Assistance strategies for robotized laparoscopy

Robotizing laparoscopic surgery not only allows achieving better accuracy to operate when a scale factor is applied between master and slave or thanks to the use of tools with 3 DoF, which cannot be used in conventional manual surgery, but also due to additional informatic support. Relying on computer assistance different strategies that facilitate the task of the surgeon can be incorporated, either in the form of autonomous navigation or cooperative guidance, providing sensory or visual feedback, or introducing certain limitations of movements. This paper describes different ways of assistance aimed at improving the work capacity of the surgeon and achieving more safety for the patient, and the results obtained with the prototype developed at UPC.Peer ReviewedPostprint (author's final draft

Reaching a modular, domain-agnostic and containerized development in biomedical Natural Language Processing systems.

The last century saw an exponential increase in scientific publications in the biomedical domain. Despite the potential value of this knowledge; most of this data is only available as unstructured textual literature, which have limited their systematic access, use and exploitation. This limitation can be avoided, or at least mitigated, by relying on text mining techniques to automatically extract relevant data and structure it from textual documents. A significant challenge for scientific software applications, including Natural Language Processing (NLP) systems, consists in providing facilities to share, distribute and run such systems in a simple and convenient way. Software containers can host their own dependencies and auxiliary programs, isolating them from the execution environment. In addition, a workflow manager can be used for the automated orchestration and execution of the text mining pipelines. Our work is focused in the study and design of new techniques and approaches to construct, develop, validate and deploy NLP components and workflows with sufficient genericity, scalability and interoperability allowing their use and instantiation across different domains. The results and techniques acquired will be applied in two main uses cases: the detection of relevant information from preclinical toxicological reports, under the eTRANSAFE project [1]; and the indexation of biomaterials publications with relevant concepts as part as the DEBBIE project

Designing a cloud and HPC based M&S platform to Investigate the IVD diseases mechanisms

The main objective of the PhD proposal consists of the creation of a platform for IVD Models & Simulations (M&S) tools and their integration into automated workflows, within the HORIZON MSCA Disc4All project. Based on the European Open Science Cloud (EOSC) vision, the expected platform will be a Cloud-based one, furnished with a front-end, to guarantee reproducibility, accessibility and easy use for experts and non-experts. The development of an automated and specialized platform can represent the best hybrid technology with perks on both healthcare data management and computational environments exploitation, given the use of Cloud infrastructures on healthcare software and databases. Though rendering automatic not only the database, but prediction and simulation models in a user-friendly integrated system, may facilitate a difficult diagnosis and forward therapy, especially considering the various forces at play in a multi-omics data analysis of its kind

FAIRsoft - A practical implementation of FAIR principles for research software

Computational tools are increasingly becoming constitutive parts of scientific research, from experimentation and data collection to the dissemination and storage of results. Unfortunately, however, research software is not subjected to the same requirements as other methods of scientific research: being peer-reviewed, being reproducible and allowing one to build upon another’s work. This situation is detrimental to the integrity and advancement of scientific research, leading to computational methods frequently being impossible to reproduce and/or verify [1]. Moreover, they are often opaque, direcly unavailable or impossible to use by others [2]. One step to address this problem could be formulating a set of principles that research software should meet to ensure its quality and sustainability, resembling the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles [3]. The FAIR Data Principles were created to solve similar issues affecting scholarly data, namely great difficulty of sharing and accessibility, and are currently widely recognized accross fileds. We present here FAIRsoft, our initial effort to assess the quality of research software using a FAIR-like framework, as a first step towards its implementation in OpenEBench [4], the ELIXIR benchmarking platform

ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution

The authors thank the Hematopathology Collection registered at the Biobank of Hospital Clínic—Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) as well as Sílvia Martín for the technical support. This study was supported by the “la Caixa” Foundation (CLLEvolution-LCF/PR/HR17/52150017, Health Research 2017 Program HR17-00221, to EC), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (810287, BCLLatlas, to EC, and HH), CERCA Program/Generalitat de Catalunya, Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-1142 (to EC), CIBERONC (CB16/12/00225 to EC), Ministerio de Ciencia e Innovación PID2020-117185RB-I00 (to XSP), FEDER: European Regional Development Fund “Una manera de hacer Europa”, and Fundación Asociación Española Contra el Cáncer FUNCAR-PRYGN211258SUÁR (to XSP). The authors thankfully acknowledge the computer resources at MareNostrum4 and the technical support provided by Barcelona Supercomputing Center (RES activity BCV-2018-3-0001). FN acknowledge research support from the American Association for Cancer Research (2021 AACR-Amgen Fellowship in Clinical/Translational Cancer Research, Grant Number 21-40-11-NADE), the European Hematology Association (EHA Junior Research Grant 2021, Grant Number RG-202012-00245), and the Lady Tata Memorial Trust (International Award for Research in Leukemia 2021–2022, Grant Number LADY_TATA_21_3223). EC is an Academia Researcher of the “Institució Catalana de Recerca i Estudis Avançats” (ICREA) of the Generalitat de Catalunya. This work was partially developed at the Centre Esther Koplowitz (CEK, Barcelona, Spain).Peer Reviewed"Article signat per 11 autors/es: Romina Royo, Laura Magnano, Julio Delgado, Sara Ruiz-Gil, Josep Ll. Gelpí, Holger Heyn, Malcom A. Taylor, Tatjana Stankovic, Xose S. Puente, Ferran Nadeu & Elías Campo"Postprint (published version

jmpegg 1.0 – the pure java implementation of the MPEG-G ISO/IEC 23092 standard

jmpegg library provides MPEG-G files encoding/decoding features. The library is written in a pure java language without external dependencies. The library also supports conversion between MPEG-G and well-known genomic formats.High-throughput sequencing technologies consistently produce overwhelming amount of genomic data. This data is extremely important for the biomedical research and has an enormous impact on the progress in healthcare system. Considering the amount of generated sequencing data, data storage capacity became the principal concern for organizations like European Genome-phenome Archive (EGA) or Database of Genotypes and Phenotypes (dbGaP). The efficient and standard storage format is an important part of forging interoperability between different organizations. Several global initiatives such as ELIXIR and GA4GH already established the strategic partnership in standardization of genomic data formats andAPIs. On the other hand, other initiatives to provide a secure and efficient compressed format have appeared, such as MPEG-G (ISO/IEC 23092), developed by the MPEG working group of ISO (ISO/IEC JTC1 SC29/WG11). MPEG-G, also supported by ISO/TC 276 on Biotechnology, is making efforts for a better alignment and integration with approaches taken by other initiatives such as GA4GH.Postprint (published version

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based plartform for biomolecular simulations.

We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users' own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users' projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs

Decreased kidney graft survival in low immunological risk patients showing inflammation in normal protocol biopsies

Introduction The pros and cons for implementing protocol biopsies (PB) after kidney transplantation are still a matter of debate. We aimed to address the frequency of pathological findings in PB, to analyze their impact on long-term graft survival (GS) and to analyze the risk factors predicting an abnormal histology. Methods We analyzed 946 kidney PB obtained at a median time of 6.5 (±2.9) months after transplantation. Statistics included comparison between groups, Kaplan-Meier and multinomial logistic regression analysis. Results and Discussion PB diagnosis were: 53.4% normal; 46% IFTA; 12.3% borderline and 4.9% had subclinical acute rejection (SCAR). Inflammation had the strongest negative impact on GS. Therefore we split the cases into: "normal without inflammation", "normal with inflammation", "IFTA without inflammation", "IFTA with inflammation" and "rejection" (including SCAR and borderline). 15-year GS in PB diagnosed normal with inflammation was significantly decreased in a similar fashion as in rejection cases. Among normal biopsies, inflammation increased significantly the risk of 15-y graft loss (P = 0.01). Variables that predicted an abnormal biopsy were proteinuria, previous AR and DR-mismatch. Conclusion We conclude that inflammation in normal PB is associated with a significantly lower 15-y GS, comparable to rejection or IFTA with inflammation

Acute renal failure induced by acute interstitial nephritis secondary to cocaine

Document publicat també en castellàCocaine has been used by 2.6% of the Spanish population aged between 15 and 64 at some point in their life, making it one of the most consumed illegal drugs after cannabis.1 Cocaine use is associated with multiple complications: neurological, cardiovascular, psychiatric, pulmonary, gastrointestinal and nephrological. Renal complications associated with cocaine use have received little attention, despite the existence of several mechanisms, in addition to secondary high blood pressure, that can cause acute renal failure (ARF) or worsen a pre-existing case of chronic renal failure. Drug-induced acute interstitial nephritis (DIAIN) represents a high percentage of acute renal failure in clinical practice. Some studies indicate that DIAIN is the lesion responsible for renal failure in about 15% of biopsies with ARF. Furthermore, in many cases of DIAIN, no biopsy is performed and diagnosis is based on clinical data and recent administration of a new drug which, as described below, is sometimes not very easy to identify

Vision based robot assistance in TTTS fetal surgery

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.This paper presents an accurate and robust tracking vision algorithm for Fetoscopic Laser Photo-coagulation (FLP) surgery for Twin-Twin Transfusion Syndrome (TTTS). The aim of the proposed method is to assist surgeons during anastomosis localization, coagulation and review using a tele-operated robotic system. The algorithm computes the relative position of the fetoscope tool tip with respect to the placenta, via local vascular structure registration.The algorithm uses image features (local superficial vascular structures of the placenta’s surface) to automatically match consecutive fetoscopic images. It is composed of three sequential steps: image processing (filtering, binarization and vascular structures segmentation); relevant Points Of Interest (POIs) seletion; and image registration between consecutive images.The algorithm has to deal with the low quality of fetoscopic images, the liquid and dirty environment inside the placenta jointly with the thin diameter of the fetoscope optics and low amount of environment light reduces the image quality. The obtained images are blurred, noisy and with very poor color components.The tracking system has been tested using real video sequences of FLP surgery for TTTS. The computational performance enables real time tracking, locally guiding the robot over the placenta’s surface with enough accuracy.Peer ReviewedPostprint (author's final draft