertaken.Interviews were conducted using virtual meeting software.Fourteen participants were enrolled between 2nd of June 2021 and 6th of September 2021. Participants were from the following roles: medical gastroenterology and radiology doctors, IBD nurse specialists, patients living with IBD, healthcare service managers. Participants reported that perceived barriers included reliance on established imaging and care pathways, reluctance to change, lack of trust in ultrasound in relation to perceived lack of precision and the initial financial and time outlay in establishing an ultrasound service. Participants were enthusiastic for the uptake of ultrasound and discussed enablers to ultrasound uptake including the benefits to patients in terms of reduction in waiting times and earlier diagnosis and treatment allocation, reduced number of hospital appointments and patients having better understanding of their health.There are perceived barriers to achieving implementation of ultrasound. There is scant literature to effectively assess these reported barriers. Therefore, there is further research required in the areas of the impact of the use of ultrasound for the assessment of IBD in the UK.© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.
  Keywords: GASTROENTEROLOGY; Inflammatory bowel disease; Ultrasound
raw_completion_output: |-
  genes: N/A
  exposures: Ultrasound
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - NCIT:C17230
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
named_entities:
  - id: NCIT:C17230
    label: Ultrasound
input_text: |-
  Title: Health Disparities in Inflammatory Bowel Disease Care Driven by Rural Versus Urban Residence: Challenges and Potential Solutions.
  Abstract: 
  Keywords: 
raw_completion_output: |-
  genes: N/A
  exposures: rural or urban residence
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - rural or urban residence
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Anaerobes in specific infectious and noninfectious diseases: new developments.
  Abstract: With the buildup of new research data, newer associations between anaerobic bacteria and diseases/conditions were evaluated. The aim of the mini-review was to draw attention and to encourage further multidisciplinary studies of the associations. We considered microbiome-disease correlations such as a decrease of fecal Faecalibacterium prausnitzii abundance in inflammatory bowel disease (IBD) and IBD recurrence, suggesting that F. prausnitzii could be a good biomarker for IBD. A link of subgingival Porphyromonas gingivalis with cardiovascular diseases was reported. Decreased Roseburia abundance was observed in the gut of Alzheimer's and Parkinson's disease patients. Akkermansia muciniphila was found to improve adipose/glucose metabolism, however, its intestinal abundance was observed in neurodegenerative diseases as well. Severe Clostridioides difficile infections have been reported in neonates and young children. Carcinogenic potential of anaerobes has been suggested. Fusobacterium nucleatum was implicated in the development of oral and colorectal cancer, Porphyromonas gingivalis and Tannerella forsythia were linked to esophageal cancer and Cutibacterium acnes subsp. defendens was associated with prostate cancer. However, there are some controversies about the results. In a Swedish longitudinal study, neither P. gingivalis nor T. forsythia exhibited oncogenic potential. The present data can enrich knowledge of anaerobic bacteria and their multifaceted significance for health and disease and can draw future research directions. However, more studies on large numbers of patients over prolonged periods are needed, taking into account the possible changes in the microbiota over time.Copyright © 2023 Elsevier Ltd. All rights reserved.
  Keywords: Anaerobes; C. difficile; Cancer; Inflammatory bowel disease; Neurodegenerative diseases; Obesity
raw_completion_output: |-
  genes: N/A
  exposures: anaerobic bacteria
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - anaerobic bacteria
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: A case of colonic perforation in collagenous colitis without diarrheal symptoms.: A case report.
  Abstract: Collagenous colitis is an inflammatory disease characterized by hyperplasia of the collagen band beneath the colonic mucous membrane. Chronic diarrhea is a characteristic clinical symptom. The disease is often diagnosed accidentally on colonoscopy for chronic diarrhea, and patients without chronic diarrhea have few chances to suspect the disease.The patient was a 75-year-old woman. The chief complaint was sudden upper abdominal pain and vomiting. There were no important findings regarding the consumed food or bowel habits (no diarrhea). Computed tomography revealed wall thickness and a small amount of free air around the descending colon. An emergency laparotomy was performed with the diagnosis of spontaneous colonic perforation. Intra-operative findings revealed a longitudinal ulcer and micro-perforation to the mesenterial side at the descending colon. Pathological findings revealed subepithelial collagenous band in the submucosal background of the ulcer, and which was diagnosed as collagenous colitis.Intestinal perforation in collagenous colitis is extremely rare. It was considered that perforation was caused by a transient increase in intestinal pressure in the background of collagenous colitis. Further, to the best of our knowledge, this is the first report of a critical case which presented without the characteristic symptom of chronic diarrhea.We report a rare case of colonic perforation of the collagenous colitis.Copyright © 2023. Published by Elsevier Ltd.
  Keywords: Chronic diarrhea; Collagenous colitis; Colonic perforation; Proton pomp inhibitor
raw_completion_output: |-
  genes: N/A
  exposures: proton pomp inhibitor
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - proton pomp inhibitor
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Psychosocial factors associated with j-pouch surgery for patients with IBD: a scoping review.
  Abstract: Ulcerative colitis and Crohn's disease are subtypes of inflammatory bowel disease: a chronic condition of unclear etiology characterized by inflammation of the small and large intestine. Inflammatory bowel disease is managed with diet, medications, and surgeries, with the most common surgery, recommended to ulcerative colitis patients being j-pouch surgery.To assess the current literature concerning psychosocial factors associated with j-pouch surgery for patients with inflammatory bowel disease.A systematic scoping review of the empirical and grey literature was conducted for original research on j-pouch surgery and psychosocial variables. Eight databases were searched: Medline, PsychInfo, CINAHL, EBM Reviews, ProQuest Dissertations and Theses Global, ResearchGate, Prospero, and PrePubMed.Thirty-nine articles were identified. Many studies (n = 18) adopted a case-series design, and none examined psychosocial interventions. The most popular psychosocial variables assessed were quality of life (n = 34) and those associated with sexual health and functioning (n = 9).Despite being an established surgical procedure, little research has examined the psychosocial implications of j-pouch surgery. As such, clinicians lack a robust understanding of how this procedure affects patients' psychiatric and social status and adaptive abilities. There is a need for high-quality research utilizing validated measures and rigorous design methodologies with control populations.© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
  Keywords: Crohn’s; IBD; Inflammatory bowel disease; Psychosocial; Scoping review; Ulcerative colitis
raw_completion_output: |-
  genes: N/A
  exposures: N/A
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - N/A
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Validation and reference scores of the Transition Readiness Assessment Questionnaire in adolescent and young adult IBD patients.
  Abstract: Transition readiness can predict a successful transition from paediatric to adult care. This study aimed to validate and develop age-dependent reference scores for the (Dutch version of) Transition Readiness Assessment Questionnaire (TRAQ), in adolescents and young adults (AYA) with inflammatory bowel disease (IBD).TRAQ has 20 items (score 1-5) distributed over five domains (total sum score 100) and is completed by AYA. Following the COSMIN methodology, we conducted the translation, back-to back translation, pretesting, and validation of the final TRAQ-NL questionnaire. We used a RASCH model for structural validation, hypothesis testing for construct validity, and Cronbach's alpha to demonstrate reliability. Reference scores were calculated using percentiles.250 TRAQ questionnaires were evaluated in 136 AYA with IBD (56% Crohn's disease, 58% male, median age 17.5 years (range 15.7-20.4)).The overall mean item score was 3.87 (range 1.45-5). With good reliability (Cronbach's alpha 0.87), TRAQ-NL discriminated well between knowledge levels, especially in the lower levels. Transition readiness was defined as low, moderate, adequate, or excellent in patients with TRAQ percentile scores <25th (< 3.375 mean item score), 25th-50th (3.375 - 3.9), 50th-90th (3.91- 4.7) or >90th (>4.7). Younger patients, concomitant illness, fewer visits to the transition clinic, and parental dependence were associated with significantly lower TRAQ scores.TRAQ(-NL) is reliable and valid, with age-dependent percentile scores to identify (in)adequate transfer readiness. TRAQ can now be more easily used as a patient-reported outcome measure to monitor transition readiness longitudinally in routine care for adolescent and young adult IBD patients.Copyright © 2023 by European Society for European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition.
  Keywords: 
raw_completion_output: |-
  genes: N/A
  exposures: inflammatory bowel disease
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - inflammatory bowel disease
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Clinical Utility of the Neutrophil-to-Bilirubin Ratio in the Detection of Disease Activity in Ulcerative Colitis.
  Abstract: Ulcerative colitis (UC) is a chronic relapsing remitting form of inflammatory bowel disease (IBD). Current disease monitoring includes evaluation of symptoms, fecal calprotectin, and colonoscopy. Due to limited availability of the latter two modalities in China, we sought a readily available, inexpensive, disease monitoring laboratory assessment. We recently identified a novel serological index (the neutrophil-to-bilirubin ratio, NBR) for monitoring disease activity in Crohn's disease. However, the clinical significance has not been evaluated in UC. Here, we aimed to verify the hypothesis that NBR might be useful in monitoring clinical and endoscopic activity in patients with UC.To test our hypothesis, we conducted a single-center, retrospective study including a total of 188 patients with UC and 145 non-IBD controls. NBR was calculated to determine its practical value in monitoring disease activity (including clinical and endoscopic activity). Disease activity of UC was determined by the partial Mayo score and the Mayo endoscopic score (MES) system.NBR was significantly higher in patients with UC than that in controls (12.10, IQR: 9.85-16.69 versus 5.06, IQR: 3.94-6.55; p < 0.001) and showed positive correlations with clinical and endoscopic disease activity in UC. Additionally, NBR was significantly lower in patients with endoscopic mucosal healing (MH) than that in those without endoscopic MH (8.81, IQR: 6.67-11.67 versus 13.51, IQR: 11.04-18.71; p < 0.001). Serial evaluation of NBR in a subset of patients demonstrated that NBR was significantly decreased during the MH stage compared with that during the endoscopically active stage.Our study suggests that NBR may be a promising candidate for assessing disease activity in UC, with potential for widespread clinical use and significant clinical implications.© 2023 Huang et al.
  Keywords: bilirubin; mucosal healing; neutrophil-to-bilirubin ratio; ulcerative colitis
raw_completion_output: |-
  genes: N/A
  exposures: bilirubin
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - bilirubin
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Pretreatment with Bifidobacterium longum BAA2573 ameliorates dextran sulfate sodium (DSS)-induced colitis by modulating gut microbiota.
  Abstract: Inflammatory bowel disease (IBD) is a chronic lifelong inflammatory disease. Probiotics such as Bifidobacterium longum are considered to be beneficial to the recovery of intestinal inflammation by interaction with gut microbiota. Our goals were to define the effect of the exclusive use of BAA2573 on dextran sulfate sodium (DSS)-induced colitis, including improvement of symptoms, alleviation of histopathological damage, and modulation of gut microbiota.In the present study, we pretreated C57BL/6J mice with Bifidobacterium longum BAA2573, one of the main components in an over-the-counter (OTC) probiotic mixture BIFOTO capsule, before modeling with DSS. 16S rDNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based non-targeted metabolomic profiling were performed with the collected feces.We found that pretreatment of Bifidobacterium longum BAA2573 given by gavage significantly improved symptoms and histopathological damage in DSS-induced colitis mice. After the BAA2573 intervention, 57 genera and 39 metabolites were significantly altered. Pathway enrichment analysis demonstrated that starch and sucrose metabolism, vitamin B6 metabolism, and sphingolipid metabolism may contribute to ameliorating colitis. Moreover, we revealed that the gut microbiome and metabolites were interrelated in the BAA2573 intervention group, while Alistipes was the core genus.Our study demonstrates the impact of BAA2573 on the gut microbiota and reveals a possible novel adjuvant therapy for IBD patients.Copyright © 2023 Lin, Hao, Zhou, Huang, Wang, Liu and Li.
  Keywords: DSS-induced colitis; bifidobacterium longum; gut microbiota; inflammatory bowel disease; metabolites; probiotics
raw_completion_output: |-
  genes: N/A
  exposures: Bifidobacterium longum BAA2573; dextran sulfate sodium (DSS)
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - Bifidobacterium longum BAA2573
    - dextran sulfate sodium (DSS)
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Application of abdominal ultrasonography in surgical necrotizing enterocolitis: a retrospective study.
  Abstract: Necrotizing enterocolitis (NEC) is a severe inflammatory bowel disease that may lead to perforation, causing high morbidity and mortality in preterm infants. Abdominal ultrasound (AUS) has been shown to provide benefits in diagnosing and managing NEC in recent years.This study focused on the utility of AUS in the diagnosis and evaluation of surgical NEC.In this retrospective study, available data of the patients diagnosed from January 2019 to June 2022 were reviewed. The sensitivity and specificity of AUS in diagnosing a perforation were analyzed. Typical cases for the application of AUS in monitoring and evaluating the progression, complications, and sequela of NEC were described.There were 69 neonates diagnosed with NEC and examined by AUS, of whom eight patients developed a perforation. AUS was used for diagnosing a perforation in eight patients with key features of pneumoperitoneum and/or complex ascites, allowing us to find four locations of perforation, with a sensitivity and specificity of 100%.AUS plays an important role in diagnosing and evaluating surgical NEC in newborn infants, with good sensitivity and specificity.Copyright © 2023 Chen, Yao, Xu, Liao, Li, Mai, Xie, He and Li.
  Keywords: abdominal ultrasound; necrotizing enterocolitis; newborn infant; perforation; surgical
raw_completion_output: |-
  genes: N/A
  exposures: N/A
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - N/A
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Hericium erinaceus, a medicinal fungus with a centuries-old history: Evidence in gastrointestinal diseases.
  Abstract: Hericium erinaceus is an edible and medicinal mushroom commonly used in traditional Chinese medicine for centuries. Several studies have highlighted its therapeutic potential for gastrointestinal disorders such as gastritis and inflammatory bowel diseases. In addition, some components of this mushroom appear to possess strong antineoplastic capabilities against gastric and colorectal cancer. This review aims to analyse all available evidence on the digestive therapeutic potential of this fungus as well as the possible underlying molecular mechanisms.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.
  Keywords: Colorectal cancer; Fungus; Gastric cancer; Gastritis; Hericium erinaceus; Inflammatory bowel diseases
raw_completion_output: |-
  genes: N/A
  exposures: Hericium erinaceus
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - Hericium erinaceus
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Circulating Cell-Free DNA in Inflammatory Bowel Disease: Liquid Biopsies with Mechanistic and Translational Implications.
  Abstract: This review examines the role of circulating cell-free DNA (cfDNA) as potential drivers of inflammation and their potential application as mechanistic biomarkers in Inflammatory Bowel Diseases (IBD). These DNA fragments contain significant information about their origins, the underlying host pathology leading to their release, and possess properties that can fuel the inflammatory process. Recent advances in sequencing and analytical approaches have made the translation of cfDNA into clinical practice a promising prospect. We focus on the functional relevance of cfDNA in the inflammatory process and discuss its potential for future assessments of IBD activity and identification of therapeutic options.Copyright: © 2023 Ho GT et al.
  Keywords: CD; IBD; UC; cfDNA; liquid biopsy; mitochondria
raw_completion_output: |-
  genes: 
  exposures: 
  gene_exposures_relationships: 

  (Note: No specific genes or exposures are mentioned in the text)
prompt: |+
  From the text below, extract the following entities in the following format:

  genes: <semicolon-separated list of genes>
  exposures: <a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change>
  gene_exposures_relationships: <semicolon-separated list of gene to molecular activity relationships>


  Text:
  Title: Circulating Cell-Free DNA in Inflammatory Bowel Disease: Liquid Biopsies with Mechanistic and Translational Implications.
  Abstract: This review examines the role of circulating cell-free DNA (cfDNA) as potential drivers of inflammation and their potential application as mechanistic biomarkers in Inflammatory Bowel Diseases (IBD). These DNA fragments contain significant information about their origins, the underlying host pathology leading to their release, and possess properties that can fuel the inflammatory process. Recent advances in sequencing and analytical approaches have made the translation of cfDNA into clinical practice a promising prospect. We focus on the functional relevance of cfDNA in the inflammatory process and discuss its potential for future assessments of IBD activity and identification of therapeutic options.Copyright: © 2023 Ho GT et al.
  Keywords: CD; IBD; UC; cfDNA; liquid biopsy; mitochondria

  ===

extracted_object: {}
input_text: |-
  Title: Early life oral antibiotics are associated with pediatric-onset inflammatory bowel disease - a nationwide study.
  Abstract: Early-life environmental triggers are thought to play a larger role in pediatric-onset inflammatory bowel disease (pIBD) compared to adult-onset IBD. We aimed to assess the risk of developing pIBD after exposure to oral antibiotics during the first five years of life.In a nation-wide cohort study, we identified all patients diagnosed with pIBD (< 18 years at diagnosis) in Denmark between 1995-2018 from the National Patient Registry and matched them with up to ten reference individuals. Antibiotic exposure was defined as being prescribed antibiotics during first five years of life. Data were retrieved from the National Prescription Register. Outcome was developing pIBD. Risk estimates are presented by Hazard ratios (HR) with 95% confidence intervals (CI).We identified 1,927 pIBD patients and 18,318 reference individuals. Oral antibiotic exposure during the first five years of life was associated with a higher risk of developing pIBD (HR = 1.33 [95%CI: 1.2-1.5], p <0.0001). The risk was also increased if patients had ≥ four antibiotic prescriptions compared to no antibiotics (HR = 1.33 [95%CI: 1.2-1.5], p <0.0001). Broad-spectrum antibiotics increased the risk of pIBD compared to narrow-spectrum antibiotics (HR: 1.29, [95%CI 1.2-1.4], p<0.0001). When stratified by IBD subtypes, only Crohn's disease was significantly associated with exposure to antibiotics (HR = 1.37 [95%CI: 1.1-1.7], p=0.002).In this nationwide registry-based study, we found that oral antibiotic exposure during first five years of life, was associated with an increased risk of pIBD. Repeated antibiotic exposures increased risk estimates.Copyright © 2023 by European Society for European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition.
  Keywords: 
raw_completion_output: |-
  genes: N/A
  exposures: oral antibiotics
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - oral antibiotics
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Prevalence of NUDT15 genetic variants and incidence of thiopurine-induced leukopenia in Inflammatory Bowel Disease: A systematic review and meta-analysis.
  Abstract: Nudix hydrolase 15 (NUDT15) genetic variants confer an increased risk of thiopurine-induced leukopenia (TIL), however their global prevalence in Inflammatory Bowel Disease (IBD) patients is unknown. We aimed to evaluate the global prevalence of NUDT15 variants in IBD patients and incidence of TIL in these patients.Six databases were searched from inception until July 2022. Studies reporting the frequency of any NUDT15 variant and/or frequency of leukopenia in adult IBD patients with these variants, were included. A random effects model was performed to estimate the pooled prevalence of variants, incidence of early (≤8 weeks) and late (>8 weeks) leukopenia, and relative risk of developing leukopenia.20 studies comprising 5232 patients were included. The pooled prevalence of the *1/*3 c.415C>T C/T diplotype was 13% (95% CI: 10-18%), *3/*3 c.415C>T T/T diplotype was 2% (95% CI: 1-2%), *1/*5 c.52G>A G/A diplotype was 2% (95% CI: 1-3%) and *1/*6 c.36_37insGGAGTC ins/- diplotype was 7% (95% CI: 4-12%). The pooled prevalence of *1/*3 was high in Japanese (20%, 95% CI: 16-24%) and Chinese patients (18%, 95% CI: 12-27%). The incidence of early leukopenia was 20% (95% CI: 16-26%) in *1/*3 patients, 99% (95% CI: 7-100%) in *3/*3 patients and 49% (95% CI: 29-69%) in *1/*6 patients. The incidence of late leukopenia was 36% (95% CI: 26-49%) in *1/*3 patients.NUDT15 variants are common and strongly predict TIL in IBD patients. Pre-treatment NUDT15 genotyping should be considered particularly in Asian populations to guide thiopurine dosing and prevent myelotoxicity.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com.
  Keywords: 
            NUDT15
          ; inflammatory bowel disease; leukopenia; thiopurines
raw_completion_output: |-
  genes: NUDT15
  exposures: thiopurines
  gene_exposures_relationships: NUDT15 variants predict thiopurine-induced leukopenia (TIL) in IBD patients.
prompt: |+
  From the text below, extract the following entities in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  NUDT15 variants predict thiopurine-induced leukopenia (TIL) in IBD patients.

  ===

extracted_object:
  genes:
    - HGNC:23063
  exposures:
    - thiopurines
  gene_exposures_relationships:
    - molecular_activity: thiopurine-induced leukopenia
      gene: HGNC:23063
named_entities:
  - id: HGNC:23063
    label: NUDT15
input_text: |-
  Title: Lack of benefit for early escalation to advanced therapies in ulcerative colitis: critical appraisal of current evidence.
  Abstract: Although ulcerative colitis (UC) shares many common pathways and therapeutic options with Crohn's disease (CD), CD patients are four times more likely to undergo surgery 10 years into their disease in biologic era and are more likely to have extraintestinal manifestations than UC patients. Early treatment in CD has been demonstrated to modify natural history of disease and potentially delay surgery. Previous reviews on this topic borrowed their evidence from CD to make UC-specific recommendations. This review highlights the emergence of UC-specific data from larger cohort studies and a comprehensive individual patient data systemic review and meta-analysis to critically appraise the evidence on utility of early escalation to advanced therapies with respect to short-, medium-, and long-term outcomes. In UC, the utility of the early escalation concept for the purposes of changing the natural history, including reducing colectomy and hospitalisations, is not supported by the available data. Data on targeting clinical, biochemical, endoscopic, and histological outcomes are needed to demonstrate that they are meaningful with regards to achieving reductions in hospitalization and surgery, improving quality of life, and minimizing disability. The analyses of different populations of UC patients, such as those with "relapsing & remitting" disease or with severe or complicated disease course, are urgently needed. The costs and risk/benefit profile of some of the newer advanced therapies should be carefully considered. In this clinical landscape, it appears premature to advocate an indiscriminate 'one size fits all' approach to escalating to advanced therapies early during the course of UC.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com.
  Keywords: disease duration; early escalation; escalation to advance therapies; ulcerative colitis
raw_completion_output: |-
  genes: N/A
  exposures: advanced therapies
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - advanced therapies
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.
  Abstract: Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.
  Keywords: Bacteroides; inflammatory bowel disease; microbiome; structural biology; type VI secretion system
raw_completion_output: |-
  genes: Ntox15, Tde1, Tdi1, Tde2, structural genes
  exposures: type VI secretion system, Tde1, T6SS, fecal metagenomes, inflammatory bowel disease
  gene_exposures_relationships: Tdi1 interacts with Tde nucleases and disrupts their active and DNA-binding sites in response to Tde1 exposure, Tde and T6SS structural genes are enriched in fecal metagenomes from ulcerative colitis subjects.
prompt: |+
  From the text below, extract the following entities in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  Tdi1 interacts with Tde nucleases and disrupts their active and DNA-binding sites in response to Tde1 exposure, Tde and T6SS structural genes are enriched in fecal metagenomes from ulcerative colitis subjects.

  ===

extracted_object:
  genes:
    - Ntox15, Tde1, Tdi1, Tde2, structural genes
  exposures:
    - type VI secretion system, Tde1, T6SS, fecal metagenomes, inflammatory bowel
      disease
  gene_exposures_relationships:
    - molecular_activity: Tde1 exposure
      gene: Tdi1
input_text: |-
  Title: Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer.
  Abstract: The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.© 2023. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.
  Keywords: 16SrRNA; 18SrRNA; Crohn’s disease; Metabarcoding; Mycobiome; Ulcerative colitis
raw_completion_output: |-
  genes: N/A
  exposures: N/A
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - N/A
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
input_text: |-
  Title: Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis.
  Abstract: Ulcerative colitis is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the ulcerative colitis ecosystem, here we use imaging mass cytometry and single-cell RNA sequencing to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction in the ulcerative colitis region, occurring only for tissue-resident macrophages. Reactive oxygen species levels are higher in the ulcerative colitis region, but reactive oxygen species scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct reactive oxygen species vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF production during ulcerative colitis via a cytokine production network formed with T and B cells. Our study suggests components of a mechanism for the observed macrophage disappearance reaction of resident macrophages, providing mechanistic hints for macrophage disappearance reaction in other inflammation or infection situations.© 2023. The Author(s).
  Keywords: 
raw_completion_output: |-
  genes: SOD2; TNF
  exposures: reactive oxygen species
  gene_exposures_relationships: SOD2 <-> reactive oxygen species
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  SOD2 <-> reactive oxygen species

  ===

extracted_object:
  genes:
    - HGNC:11180
    - HGNC:11892
  exposures:
    - CHEBI:26523
  gene_exposures_relationships:
    - molecular_activity: CHEBI:26523
      gene: HGNC:11180
named_entities:
  - id: HGNC:11180
    label: SOD2
  - id: HGNC:11892
    label: TNF
  - id: CHEBI:26523
    label: reactive oxygen species
input_text: |-
  Title: Differences in gut microbiota and fecal bile acids between Caucasian and Hispanic children and young adults with ulcerative colitis.
  Abstract: Ulcerative Colitis (UC) is an inflammatory bowel disease (IBD) that has been associated with gut dysbiosis. Changes in the gut microbiome lead to changes in bile acids (BA) metabolism, which changes the BA profiles in patients with UC. We conducted this study to investigate the differences in bile acids and gut microbiota between Hispanic and Caucasian children and young adults with UC. Twenty-seven Caucasian and 20 Hispanic children and young adults with UC were enrolled in the study. BAs were extracted from the subjects' stool samples and analyzed by liquid chromatography-mass spectrometry. Microbial DNA was also extracted from the stool samples to perform 16s rRNA amplicon sequencing. The median levels of cholic acid and taurolithocholic acid were found to be significantly higher in Hispanic children and young adults with UC compared to their Caucasian counterparts. The abundance of the gut microbiota that metabolizes BAs such as Proteobacteria, Pseudomonadaceae, Pseudomonas, Ruminococcus gnavus, and Escherichia coli were also all significantly higher in Hispanic children and young adults as well. The distinct BA profile that we found in Hispanic children and young adults with UC, in addition to the unique composition of their gut microbiome, provide them with a protective gut environment against inflammation, which is contrary to the common believe that Hispanics have worse IBD.© 2023 The Authors. Physiological Reports published by Wiley Periodicals LLC on behalf of The Physiological Society and the American Physiological Society.
  Keywords: 
raw_completion_output: |-
  genes: N/A 
  exposures: bile acids (BA), Proteobacteria, Pseudomonadaceae, Pseudomonas, Ruminococcus gnavus, Escherichia coli  
  gene_exposures_relationships: N/A
prompt: |+
  Split the following piece of text into fields in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  N/A

  ===

extracted_object:
  genes:
    - N/A
  exposures:
    - CHEBI:32594
  gene_exposures_relationships:
    - molecular_activity: N/A
      gene: N/A
named_entities:
  - id: CHEBI:32594
    label: bile acids (BA), Proteobacteria, Pseudomonadaceae, Pseudomonas, Ruminococcus
      gnavus, Escherichia coli
input_text: |-
  Title: Targeting 14-3-3ζ by a small-molecule compound AI-34 maintains epithelial barrier integrity and alleviates colitis in mice via stabilizing β-catenin.
  Abstract: Aberrant intestinal epithelial barrier function is the primary pathology of Ulcerative colitis (UC), making it a desirable drug target. In this study, our small-molecule compound AI-34 exerted a significant protective effect in an LPS-induced epithelial barrier injury model. In vitro, AI-34 treatment significantly decreased cell permeability, increased transmembrane resistance, and maintained the junctional protein (ZO-1 and E-cadherin) levels in monolayer cells. Using the LiP-small molecule mapping approach (LiP-SMap), we demonstrated that AI-34 binds to 14-3-3ζ. AI-34 promoted the interaction between 14-3-3ζ and β-catenin, decreasing the ubiquitination of β-catenin and thus maintaining intestinal epithelial barrier function. Finally, AI-34 triggered the stabilization of β-catenin mediated by 14-3-3ζ, provoking a significant improvement in the DSS-induced colitis model. Our findings suggest that AI-34 may be a promising candidate for UC treatment.Copyright © 2023 The Authors. Production and hosting by Elsevier B.V. All rights reserved.
  Keywords: 14-3-3ζ; Colitis; Small-molecule compound; β-catenin
raw_completion_output: |-
  genes: None mentioned
  exposures: AI-34
  gene_exposures_relationships: 14-3-3ζ binds to AI-34, AI-34 promotes interaction between 14-3-3ζ and β-catenin, AI-34 triggers stabilization of β-catenin mediated by 14-3-3ζ.
prompt: |+
  From the text below, extract the following entities in the following format:

  molecular_activity: <the name of the exposure, such as a exposure to a chemical toxin.>
  gene: <the name of the gene in the pair. This comes second in the pair.>


  Text:
  14-3-3ζ binds to AI-34, AI-34 promotes interaction between 14-3-3ζ and β-catenin, AI-34 triggers stabilization of β-catenin mediated by 14-3-3ζ.

  ===

extracted_object:
  genes:
    - None mentioned
  exposures:
    - AI-34
  gene_exposures_relationships:
    - molecular_activity: exposure to AI-34
      gene: β-catenin