Search results
Found 9282 matches for
Microbiome diversity protects against pathogens by nutrient blocking.
The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack the ability to predict which communities will be protective. We studied how human gut bacteria influence colonization of two major bacterial pathogens, both in vitro and in gnotobiotic mice. Whereas single species alone had negligible effects, colonization resistance greatly increased with community diversity. Moreover, this community-level resistance rested critically upon certain species being present. We explained these ecological patterns through the collective ability of resistant communities to consume nutrients that overlap with those used by the pathogen. Furthermore, we applied our findings to successfully predict communities that resist a novel target strain. Our work provides a reason why microbiome diversity is beneficial and suggests a route for the rational design of pathogen-resistant communities.
Developing consensus on core outcome sets of domains for acute, the transition from acute to chronic, recurrent/episodic, and chronic pain: results of the INTEGRATE-pain Delphi process
Background: Pain is the leading cause of disability worldwide among adults and effective treatment options remain elusive. Data harmonization efforts, such as through core outcome sets (COS), could improve care by highlighting cross-cutting pain mechanisms and treatments. Existing pain-related COS often focus on specific conditions, which can hamper data harmonization across various pain states. Methods: Our objective was to develop four overarching COS of domains/subdomains (i.e., what to measure) that transcend pain conditions within different pain categories. We hosted a meeting to assess the need for these four COS in pain research and clinical practice. Potential COS domains/subdomains were identified via a systematic literature review (SLR), meeting attendees, and Delphi participants. We conducted an online, three step Delphi process to reach a consensus on domains to be included in the four final COS. Survey respondents were identified from the SLR and pain-related social networks, including multidisciplinary health care professionals, researchers, and people with lived experience (PWLE) of pain. Advisory boards consisting of COS experts and PWLE provided advice throughout the process. Findings: Domains in final COS were generally related to aspects of pain, quality of life, and physical function/activity limitations, with some differences among pain categories. This effort was the first to generate four separate, overarching COS to encourage international data harmonization within and across different pain categories. Interpretation: The adoption of the COS in research and clinical practice will facilitate comparisons and data integration around the world and across pain studies to optimize resources, expedite therapeutic discovery, and improve pain care. Funding: Innovative Medicines Initiative 2 Join Undertaking; European Union Horizon 2020 research innovation program, European Federation of Pharmaceutical Industries and Associations (EFPIA) provided funding for IMI-PainCare. RDT acknowledges grants from Esteve and TEVA.
Residual Aligner-based Network (RAN): Motion-separable structure for coarse-to-fine discontinuous deformable registration.
Deformable image registration, the estimation of the spatial transformation between different images, is an important task in medical imaging. Deep learning techniques have been shown to perform 3D image registration efficiently. However, current registration strategies often only focus on the deformation smoothness, which leads to the ignorance of complicated motion patterns (e.g., separate or sliding motions), especially for the intersection of organs. Thus, the performance when dealing with the discontinuous motions of multiple nearby objects is limited, causing undesired predictive outcomes in clinical usage, such as misidentification and mislocalization of lesions or other abnormalities. Consequently, we proposed a novel registration method to address this issue: a new Motion Separable backbone is exploited to capture the separate motion, with a theoretical analysis of the upper bound of the motions' discontinuity provided. In addition, a novel Residual Aligner module was used to disentangle and refine the predicted motions across the multiple neighboring objects/organs. We evaluate our method, Residual Aligner-based Network (RAN), on abdominal Computed Tomography (CT) scans and it has shown to achieve one of the most accurate unsupervised inter-subject registration for the 9 organs, with the highest-ranked registration of the veins (Dice Similarity Coefficient (%)/Average surface distance (mm): 62%/4.9mm for the vena cava and 34%/7.9mm for the portal and splenic vein), with a smaller model structure and less computation compared to state-of-the-art methods. Furthermore, when applied to lung CT, the RAN achieves comparable results to the best-ranked networks (94%/3.0mm), also with fewer parameters and less computation.
Fibroblasts Derived From Vestibular Schwannoma Express Protumorogenic Markers.
BACKGROUND AND AIM: Vestibular schwannomas (VSs), despite being histologically benign, cause significant morbidity because of their challenging intracranial location and the propensity for growth. The role of the stroma and particularly fibroblasts, in the progression of VS, is not completely understood. This study examines the profile of fibroblasts in VS. METHODS: Seventeen patients undergoing surgical excision of VS were recruited into the study. Reverse transcription with quantitative polymerase chain reaction (RT-qPCR) was performed on VS tissue samples and fibroblast-associated molecules examined. Immunofluorescence and immunohistochemistry in VS tissue were used to study the expression of fibroblast markers CD90 and podoplanin in situ. Fibroblast cultures were established from VS, and RT-qPCR analysis was performed on a panel of fibroblast markers on VS and control tissue fibroblasts. RESULTS: Several fibroblast-associated molecules including members of galectin family and matrix metalloproteinases were found to be expressed in VS tissue on RT-qPCR analysis. In situ, expression of CD90 and podoplanin was observed in VS tissue both on immunohistochemistry and immunofluorescence. RT-qPCR analysis of fibroblasts from VS and control vestibular neuroepithelium (NE) showed a higher expression of several molecules of the galectin and matrix metalloproteinases family on VS fibroblasts compared with NE fibroblasts. CONCLUSION: This work examines fibroblasts from VS and shows qualitative differences from NE fibroblasts on RT-qPCR. Further understanding of the fibroblast function in the progression of VS will potentially unveil new targets to manage VS growth.
Endoscopic characterization of neoplastic and non-neoplastic lesions in inflammatory bowel disease: systematic review in the era of advanced endoscopic imaging.
BACKGROUND: Current guidelines strongly recommend the use of validated classifications to support optical diagnosis of lesions with advanced endoscopic imaging in the lower gastrointestinal tract. However, the optimal strategy in inflammatory bowel disease (IBD) is still a matter of debate. OBJECTIVES: To analyze the accuracy of endoscopic classifications or single predictors for in vivo lesion characterization during endoscopic surveillance of IBD with advanced endoscopic imaging. DESIGN: Systematic review. DATA SOURCES AND METHODS: Medline and PubMed were used to extract all studies which focused on lesion characterization of neoplastic and non-neoplastic lesions in IBD. The diagnostic accuracy of endoscopic classifications and single endoscopic predictors for lesion characterization were analyzed according to type of patients, lesions, and technology used. When available, the rates of true and false positives or negatives for neoplasia were pooled and the sensitivity (SE), specificity (SP), positive predictive value, and negative predictive value (NPV) were calculated. RESULTS: We included 35 studies (2789 patients; 5925 lesions - 1149 neoplastic). Advanced endoscopic imaging included dye-based chromoendoscopy, virtual chromoendoscopy (VCE), magnification and high-definition endoscopy, confocal laser endomicroscopy (CLE), endocytoscopy, and autofluorescence imaging. The Kudo classification of pit patterns was most frequently used, with pooled SE 83%, SP 83%, and NPV 95%. The endoscopic criteria with the highest accuracy, with minimum SE ⩾ 90%, SP ⩾ 80%, and NPV ⩾ 90% were: the Kudo-IBD classification used with VCE (Fuji Intelligent Color Enhancement and i-SCAN); combined irregular surface and vascular patterns used with narrow band imaging; the Mainz classification used with CLE. Multiple clinical and technical factors were found to influence the accuracy of optical diagnosis in IBD. CONCLUSION: No single endoscopic factor has yet shown sufficient accuracy for lesion characterization in IBD surveillance. Conventional classifications developed in the non-IBD setting have lower accuracy in IBD. The use of new classifications adapted for IBD (Kudo-IBD), and new technologies based on in vivo microscopic analysis show promise.
Mmp14 is required for matrisome homeostasis and circadian rhythm in fibroblasts.
The circadian clock in tendon regulates the daily rhythmic synthesis of collagen-I and the appearance and disappearance of small-diameter collagen fibrils in the extracellular matrix. How the fibrils are assembled and removed is not fully understood. Here, we first showed that the collagenase, membrane type I-matrix metalloproteinase (MT1-MMP, encoded by Mmp14), is regulated by the circadian clock in postnatal mouse tendon. Next, we generated tamoxifen-induced Col1a2-Cre-ERT2::Mmp14 KO mice (Mmp14 conditional knockout (CKO)). The CKO mice developed hind limb dorsiflexion and thickened tendons, which accumulated narrow-diameter collagen fibrils causing ultrastructural disorganization. Mass spectrometry of control tendons identified 1195 proteins of which 212 showed time-dependent abundance. In Mmp14 CKO mice 19 proteins had reversed temporal abundance and 176 proteins lost time dependency. Among these, the collagen crosslinking enzymes lysyl oxidase-like 1 (LOXL1) and lysyl hydroxylase 1 (LH1; encoded by Plod2) were elevated and had lost time-dependent regulation. High-pressure chromatography confirmed elevated levels of hydroxylysine aldehyde (pyridinoline) crosslinking of collagen in CKO tendons. As a result, collagen-I was refractory to extraction. We also showed that CRISPR-Cas9 deletion of Mmp14 from cultured fibroblasts resulted in loss of circadian clock rhythmicity of period 2 (PER2), and recombinant MT1-MMP was highly effective at cleaving soluble collagen-I but less effective at cleaving collagen pre-assembled into fibrils. In conclusion, our study shows that circadian clock-regulated Mmp14 controls the rhythmic synthesis of small diameter collagen fibrils, regulates collagen crosslinking, and its absence disrupts the circadian clock and matrisome in tendon fibroblasts.
A partial human LCK defect causes a T cell immunodeficiency with intestinal inflammation.
Lymphocyte-specific protein tyrosine kinase (LCK) is essential for T cell antigen receptor (TCR)-mediated signal transduction. Here, we report two siblings homozygous for a novel LCK variant (c.1318C>T; P440S) characterized by T cell lymphopenia with skewed memory phenotype, infant-onset recurrent infections, failure to thrive, and protracted diarrhea. The patients' T cells show residual TCR signal transduction and proliferation following anti-CD3/CD28 and phytohemagglutinin (PHA) stimulation. We demonstrate in mouse models that complete (Lck-/-) versus partial (LckP440S/P440S) loss-of-function LCK causes disease with differing phenotypes. While both Lck-/- and LckP440S/P440S mice exhibit arrested thymic T cell development and profound T cell lymphopenia, only LckP440S/P440S mice show residual T cell proliferation, cytokine production, and intestinal inflammation. Furthermore, the intestinal disease in the LckP440S/P440S mice is prevented by CD4+ T cell depletion or regulatory T cell transfer. These findings demonstrate that P440S LCK spares sufficient T cell function to allow the maturation of some conventional T cells but not regulatory T cells-leading to intestinal inflammation.