Linking Theory and Practice of Digital Libraries
26th International Conference on Theory and Practice of Digital Libraries, TPDL 2022, Padua, Italy, September 20–23, 2022, Proceedings
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Article
Open AccessA distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche
Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2–5. Hi...
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Article
Open AccessMicrobial composition associated with biliary stents in patients undergoing pancreatic resection for cancer
Malignant bile duct obstruction is typically treated by biliary stenting, which however increases the risk of bacterial infections. Here, we analyzed the microbial content of the biliary stents from 56 patient...
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Article
Open AccessLongitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma
Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut m...
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Article
Open AccessInfluence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial
Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its crede...
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Article
Open AccessFavorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases
We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently...
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Article
Open AccessData management plans as linked open data: exploiting ARGOS FAIR and machine actionable outputs in the OpenAIRE research graph
Open Science Graphs (OSGs) are scientific knowledge graphs representing different entities of the research lifecycle (e.g. projects, people, research outcomes, institutions) and the relationships among them. T...
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Article
Open AccessExtending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information f...
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Article
Open AccessThe person-to-person transmission landscape of the gut and oral microbiomes
The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of th...
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Chapter and Conference Paper
A Graph Neural Network Approach for Evaluating Correctness of Groups of Duplicates
Unlabeled entity deduplication is a relevant task already studied in the recent literature. Most methods can be traced back to the following workflow: entity blocking phase, in-block pairwise comparisons betwe...
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Chapter and Conference Paper
Tracing Data Footprints: Formal and Informal Data Citations in the Scientific Literature
Data citation has become a prevalent practice within the scientific community, serving the purpose of facilitating data discovery, reproducibility, and credit attribution. Consequently, data has gained signifi...
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Chapter and Conference Paper
A Primer on Open Science-Driven Repository Platforms
Following Open Science mandates, institutions and communities increasingly demand repositories with native support for publishing scientific literature together with research data, software, and other research...
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Article
Open AccessNAVIGATOR: an Italian regional imaging biobank to promote precision medicine for oncologic patients
NAVIGATOR is an Italian regional project boosting precision medicine in oncology with the aim of making it more predictive, preventive, and personalised by advancing translational research based on quantitativ...
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Article
Open AccessVariability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases
Fecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides difficile infection and is considered a promising treatment for other microbiome-related disorders, but a comprehensive ...
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Article
Open AccessCross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linke...
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Chapter and Conference Paper
“Knock Knock! Who’s There?” A Study on Scholarly Repositories’ Availability
Scholarly repositories are the cornerstone of modern open science, and their availability is vital for enacting its practices. To this end, scholarly registries such as FAIRsharing, re3data, OpenDOAR and ROAR ...
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Book and Conference Proceedings
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Article
Open AccessMetagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding o...
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Article
Open AccessGenomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Des...
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Article
Open AccessA workflow language for research e-infrastructures
Research e-infrastructures are “systems of systems,” patchworks of resources such as tools and services, which change over time to address the evolving needs of the scientific process. In such environments, re...
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Article
Open AccessData science: a game changer for science and innovation
This paper shows data science’s potential for disruptive innovation in science, industry, policy, and people’s lives. We present how data science impacts science and society at large in the coming years, inclu...
