Interpretable Medical Image Classification using Prototype Learning and Privileged Information

Interpretability is often an essential requirement in medical imaging. Advanced deep learning methods are required to address this need for explainability and high performance. In this work, we investigate whether additional information available during the training process can be used to create an understandable and powerful model. We propose an innovative solution called Proto-Caps that leverages the benefits of capsule networks, prototype learning and the use of privileged information. Evaluating the proposed solution on the LIDC-IDRI dataset shows that it combines increased interpretability with above state-of-the-art prediction performance. Compared to the explainable baseline model, our method achieves more than 6 % higher accuracy in predicting both malignancy (93.0 %) and mean characteristic features of lung nodules. Simultaneously, the model provides case-based reasoning with prototype representations that allow visual validation of radiologist-defined attributes.Comment: MICCAI 2023 Medical Image Computing and Computer Assisted Interventio

Trends in the start of the wet season over Africa

A quarter of a century of daily rainfall data from the Global Telecommunications System are used to define the temporal and spatial variability of the start of the wet season over Africa and surrounding extreme south of Europe and parts of the Middle East. From 1978 to 2002, the start of the wet season arrived later in the year for the majority of the region, as time progressed. In some parts of the continent, there was an annual increase in the start date of up to 4 days per year. On average, the start of the wet season arrived 9–21 days later from 1978 to 2002, depending on the threshold used to define the start of the rains (varying from 10–30 mm over 2 days, with no dry period in the following 10 days). It is noted that the inter-annual variability of the start of the wet season is high with the range of start dates varying on average from 116 to 142 days dependent on the threshold used to determine the start date. These results may have important implications for agriculturists on all levels (from the individual farmer to those responsible for regional food supply), as knowledge of potential future climate changes starts to play an increasingly important role in the agricultural decision-making process, such as sowing and harvesting times

Formaldehyde (HCHO) in air, snow and interstitial air at Concordia (East Antarctic plateau) in summer

During the 2011/12 and 2012/13 austral summers, HCHO was investigated for the first time in ambient air, snow, and interstitial air at the Concordia site, located near Dome C on the East Antarctic Plateau, by deploying an Aerolaser AL-4021 analyzer. Snow emission fluxes were estimated from vertical gradients of mixing ratios observed at 1 cm and 1 m above the snow surface as well as in interstitial air a few centimeters below the surface and in air just above the snowpack. Typical flux values range between 1 and 2 × 1012 molecules m−2 s−1 at night and 3 and 5 × 1012 molecules m−2 s−1 at noon. Shading experiments suggest that the photochemical HCHO production in the snowpack at Concordia remains negligible compared to temperature-driven air–snow exchanges. At 1 m above the snow surface, the observed mean mixing ratio of 130 pptv and its diurnal cycle characterized by a slight decrease around noon are quite well reproduced by 1-D simulations that include snow emissions and gas-phase methane oxidation chemistry. Simulations indicate that the gas-phase production from CH4 oxidation largely contributes (66%) to the observed HCHO mixing ratios. In addition, HCHO snow emissions account for ~ 30% at night and ~ 10% at noon to the observed HCHO levels

Characterization of the boundary layer at Dome C (East Antarctica) during the OPALE summer campaign

The regional climate model MAR was run for the region of Dome C located on the East Antarctic plateau, during Antarctic summer 2011–2012, in order to refine our understanding of meteorological conditions during the OPALE observation campaign. A very high vertical resolution is set up in the lower troposphere, with a grid spacing of roughly 2 m. Comparisons are made with observed temperatures and winds near the surface and from a 45 m high tower as well as sodar and radiation data. MAR is generally in very good agreement with the observations but sometimes underestimates cloud formation, leading to an underestimation of the simulated downward long-wave radiation. Absorbed short-wave radiation may also be slightly overestimated due to an underestimation of the snow albedo and this influences the surface energy budget and atmospheric turbulence. Nevertheless the model provides sufficiently reliable information that represent key parameters when discussing the representativeness of chemical measurements made nearby the ground surface during field campaigns conducted at the Concordia site located at Dome C (3233 m a.s.l.)

Important role of the mid-tropospheric atmospheric circulation in the recent surface melt increase over the Greenland ice sheet [brief communication]

Since 2007, there has been a series of surface melt records over the Greenland ice sheet (GrIS), continuing the trend towards increased melt observed since the end of the 1990's. The last two decades are characterized by an increase of negative phases of the North Atlantic Oscillation (NAO) favouring warmer and drier summers than normal over GrIS. In this context, we use a circulation type classification based on daily 500 hPa geopotential height to evaluate the role of atmospheric dynamics in this surface melt acceleration for the last two decades. Due to the lack of direct observations, the interannual melt variability is gauged here by the summer (June-July-August) mean temperature from reanalyses at 700 hPa over Greenland; analogous atmospheric circulations in the past show that �70 of the 1993-2012 warming at 700 hPa over Greenland has been driven by changes in the atmospheric flow frequencies. Indeed, the occurrence of anticyclones centred over the GrIS at the surface and at 500 hPa has doubled since the end of 1990's, which induces more frequent southerly warm air advection along the western Greenland coast and over the neighbouring Canadian Arctic Archipelago (CAA). These changes in the NAO modes explain also why no significant warming has been observed these last summers over Svalbard, where northerly atmospheric flows are twice as frequent as before. Therefore, the recent warmer summers over GrIS and CAA cannot be considered as a long-term climate warming but are more a consequence of NAO variability affecting atmospheric heat transport. Although no global model from the CMIP5 database projects subsequent significant changes in NAO through this century, we cannot exclude the possibility that the observed NAO changes are due to global warming. © 2013 Author(s)

Variation of prostate-specific antigen expression in different tumour growth patterns present in prostatectomy specimens

A series of 55 randomly chosen radical prostatectomy specimens was analyzed for expression of prostate-specific antigen (PSA) by immunohistochemical techniques. Tissue sections were selected in such a manner that in addition to glandular benign prostatic hyperplasia (BPH), one or more different prostatic tumour growth patterns were present. Four monoclonal antibodies, directed against three different PSA epitopes, and one polyclonal anti-PSA antiserum were used. Expression of PSA was compared with that of prostate-specific acid phosphatase (PAP), recognized by two different polyclonal antisera. A critical dilution aimed at a maximum of staining intensity on BPH tissue sections was chosen for all antibodies. Anti-PSA and anti-PAP antisera stained essentially all BPH samples (over 90%). Irrespective of the nature of the antibodies used, PSA expression was found to be decreased in prostatic carcinoma. A clear cut relationship was found between immunoreactivity for PSA and the degree of differentiation of the tumour area. Under the experimental conditions used the PSA monoclonal antibodies stained only 1 out of 10 undifferentiated carcinomas, whereas 50% to 70% of the well- and moderately-differentiated carcinomas showed immunoreactivity. This correlation was less pronounced with the PAP staining pattern. If the PSA antibody titer was raised the percentage of clearly staining undifferentiated carcinomas could be considerably increased (up to 60%-100%), indicating that PSA expression is not absent, but lowered in most (if not all) undifferentiated carcinomas

Effects of a multi-faceted program to increase influenza vaccine coverage among health care workers:A hospital-based cluster randomized controlled trial

Background: Immunizing health care workers (HCWs) against influenza has proven to protect their patients. Despite recommentations of the World Health Organization and the Dutch Health Council, influenza vaccine uptake among hospital HCWs remains low in the Netherlands Objectives: To assess the effects of implementing a hospital- based multi-faceted influenza immunization program on vaccine coverage in health care workers (HCW) and on patient morbidity. Methods: We conducted a cluster randomized controlled trial among all eight University Medical Centers (UMC) of The Netherlands during the influenza seasons of 2009- 2010 and 2010-2011. Participants were hospital staff of three intervention (n = 27,900 in 2009), three control (n = 22,451) and two external non-randomized intervention UMCs (n = 16,893), and 3,367 patients admitted to the departments of pediatrics and internal medicine during both influenza epidemics. We offered a vaccination implementation progran to staff of intervention and external UMCs, but not to control UMCs. The primary outcome measure was influenza vaccine coverage among HCW. Secondary outcome measures were work absenteeism and patient morbidity. Results: In 2009, the coverage of seasonal, first pandemic and second pandemic vaccine was 32.3%, 61.7% and 45.8% in the intervention UMCs. Corresponding figures for control UMCs were significantly lower at 20.4%, 38.0%, and 17.8%, respectively (p <0.05). In 2010, the coverage of the seasonal vaccine was 28.6% and 17.8% in intervention and control UMCs, respectively (p <0.05). During their stay, influenza and/or pneumonia was reduced in patients of intervention UMCs compared to control UMCs (work in progress). Rates of HCWs' absenteeism and influenza testing rates during epidemics were higher in intervention than control UMCs. Conclusions: Adoption of the program improved the influenza vaccine coverage among hospital staff. An increase in coverage was associated with decreased patient morbidity from influenza and/or pneumonia

Expression of CD3-ζ on T-cells in primary cervical carcinoma and in metastasis-positive and -negative pelvic lymph nodes

Lymphocytic infiltrate is often present in cervical cancer lesions, possibly reflecting an ongoing, but ineffective, immune response to the tumour. Recently, evidence has accumulated for systemically impaired T-cell functions in cancer patients, associated with decreased expression of signal-transducing zeta (ζ) chain dimer molecules on circulating T-cells and NK-cells. Here, we report on the intralesional down-regulation of ζ chain expression on T-cells in cervical carcinoma. Paraffin-embedded or snap-frozen sections from 24 different cervical cancer specimens were studied. Paraffin-embedded tumour-positive (n = 7) and tumour-negative (n = 15) pelvic lymph nodes were also included in the study. Immunostaining was performed on consecutive sections with antibodies specific for CD3-ɛ or the CD3-associated ζ chain dimer. Antigen retrieval by sodium citrate/microwave treatment was essential for ζ staining of paraffin sections. The amount of ζ positive cells was quantitated and related to the number of CD3-ɛ+ cells in corresponding tumour areas. Of the 24 cervical cancer specimens studied, ζ chain dimer expression was reduced in seven cases and strongly reduced in the other 17 samples. In tonsil control sections, CD3-ɛ and CD3-ζ were always co-expressed in almost equal numbers. Also, both tumour-negative and -positive lymph nodes showed ζ chain expression which equalled that of CD3-ɛ expression. These data indicate that a decreased expression of signal-transducing ζ molecules on tumour-infiltrating T-cells is frequent in cervical cancer. The apparently unimpaired ζ chain expression within draining lymph nodes suggests that local tumour-derived factors at the primary site are instrumental in ζ chain down-regulation. © 1999 Cancer Research Campaig