Generalizable Denoising of Microscopy Images using Generative Adversarial Networks and Contrastive Learning

Microscopy images often suffer from high levels of noise, which can hinder further analysis and interpretation. Content-aware image restoration (CARE) methods have been proposed to address this issue, but they often require large amounts of training data and suffer from over-fitting. To overcome these challenges, we propose a novel framework for few-shot microscopy image denoising. Our approach combines a generative adversarial network (GAN) trained via contrastive learning (CL) with two structure preserving loss terms (Structural Similarity Index and Total Variation loss) to further improve the quality of the denoised images using little data. We demonstrate the effectiveness of our method on three well-known microscopy imaging datasets, and show that we can drastically reduce the amount of training data while retaining the quality of the denoising, thus alleviating the burden of acquiring paired data and enabling few-shot learning. The proposed framework can be easily extended to other image restoration tasks and has the potential to significantly advance the field of microscopy image analysis

Automatic classification of human facial features based on their appearance

[EN] Classification or typology systems used to categorize different human body parts have existed for many years. Nevertheless, there are very few taxonomies of facial features. Ergonomics, forensic anthropology, crime prevention or new human-machine interaction systems and online activities, like e-commerce, e-learning, games, dating or social networks, are fields in which classifications of facial features are useful, for example, to create digital interlocutors that optimize the interactions between human and machines. However, classifying isolated facial features is difficult for human observers. Previous works reported low inter-observer and intra-observer agreement in the evaluation of facial features. This work presents a computer-based procedure to automatically classify facial features based on their global appearance. This procedure deals with the difficulties associated with classifying features using judgements from human observers, and facilitates the development of taxonomies of facial features. Taxonomies obtained through this procedure are presented for eyes, mouths and noses.Fuentes-Hurtado, F.; Diego-Mas, JA.; Naranjo Ornedo, V.; Alcañiz Raya, ML. (2019). Automatic classification of human facial features based on their appearance. PLoS ONE. 14(1):1-20. https://doi.org/10.1371/journal.pone.0211314S120141Damasio, A. R. (1985). Prosopagnosia. Trends in Neurosciences, 8, 132-135. doi:10.1016/0166-2236(85)90051-7Bruce, V., & Young, A. (1986). Understanding face recognition. British Journal of Psychology, 77(3), 305-327. doi:10.1111/j.2044-8295.1986.tb02199.xTodorov, A. (2011). Evaluating Faces on Social Dimensions. Social Neuroscience, 54-76. doi:10.1093/acprof:oso/9780195316872.003.0004Little, A. C., Burriss, R. P., Jones, B. C., & Roberts, S. C. (2007). 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Is salinity the main ecologic factor that shapes the distribution of two endemic Mediterranean plant species of the genus Gypsophila?

The final publication is available at Springer via http://dx.doi.org/10.1007/s11104-014-2218-2Aims Responses to salt stress of two Gypsophila species that share territory, but with different ecological optima and distribution ranges, were analysed. G. struthium is a regionally dominant Iberian endemic gypsophyte, whereas G. tomentosa is a narrow endemic reported as halophyte. Theworking hypothesis is that salt tolerance shapes the presence of these species in their specific habitats. Methods Taking a multidisciplinary approach, we assessed the soil characteristics and vegetation structure at the sampling site, seed germination and seedling development, growth and flowering, synthesis of proline and cation accumulation under artificial conditions of increasing salt stress and effect of PEG on germination and seedling development. Results Soil salinity was low at the all sampling points where the two species grow, but moisture was higher in the area of G. tomentosa. Differences were found in the species salt and drought tolerance. The different parameters tested did not show a clear pattern indicating the main role of salt tolerance in plant distribution. Conclusions G. tomentosa cannot be considered a true halophyte as previously reported because it is unable to complete its life cycle under salinity. The presence of G. tomentosa in habitats bordering salt marshes is a strategy to avoid plant competition and extreme water stressSoriano, P.; Moruno Manchón, JF.; Boscaiu Neagu, MT.; Vicente Meana, Ó.; Hurtado, A.; Llinares Palacios, JV.; Estrelles, E. (2014). Is salinity the main ecologic factor that shapes the distribution of two endemic Mediterranean plant species of the genus Gypsophila?. Plant and Soil. 384(1-2):363-379. doi:10.1007/s11104-014-2218-2S3633793841-2Alonso MA (1996) Flora y vegetación del Valle de Villena (Alicante). 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Adaptation of the Wound Healing Questionnaire universal-reporter outcome measure for use in global surgery trials (TALON-1 study): mixed-methods study and Rasch analysis

BackgroundThe Bluebelle Wound Healing Questionnaire (WHQ) is a universal-reporter outcome measure developed in the UK for remote detection of surgical-site infection after abdominal surgery. This study aimed to explore cross-cultural equivalence, acceptability, and content validity of the WHQ for use across low- and middle-income countries, and to make recommendations for its adaptation.MethodsThis was a mixed-methods study within a trial (SWAT) embedded in an international randomized trial, conducted according to best practice guidelines, and co-produced with community and patient partners (TALON-1). Structured interviews and focus groups were used to gather data regarding cross-cultural, cross-contextual equivalence of the individual items and scale, and conduct a translatability assessment. Translation was completed into five languages in accordance with Mapi recommendations. Next, data from a prospective cohort (SWAT) were interpreted using Rasch analysis to explore scaling and measurement properties of the WHQ. Finally, qualitative and quantitative data were triangulated using a modified, exploratory, instrumental design model.ResultsIn the qualitative phase, 10 structured interviews and six focus groups took place with a total of 47 investigators across six countries. Themes related to comprehension, response mapping, retrieval, and judgement were identified with rich cross-cultural insights. In the quantitative phase, an exploratory Rasch model was fitted to data from 537 patients (369 excluding extremes). Owing to the number of extreme (floor) values, the overall level of power was low. The single WHQ scale satisfied tests of unidimensionality, indicating validity of the ordinal total WHQ score. There was significant overall model misfit of five items (5, 9, 14, 15, 16) and local dependency in 11 item pairs. The person separation index was estimated as 0.48 suggesting weak discrimination between classes, whereas Cronbach's α was high at 0.86. Triangulation of qualitative data with the Rasch analysis supported recommendations for cross-cultural adaptation of the WHQ items 1 (redness), 3 (clear fluid), 7 (deep wound opening), 10 (pain), 11 (fever), 15 (antibiotics), 16 (debridement), 18 (drainage), and 19 (reoperation). Changes to three item response categories (1, not at all; 2, a little; 3, a lot) were adopted for symptom items 1 to 10, and two categories (0, no; 1, yes) for item 11 (fever).ConclusionThis study made recommendations for cross-cultural adaptation of the WHQ for use in global surgical research and practice, using co-produced mixed-methods data from three continents. Translations are now available for implementation into remote wound assessment pathways

Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries

Background Anastomotic leak affects 8 per cent of patients after right colectomy with a 10-fold increased risk of postoperative death. The EAGLE study aimed to develop and test whether an international, standardized quality improvement intervention could reduce anastomotic leaks. Methods The internationally intended protocol, iteratively co-developed by a multistage Delphi process, comprised an online educational module introducing risk stratification, an intraoperative checklist, and harmonized surgical techniques. Clusters (hospital teams) were randomized to one of three arms with varied sequences of intervention/data collection by a derived stepped-wedge batch design (at least 18 hospital teams per batch). Patients were blinded to the study allocation. Low- and middle-income country enrolment was encouraged. The primary outcome (assessed by intention to treat) was anastomotic leak rate, and subgroup analyses by module completion (at least 80 per cent of surgeons, high engagement; less than 50 per cent, low engagement) were preplanned. Results A total 355 hospital teams registered, with 332 from 64 countries (39.2 per cent low and middle income) included in the final analysis. The online modules were completed by half of the surgeons (2143 of 4411). The primary analysis included 3039 of the 3268 patients recruited (206 patients had no anastomosis and 23 were lost to follow-up), with anastomotic leaks arising before and after the intervention in 10.1 and 9.6 per cent respectively (adjusted OR 0.87, 95 per cent c.i. 0.59 to 1.30; P = 0.498). The proportion of surgeons completing the educational modules was an influence: the leak rate decreased from 12.2 per cent (61 of 500) before intervention to 5.1 per cent (24 of 473) after intervention in high-engagement centres (adjusted OR 0.36, 0.20 to 0.64; P < 0.001), but this was not observed in low-engagement hospitals (8.3 per cent (59 of 714) and 13.8 per cent (61 of 443) respectively; adjusted OR 2.09, 1.31 to 3.31). Conclusion Completion of globally available digital training by engaged teams can alter anastomotic leak rates. Registration number: NCT04270721 (http://www.clinicaltrials.gov)

Search for CPCP violation in D0^0→\to KS0^0_\mathrm{S}KS0^0_\mathrm{S} decays in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceA search is reported for charge-parity D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ violation in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ decays, using data collected in proton-proton collisions at $\sqrt{s}$ = 13 TeV recorded by the CMS experiment in 2018. The analysis uses a dedicated data set that corresponds to an integrated luminosity of 41.6 fb$^{-1}$, which consists of about 10 billion events containing a pair of ẖadrons, nearly all of which decay to charm hadrons. The flavor of the neutral D meson is determined by the pion charge in the reconstructed decays D$^{*+}$$\to$ D$^0\pi^+$ and D$^{*-}$$\to$ D$^0\pi^-$. The D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ asymmetry in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ is measured to be $A_{CP}$( K$^0_\mathrm{S}$K$^0_\mathrm{S}$) = (6.2 $\pm$ 3.0 $\pm$ 0.2 $\pm$ 0.8)%, where the three uncertainties represent the statistical uncertainty, the systematic uncertainty, and the uncertainty in the measurement of the D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry in the D$^0$ $\to$ K$^0_\mathrm{S}\pi^+\pi^-$ decay. This is the first D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry measurement by CMS in the charm sector as well as the first to utilize a fully hadronic final state

Search for heavy neutral leptons in final states with electrons, muons, and hadronically decaying tau leptons in proton-proton collisions at s\sqrt{s} =13 TeV

International audienceA search for heavy neutral leptons (HNLs) of Majorana or Dirac type using proton-proton collision data at $\sqrt{s}$ =13 TeV is presented. The data were collected by the CMS experiment at the CERN LHC and correspond to an integrated luminosity of 138 fb$^{-1}$. Events with three charged leptons (electrons, muons, and hadronically decaying tau leptons) are selected, corresponding to HNL production in association with a charged lepton and decay of the HNL to two charged leptons and a standard model (SM) neutrino. The search is performed for HNL masses between 10 GeV and 1.5 TeV. No evidence for an HNL signal is observed in data. Upper limits at 95% confidence level are found for the squared coupling strength of the HNL to SM neutrinos, considering exclusive coupling of the HNL to a single SM neutrino generation, for both Majorana and Dirac HNLs. The limits exceed previously achieved experimental constraints for a wide range of HNL masses, and the limits on tau neutrino coupling scenarios with HNL masses above the W boson mass are presented for the first time

Search for the Z boson decay to ττμμ\tau\tau\mu\mu in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceThe first search for the Z boson decay to $\tau\tau\mu\mu$ at the CERN LHC is presented, based on data collected by the CMS experiment at the LHC in proton-proton collisions at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 138 fb$^{-1}$. The data are compatible with the predicted background. For the first time, an upper limit at the 95% confidence level of 6.9 times the standard model expectation is placed on the ratio of the Z $\to$ $\tau\tau\mu\mu$ to Z $\to$ 4$\mu$ branching fractions. Limits are also placed on the six flavor-conserving four-lepton effective-field-theory operators involving two muons and two tau leptons, for the first time testing all such operators

Searches for Higgs boson production through decays of heavy resonances

The discovery of the Higgs boson has led to new possible signatures for heavy resonance searches at the LHC. Since then, search channels including at least one Higgs boson plus another particle have formed an important part of the program of new physics searches. In this report, the status of these searches by the CMS Collaboration is reviewed. Searches are discussed for resonances decaying to two Higgs bosons, a Higgs and a vector boson, or a Higgs boson and another new resonance, with proton-proton collision data collected at $\sqrt{s}=$ 13 TeV in the years 2016-2018. A combination of the results of these searches is presented together with constraints on different beyond-the-standard model scenarios, including scenarios with extended Higgs sectors, heavy vector bosons and extra dimensions. Studies are shown for the first time by CMS on the validity of the narrow-width approximation in searches for the resonant production of a pair of Higgs bosons. The potential for a discovery at the High Luminosity LHC is also discussed.The discovery of the Higgs boson has led to new possible signatures for heavy resonance searches at the LHC. Since then, search channels including at least one Higgs boson plus another particle have formed an important part of the program of new physics searches. In this report, the status of these searches by the CMS Collaboration is reviewed. Searches are discussed for resonances decaying to two Higgs bosons, a Higgs and a vector boson, or a Higgs boson and another new resonance, with proton-proton collision data collected at $\sqrt{s}$ = 13 TeV in the years 2016-2018. A combination of the results of these searches is presented together with constraints on different beyond-the-standard model scenarios, including scenarios with extended Higgs sectors, heavy vector bosons and extra dimensions. Studies are shown for the first time by CMS on the validity of the narrow-width approximation in searches for the resonant production of a pair of Higgs bosons. The potential for a discovery at the High Luminosity LHC is also discussed