<i>Active</i> provenance for Data-Intensive workflows: engaging users and developers

We present a practical approach for provenance capturing in Data-Intensive workflow systems. It provides contextualisation by recording injected domain metadata with the provenance stream. It offers control over lineage precision, combining automation with specified adaptations. We address provenance tasks such as extraction of domain metadata, injection of custom annotations, accuracy and integration of records from multiple independent workflows running in distributed contexts. To allow such flexibility, we introduce the concepts of programmable Provenance Types and Provenance Configuration.Provenance Types handle domain contextualisation and allow developers to model lineage patterns by re-defining API methods, composing easy-to-use extensions. Provenance Configuration, instead, enables users of a Data-Intensive workflow execution to prepare it for provenance capture, by configuring the attribution of Provenance Types to components and by specifying grouping into semantic clusters. This enables better searches over the lineage records. Provenance Types and Provenance Configuration are demonstrated in a system being used by computational seismologists. It is based on an extended provenance model, S-PROV.PublishedSan Diego (CA, USA)3IT. Calcolo scientific

Comprehensible Control for Researchers and Developers facing Data Challenges

The DARE platform enables researchers and their developers to exploit more capabilities to handle complexity and scale in data, computation and collaboration. Today’s challenges pose increasing and urgent demands for this combination of capabilities. To meet technical, economic and governance constraints, application communities must use use shared digital infrastructure principally via virtualisation and mapping. This requires precise abstractions that retain their meaning while their implementations and infrastructures change. Giving specialists direct control over these capabilities with detail relevant to each discipline is necessary for adoption. Research agility, improved power and retained return on intellectual investment incentivise that adoption. We report on an architecture for establishing and sustaining the necessary optimised mappings and early evaluations of its feasibility with two application communities.PublishedSan Diego (CA, USA)3IT. Calcolo scientific

Identifying the factors that influence surgeon's compliance with excisional margins of non-melanoma skin cancer

The rising incidence of Non Melanoma Skin Cancers (NMSC) leads to a high number of surgical procedures worldwide. The strict compliance with international guidelines with regard to excisional margins may help decrease the number of re-excision procedures and reduce the risk of NMSC recurrence. The aim of this study was to investigate the prevalence of excisional margins as recommended by the European Academy of Dermatology and Venereology (EADV) and the European Dermatology Forum (EDF) guidelines, and the factors (demographic or clinical) that influence surgeons' compliance with these guidelines.This was a prevalence study looking at surgical excisions of NMSCs performed over a period of 2 years (2011-2012). A sample size of 1669 patients was considered. Definition of excisional margins recommended by the international guidelines (EADV and EDF) were used as point of reference for the analysis. Tumor and histologic specimen size were calculated ex vivo by 5 different pathologists. The size of skin specimens was measured with a major axis and a minor axis. The same was done for the tumor present on the skin specimens. The differences between the major and minor axes of surgical specimen and tumor were calculated. These differences were subsequently divided by two, hypothesizing that the lesion had the same distance from the margins of the surgical specimen. The differences obtained were named "Delta", the formulas applied being the following: Delta major = (major axis specimen-major axis tumor)/2; Delta minor = (minor axis specimen -minor axis tumor)/2.Results show a significant statistical difference, associated with factors such as: Age of the patient, anatomical localization of the tumor, histological diagnosis, and surgeons' experience.The identification of these factors sheds light on clinicians' practice and decision-making regarding excisional margins. Hopefully a higher level of adherence to the guidelines can be achieved in the future

Forward and adjoint simulations of seismic wave propagation on fully unstructured hexahedral meshes

We present forward and adjoint spectral-element simulations of coupled acoustic and (an)elastic seismic wave propagation on fully unstructured hexahedral meshes. Simulations benefit from recent advances in hexahedral meshing, load balancing and software optimization. Meshing may be accomplished using a mesh generation tool kit such as CUBIT, and load balancing is facilitated by graph partitioning based on the SCOTCH library. Coupling between fluid and solid regions is incorporated in a straightforward fashion using domain decomposition. Topography, bathymetry and Moho undulations may be readily included in the mesh, and physical dispersion and attenuation associated with anelasticity are accounted for using a series of standard linear solids. Finite-frequency Fréchet derivatives are calculated using adjoint methods in both fluid and solid domains. The software is benchmarked for a layercake model. We present various examples of fully unstructured meshes, snapshots of wavefields and finite-frequency kernels generated by Version 2.0 ‘Sesame' of our widely used open source spectral-element package SPECFEM3

Changing in the post-surgery infective complications following the shortening of the antibiotic prophylaxis in the patients undergoing skin dermal substitutes reconstruction

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue, both in massive deep burns, extensive full-thickness wounds, and reconstruction after cancer resection. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material &amp; Methods: Infective complications at the site of SDS were compared in two groups of patients: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a &gt;24h-antibiotic prophylaxis, and subjects undergoing surgical reconstruction between May 2016 and June 2017 (PERIOD B) who received a ≤24h-antibiotic prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Univariate linear regression analysis was performed to evaluate the risk factors for infection (sex, age, ASA code, perioperative antibiotic prophylaxis, site of SDS intervention, type of SDS, dimensions of surgical area, chronic renal impairment, and diabetes mellitus). Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The 66.4% (n=77) of the study population was male, and the mean age was 73 years (22-92 years). Seventy-eight patients (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were former or current smokers, and 45 (38.8%) had an ASA code ≥3. In the 94.8% of the patients (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the arm or the hand in 9 (7.8%), the leg in 12 (10.3%) and the foot in 12 (10.3%). Among 116 patients undergoing SDS surgical reconstruction, 62 (53.4%) received a &gt;24h-prophylaxis and 54 (46.6%) received a ≤24h-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limb/foot had higher infection rate in comparison with those undergoing SDS reconstruction in chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received &gt;24h or ≤24h-antibiotic prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. No significant differences in pathogen prevalence were found (p=0.692). Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed to reduce of 6 days-per-patient the antibiotic exposure

DARE: A Reflective Platform Designed to Enable Agile Data-Driven Research on the Cloud

The DARE platform has been designed to help research developers deliver user-facing applications and solutions over diverse underlying e-infrastructures, data and computational contexts. The platform is Cloud-ready, and relies on the exposure of APIs, which are suitable for raising the abstraction level and hiding complexity. At its core, the platform implements the cataloguing and execution of fine-grained and Python-based dispel4py workflows as services. Reflection is achieved via a logical knowledge base, comprising multiple internal catalogues, registries and semantics, while it supports persistent and pervasive data provenance. This paper presents design and implementation aspects of the DARE platform, as well as it provides directions for future development.PublishedSan Diego (CA, USA)3IT. Calcolo scientific

Infective complications in patients undergoing surgical reconstruction with dermal matrix: the Modena experience

Background: Bioengineered skin dermal substitutes (SDS) represent a novel therapeutic opportunity for restoring damaged tissue1,2,3. Antimicrobial prophylaxis duration in such procedures has not been well established yet. The aim of the study was to evaluate the changing of infective complications following shortening of perioperative prophylaxis in patients undergoing surgical reconstruction with SDS. Material &amp; Methods: Infective complications at the site of SDS were compared in 2 groups: subjects undergoing surgical reconstruction between September 2014 and January 2016 (PERIOD A) who received a &gt;24H-antibiotic-prophylaxis, and between May 2016 and June 2017 (PERIOD B) who received a ≤24H-antibiotic-prophylaxis. Differences in the incidence of infection and pathogen prevalence were explored. Results: Between September 2014 and June 2017, 116 patients underwent a surgical reconstruction with a SDS. The mean age was 73-years, 77 were male (66.4%), 78 (67.2%) were positive for hypertension, 20 (17.2%) for diabetes mellitus, 16 (13.8%) for chronic renal impairment, 22 (19%) were smokers, and 45 (38.8%) had an ASA score ≥3. In the 94.8% (n=110) the reason of surgical intervention was a skin cancer. Surgical SDS reconstruction involved the scalp in 44 cases (37.9%), the face in 28 (24.1%), the chest in 11 (9.5%), the limbs in 33 (28.5%). Among 116 patients, 62 (53.4%) received &gt;24H-antibiotic and 54 (46.6%) ≤24H-antibiotic-prophylaxis. The average duration of prophylaxis in the 2 groups of patients was 6.6 days and 0.5 day, respectively. Overall incidence rate of infection was 20.7% (24/116). The most frequently isolated pathogen was S. aureus (41.6%), followed by P. aeruginosa (29.1%), P. mirabilis (8.3%), and E. faecalis (4.1%). Patients undergoing SDS reconstruction in limbs had higher infection rate in comparison with chest/head (33.3% and 15.6%, respectively; p=0.034). No differences in the infection rate were observed between the patients who received &gt;24H or ≤24H-antibiotic-prophylaxis (22.5% and 18.5%, respectively; p=0.590). The two groups resulted similar for gender, age, comorbidities, ASA score, and type of skin cancer. Discussion: As far as we know, this is the first study that compared two perioperative antibiotic prophylaxis regimes in patients undergoing SDS reconstruction. Comparing the two patient groups (≤24-hour and &gt;24-hour prophylaxis), no differences in the rate of infection were found. The result is very important: it shows that prolongation of prophylaxis in this type of surgical patients does not reduce the rate of infection. Shortening of antibiotic prophylaxis allowed to reduce of 6 days-per-patient the antibiotic exposure. It was surprising that only the reconstruction of the limbs, in comparison with other sites, was associated with a higher risk of infection (33.3 and 15.7 respectively). Nor the most critical patients (with an ASA score ≥3), nor patients undergoing major surgical reconstructions (surgical area &gt;60 cm2) resulted associated with a higher risk. Conclusion: Antibiotic prophylaxis reduction to 24 hours or less demonstrated to be beneficial to patients undergoing surgical reconstruction with SDS. Shortening of antibiotic prophylaxis did not increase infection rate, and it allowed a reduction of 6 days-per-patient the antibiotic exposure. Randomized and controlled trials, with greater population, could give a more accurate response on the duration of antibiotic prophylaxis in patients undergoing surgical SDS reconstruction

dispel4py: An Open Source Python Framework for Encoding, Mapping and Reusing Seismic Continuous Data Streams: Intensive Analysis and Data Mining

Scientific workflows are needed by many scientific communities, such as seismology, as they enable easy composition and execution of applications, enabling scientists to focus on their research without being distracted by arranging computation and data management. However, there are challenges to be addressed. In many systems users have to adapt their codes and data movement as they change from one HPC-architecture to another. They still need to be aware of the computing architectures available for achieving the best application performance. We present dispel4py, an open-source framework presented as a Python library for encoding and automating data-intensive scientific methods as a graph of operations coupled together by data-streams. It enables scientists to develop and experiment with their own data-intensive applications using their familiar work environment. These are then automatically mapped to a variety of HPC-architectures, i.e., MPI, multiprocessing, Storm and Spark frameworks, increasing the chances to reuse their applications in different computing resources. dispel4py comes with data provenance, as shown in the screenshot, and with an information registry that can be accessed transparently from within workflows. dispel4py has been enhanced with a new run-time adaptive compression strategy to reduce the data stream volume and a diagnostic tool which monitors workflow performance and computes the most efficient parallelisation to use. dispel4py has been used by seismologists in the project VERCE for seismic ambient noise cross-correlation applications and for orchestrated HPC wave simulation and data misfit analysis workflows; two data-intensive problems that are common in today's research practice. Both have been tested in several local computing resources and later submitted to a variety of European PRACE HPC-architectures (e.g. SuperMUC &amp; CINECA) for longer runs without change. Results show that dispel4py is an easy tool for developing, sharing and reusing data-intensive scientific methods