Method for coregistration of optical measurements of breast tissue with histopathology : the importance of accounting for tissue deformations

For the validation of optical diagnostic technologies, experimental results need to be benchmarked against the gold standard. Currently, the gold standard for tissue characterization is assessment of hematoxylin and eosin (H&E)-stained sections by a pathologist. When processing tissue into H&E sections, the shape of the tissue deforms with respect to the initial shape when it was optically measured. We demonstrate the importance of accounting for these tissue deformations when correlating optical measurement with routinely acquired histopathology. We propose a method to register the tissue in the H&E sections to the optical measurements, which corrects for these tissue deformations. We compare the registered H&E sections to H&E sections that were registered with an algorithm that does not account for tissue deformations by evaluating both the shape and the composition of the tissue and using microcomputer tomography data as an independent measure. The proposed method, which did account for tissue deformations, was more accurate than the method that did not account for tissue deformations. These results emphasize the need for a registration method that accounts for tissue deformations, such as the method presented in this study, which can aid in validating optical techniques for clinical use. (C) The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License

Definition of large bowel obstruction by primary colorectal cancer:A systematic review

Aim: Controversies on therapeutic strategy for large bowel obstruction by primary colorectal cancer mainly concern acute conditions, being essentially different from subacute obstruction. Clearly defining acute obstruction is important for design and interpretation of studies as well as for guidelines and daily practice. This systematic review aimed to evaluate definitions of obstruction by colorectal cancer in prospective studies. Method: A systematic search was performed in PubMed, Embase and the Cochrane Library. Eligibility criteria included randomized or prospective observational design, publication between 2000 and 2019, and the inclusion of patients with an obstruction caused by colorectal cancer. Provided definitions of obstruction were extracted with assessment of common elements. Results: A total of 16 randomized controlled trials (RCTs) and 99 prospective observational studies were included. Obstruction was specified as acute in 28 studies, complete/emergency in five, (sub)acute or similar terms in four and unspecified in 78. Five of 16 RCTs (31%) and 37 of 99 cohort studies (37%) provided a definition. The definitions included any combination of clinical symptoms, physical signs, endoscopic features and radiological imaging findings in 25 studies. The definition was only based on clinical symptoms in 11 and radiological imaging in six studies. Definitions included a radiological component in 100% of evaluable RCTs (5/5) vs. 54% of prospective observational studies (20/37, P = 0.07). Conclusion: In this systematic review, the majority of prospective studies did not define obstruction by colorectal cancer and its urgency, whereas provided definitions varied hugely. Radiological confirmation seems to be an essential component in defining acute obstruction

Statistical Model Checking for Product Lines

International audienceWe report on the suitability of statistical model checking forthe analysis of quantitative properties of product line models by an extendedtreatment of earlier work by the authors. The type of analysis thatcan be performed includes the likelihood of specific product behaviour,the expected average cost of products (in terms of the attributes of theproducts’ features) and the probability of features to be (un)installed atruntime. The product lines must be modelled in QFLan, which extendsthe probabilistic feature-oriented language PFLan with novel quantitativeconstraints among features and on behaviour and with advancedfeature installation options. QFLan is a rich process-algebraic specifi-cation language whose operational behaviour interacts with a store ofconstraints, neatly separating product configuration from product behaviour.The resulting probabilistic configurations and probabilistic behaviourconverge in a discrete-time Markov chain semantics, enablingthe analysis of quantitative properties. Technically, a Maude implementationof QFLan, integrated with Microsoft’s SMT constraint solver Z3,is combined with the distributed statistical model checker MultiVeStA,developed by one of the authors. We illustrate the feasibility of our frameworkby applying it to a case study of a product line of bikes

DC-electric-field-induced and low-frequency electromodulation second-harmonic generation spectroscopy of Si(001)-SiO2_2 interfaces

The mechanism of DC-Electric-Field-Induced Second-Harmonic (EFISH) generation at weakly nonlinear buried Si(001)-SiO$_2$ interfaces is studied experimentally in planar Si(001)-SiO$_2$-Cr MOS structures by optical second-harmonic generation (SHG) spectroscopy with a tunable Ti:sapphire femtosecond laser. The spectral dependence of the EFISH contribution near the direct two-photon $E_1$ transition of silicon is extracted. A systematic phenomenological model of the EFISH phenomenon, including a detailed description of the space charge region (SCR) at the semiconductor-dielectric interface in accumulation, depletion, and inversion regimes, has been developed. The influence of surface quantization effects, interface states, charge traps in the oxide layer, doping concentration and oxide thickness on nonlocal screening of the DC-electric field and on breaking of inversion symmetry in the SCR is considered. The model describes EFISH generation in the SCR using a Green function formalism which takes into account all retardation and absorption effects of the fundamental and second harmonic (SH) waves, optical interference between field-dependent and field-independent contributions to the SH field and multiple reflection interference in the SiO$_2$ layer. Good agreement between the phenomenological model and our recent and new EFISH spectroscopic results is demonstrated. Finally, low-frequency electromodulated EFISH is demonstrated as a useful differential spectroscopic technique for studies of the Si-SiO$_2$ interface in silicon-based MOS structures.Comment: 31 pages, 14 figures, 1 table, figures are also available at http://kali.ilc.msu.su/articles/50/efish.ht

Neurodevelopmental outcome at 5.5 years in Dutch preterm infants born at 24-26 weeks' gestational age: the EPI-DAF study

Objective After lowering the Dutch threshold for active treatment from 25 to 24 completed weeks' gestation, survival to discharge increased by 10% in extremely preterm live born infants. Now that this guideline has been implemented, an accurate description of neurodevelopmental outcome at school age is needed.Design Population-based cohort study.Setting All neonatal intensive care units in the Netherlands.Patients All infants born between 24(0/7) and 26(6/7 )weeks' gestation who were 5.5 years' corrected age (CA) in 2018-2020 were included.Main outcome measures Main outcome measure was neurodevelopmental outcome at 5.5 years. Neurodevelopmental outcome was a composite outcome defined as none, mild or moderate-to-severe impairment (further defined as neurodevelopmental impairment (NDI)), using corrected cognitive score (Wechsler Preschool and Primary Scale of Intelligence Scale-III-NL), neurological examination and neurosensory function. Additionally, motor score (Movement Assessment Battery for Children-2-NL) was assessed. All assessments were done as part of the nationwide, standardised follow-up programme.Results In the 3-year period, a total of 632 infants survived to 5.5 years' CA. Data were available for 484 infants (77%). At 5.5 years' CA, most cognitive and motor (sub)scales were significantly lower compared with the normative mean. Overall, 46% had no impairment, 36% had mild impairment and 18% had NDI. NDI-free survival was 30%, 49% and 67% in live born children at 24, 25 and 26 weeks' gestation, respectively (pDevelopmen

Preoperative image-guided identification of response to neoadjuvant chemoradiotherapy in esophageal cancer (PRIDE):a multicenter observational study

BACKGROUND: Nearly one third of patients undergoing neoadjuvant chemoradiotherapy (nCRT) for locally advanced esophageal cancer have a pathologic complete response (pCR) of the primary tumor upon histopathological evaluation of the resection specimen. The primary aim of this study is to develop a model that predicts the probability of pCR to nCRT in esophageal cancer, based on diffusion-weighted magnetic resonance imaging (DW-MRI), dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and (18)F-fluorodeoxyglucose positron emission tomography with computed tomography ((18)F-FDG PET-CT). Accurate response prediction could lead to a patient-tailored approach with omission of surgery in the future in case of predicted pCR or additional neoadjuvant treatment in case of non-pCR. METHODS: The PRIDE study is a prospective, single arm, observational multicenter study designed to develop a multimodal prediction model for histopathological response to nCRT for esophageal cancer. A total of 200 patients with locally advanced esophageal cancer - of which at least 130 patients with adenocarcinoma and at least 61 patients with squamous cell carcinoma - scheduled to receive nCRT followed by esophagectomy will be included. The primary modalities to be incorporated in the prediction model are quantitative parameters derived from MRI and (18)F-FDG PET-CT scans, which will be acquired at fixed intervals before, during and after nCRT. Secondary modalities include blood samples for analysis of the presence of circulating tumor DNA (ctDNA) at 3 time-points (before, during and after nCRT), and an endoscopy with (random) bite-on-bite biopsies of the primary tumor site and other suspected lesions in the esophagus as well as an endoscopic ultrasonography (EUS) with fine needle aspiration of suspected lymph nodes after finishing nCRT. The main study endpoint is the performance of the model for pCR prediction. Secondary endpoints include progression-free and overall survival. DISCUSSION: If the multimodal PRIDE concept provides high predictive performance for pCR, the results of this study will play an important role in accurate identification of esophageal cancer patients with a pCR to nCRT. These patients might benefit from a patient-tailored approach with omission of surgery in the future. Vice versa, patients with non-pCR might benefit from additional neoadjuvant treatment, or ineffective therapy could be stopped. TRIAL REGISTRATION: The article reports on a health care intervention on human participants and was prospectively registered on March 22, 2018 under ClinicalTrials.gov Identifier: NCT03474341

Partially distributed coordination with Reo and constraint automata

Algorithms and the Foundations of Software technolog

Sensoria Patterns: Augmenting Service Engineering with Formal Analysis, Transformation and Dynamicity

The IST-FET Integrated Project Sensoria is developing a novel comprehensive approach to the engineering of service-oriented software systems where foundational theories, techniques and methods are fully integrated into pragmatic software engineering processes. The techniques and tools of Sensoria encompass the whole software development cycle, from business and architectural design, to quantitative and qualitative analysis of system properties, and to transformation and code generation. The Sensoria approach takes also into account reconfiguration of service-oriented architectures (SOAs) and re-engineering of legacy systems. In this paper we give first a short overview of Sensoria and then present a pattern language for augmenting service engineering with formal analysis, transformation and dynamicity. The patterns are designed to help software developers choose appropriate tools and techniques to develop service-oriented systems with support from formal methods. They support the whole development process, from the modelling stage to deployment activities and give an overview of many of the research areas pursued in the Sensoria project

The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε

Replication fork stalling and accumulation of single-stranded DNA trigger the S phase checkpoint, a signalling cascade that, in budding yeast, leads to the activation of the Rad53 kinase. Rad53 is essential in maintaining cell viability, but its targets of regulation are still partially unknown. Here we show that Rad53 drives the hyper-SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε, principally following replication forks stalling induced by nucleotide depletion. Pol2 is the main target of SUMOylation within the replisome and its modification requires the SUMO-ligase Mms21, a subunit of the Smc5/6 complex. Moreover, the Smc5/6 complex co-purifies with Pol ε, independently of other replisome components. Finally, we map Pol2 SUMOylation to a single site within the N-terminal catalytic domain and identify a SUMO-interacting motif at the C-terminus of Pol2. These data suggest that the S phase checkpoint regulate Pol ε during replication stress through Pol2 SUMOylation and SUMO-binding abilit