Exploiting Patch Sizes and Resolutions for Multi-Scale Deep Learning in Mammogram Image Classification.

Recent progress in deep learning (DL) has revived the interest on DL-based computer aided detection or diagnosis (CAD) systems for breast cancer screening. Patch-based approaches are one of the main state-of-the-art techniques for 2D mammogram image classification, but they are intrinsically limited by the choice of patch size, as there is no unique patch size that is adapted to all lesion sizes. In addition, the impact of input image resolution on performance is not yet fully understood. In this work, we study the impact of patch size and image resolution on the classifier performance for 2D mammograms. To leverage the advantages of different patch sizes and resolutions, a multi patch-size classifier and a multi-resolution classifier are proposed. These new architectures perform multi-scale classification by combining different patch sizes and input image resolutions. The AUC is increased by 3% on the public CBIS-DDSM dataset and by 5% on an internal dataset. Compared with a baseline single patch size and single resolution classifier, our multi-scale classifier reaches an AUC of 0.809 and 0.722 in each dataset.

Deformable registration with intensity correction for CESM monitoring response to Neoadjuvant Chemotherapy.

This paper proposes a robust longitudinal registration method for Contrast Enhanced Spectral Mammography in monitoring neoadjuvant chemotherapy. Because breast texture intensity changes with the treatment, a non-rigid registration procedure with local intensity compensations is developed. The approach allows registering the low energy images of the exams acquired before and after the chemotherapy. The measured motion is then applied to the corresponding recombined images. The difference of registered images, called residual, makes vanishing the breast texture that did not changed between the two exams. Consequently, this registered residual allows identifying local density and iodine changes, especially in the lesion area. The method is validated with a synthetic NAC case where ground truths are available. Then the procedure is applied to 51 patients with 208 CESM image pairs acquired before and after the chemotherapy treatment. The proposed registration converged in all 208 cases. The intensity-compensated registration approach is evaluated with different mathematical metrics and through the repositioning of clinical landmarks (RMSE: 5.9 mm) and outperforms state-of-the-art registration techniques.

A 3D Mathematical Breast Texture Model With Parameters Automatically Inferred From Clinical Breast CT Images.

A numerical realistic 3D anthropomorphic breast model is useful for evaluating breast imaging applications. A method is proposed to model small and medium-scale fibroglandular and intra-glandular adipose tissues observed in the center part of clinical breast CT images. The method builds upon a previously proposed model formulated as stochastic geometric processes with mathematically tractable parameters. In this work, the medium-scale parameters were automatically and objectively inferred from breast CT images. We hypothesized that a set of random ellipsoids exhibiting cluster interaction is representative to model the medium-scale intra-glandular adipose compartments. The ellipsoids were reconstructed using a multiple birth, death and shift algorithm. Then, a Matérn cluster process was used to fit the reconstructed ellipsoid centers. Finally, distributions of the ellipsoid shapes and orientations were estimated using maximum likelihood estimators. Feasibility was demonstrated on 16 volumes of interests (VOI). To assess the realism of the 3D breast texture model, ß and LFE metrics computed in simulated projection images of simulated texture realizations and clinical images were compared. Visual realism was illustrated. For 12 out of 16 VOIs, our hypothesis on clustering interaction process is confirmed. The average ß values from simulated texture images (3.7 to 4.2) of the 12 different VOIs are higher than the average ß value from 2D clinical images (2.87). LFE of simulated texture images and clinical mammograms are similar. Compared to our previous model, whereby simulation parameters were based upon empirical observations, our inference method substantially augments the ability to generate textures with higher visual realism and larger morphological variety.

A Novel Task-Based reconstruction approach for digital breast tomosynthesis.

The reconstruction of a volumetric image from Digital Breast Tomosynthesis (DBT) measurements is an ill-posed inverse problem, for which existing iterative regularized approaches can provide a good solution. However, the clinical task is somehow omitted in the derivation of those techniques, although it plays a primary role in the radiologist diagnosis. In this work, we address this issue by introducing a novel variational formulation for DBT reconstruction, tailored for a specific clinical task, namely the detection of microcalcifications. Our method aims at simultaneously enhancing the detectability performance and enabling a high-quality restoration of the background breast tissues. Our contribution is threefold. First, we introduce an original task-based reconstruction framework through the proposition of a detectability function inspired from mathematical model observers. Second, we propose a novel total-variation regularizer where the gradient field accounts for the different morphological contents of the imaged breast. Third, we integrate the two developed measures into a cost function, minimized thanks to a new form of the Majorize Minimize Memory Gradient (3MG) algorithm. We conduct a numerical comparison of the convergence speed of the proposed method with those of standard convex optimization algorithms. Experimental results show the interest of our DBT reconstruction approach, qualitatively and quantitatively.

Dataset of costs of the mitigation hierarchy and plant translocations in France.

These data are coming from the derogation requests for the destruction of protected species in the context of construction or development work in France. These derogation requests include, among other things, the contents of an environmental impact assessment and the costs of the measures suggested to reduce the impact on the environment. In the article connected to this dataset, we studied the quality of the plant translocation protocols proposed in 95 derogation files (see Julien et al., 2022). We additionally collected during the reading of the files data that we make available here about the costs of (i) the total project, (ii) the mitigation hierarchy and (iii) the plant translocation operations and monitoring. These data complement our aforementioned paper by documenting how much translocations cost and in what proportion of the other costs reported in the projects we evaluated for quality. These data can be helpful for environmental stakeholders but also to further studies to determine the extent to which the environment is considered in land planning.

Quality assessment of mitigation translocation protocols for protected plants in France.

Mitigation translocations are increasingly used worldwide in response to land planning pressures. The quality of translocation protocols and their adjustment to the ecological traits of the translocated populations are crucial to optimise translocation success. We studied the quality of translocation protocols presented in derogation requests, a mandatory step in France to translocate a protected plant species. We analysed 103 translocation proposals for 93 different species in 92 files examined between 2018 and 2020. After tracing the history of the place of translocations in legal procedures in France, we assessed each translocation proposal according to an evaluation grid, which involved the quantity and quality of information on plant species and translocation sites in the files and the quality of translocation protocols. We have shown that the translocation protocols are of low quality, with a lot of missing information. The biology and ecology of the species suggested for translocation are not sufficiently known, nor are the ecological characteristics of the host sites. Derogation requests that received a favourable opinion from the assessment body are more likely to propose a protected host site and post-translocation monitoring. We believe that, to optimise their outcome, mitigation translocations need to be improved upstream, with more detailed protocols and better species knowledge. We highly recommend following the same guidelines for mitigation translocations as for conservation translocations.

The X-ray fluorescence screening of multiple elements in herbarium specimens from the Neotropical region reveals new records of metal accumulation in plants.

Plants have developed a diversity of strategies to take up and store essential metals in order to colonize various types of soils including mineralized soils. Yet, our knowledge of the capacity of plant species to accumulate metals is still fragmentary across the plant kingdom. In this study, we have used the X-ray fluorescence technology to analyze metal concentration in a wide diversity of species of the Neotropical flora that was not extensively investigated so far. In total, we screened more than 11 000 specimens representing about 5000 species from herbaria in Paris and Cuba. Our study provides a large overview of the accumulation of metals such as manganese, zinc, and nickel in the Neotropical flora. We report 30 new nickel hyperaccumulating species from Cuba, including the first records in the families Connaraceae, Melastomataceae, Polygonaceae, Santalaceae, and Urticaceae. We also identified the first species from this region of the world that can be considered as manganese hyperaccumulators in the genera Lomatia (Proteaceae), Calycogonium (Melastomataceae), Ilex (Aquifoliaceae), Morella (Myricaceae), and Pimenta (Myrtaceae). Finally, we report the first zinc hyperaccumulator, Rinorea multivenosa (Violaceae), from the Amazonas region. The identification of species able to accumulate high amounts of metals will become instrumental to support the development of phytotechnologies in order to limit the impact of soil metal pollution in this region of the world.

Distribution of pressure on the breast in mammography using flexible and rigid compression plates: implications on patient handling.

BACKGROUND: Breast compression in mammography is important but is a source of discomfort and has been linked to screening non-attendance. Reducing compression has little effect on breast thickness, and likely little effect on image quality, due to force being absorbed in the stiff juxta thoracic area instead of in the central breast. PURPOSE: To investigate whether a flexible compression plate can redistribute force to the central breast and whether this affects perceived pain. MATERIAL AND METHODS: Twenty-eight women recalled from mammography screening were compressed with flexible and rigid plates while retaining force and positioning, 15 in the craniocaudal (CC) view and 13 in the mediolateral oblique (MLO) view. Pressure distribution was continuously measured using pressure sensors. RESULTS: The flexible plate showed greater mean breast pressure in both views: 2.8 versus 2.3 kPa for CC (confidence interval [CI] = 0.2-0.8) and 1.0 versus 0.5 kPa for MLO (CI = 0.2-0.6). The percentage of applied force distributed to the breast was significantly higher with the flexible plate, both on CC (36% vs. 22%, CI = 1-11) and MLO (30% vs. 14%, CI = 4-13). CONCLUSION: The flexible plate redistributes pressure to the central breast, achieving a better compression, particularly in the MLO view, though much applied force is still applied to the juxta thoracic region.

Pressure-based Compression Guidance of the Breast in Digital Breast Tomosynthesis Using Flexible Paddles Compared to Conventional Compression.

OBJECTIVE: We investigated the effect of introducing a pressure-based flexible paddle on compression parameters and user and patient experience of digital breast tomosynthesis (DBT) combined with patient-assisted compression or technologist compression. METHODS: After institutional review board approval, women with a DBT appointment who gave informed consent received pressure-based flexible paddle breast compression. Eight lights on the paddle were illuminated (1.9 kPa per light) as pressure was applied, aiming for an 8-13.9 kPa target range. The compression level was applied by the technologist or the participant utilizing a remote control device. The participant's and technologist's experiences were assessed by a questionnaire. Compression parameters were compared to previous examinations. Comparative statistics were performed using t-tests. RESULTS: Pressure-based compression (PBC) was judged to be similar or more comfortable compared with previous traditional exams (80%, 83/103), and 87% (90/103) of participants would recommend PBC to friends. Pressure variability decreased for craniocaudal (CC) views (-55%, P < 0.001) and mediolateral oblique (MLO) views (-34%, P < 0.0001). Subgroup analysis showed a similar glandular dose for CC views, while breast thickness was reduced (-3.74 mm, P < 0.0001). For MLO views, both glandular dose (-0.13 mGy, P < 0.0001) and breast thickness were reduced (-6.70 mm, P < 0.0001). Mean compression parameters were similar for technologist compression and patient-assisted examinations. CONCLUSION: Use of the pressure-based flexible paddle in DBT, with or without patient-assisted compression, improved participant and technologist experience and reduced compression pressure variability, mean breast thickness, and glandular dose.

AFLP markers show low levels of clonal propagation and high genotypic diversity in the rare, southernmost populations of Linnaea borealis L. (Caprifoliaceae) in the Western Alps.

In plants, clonal propagation is a common reproductive strategy in parallel to sexual reproduction. It has both advantages and drawbacks, and the potential complete loss of sexual reproduction causes serious conservation concerns, especially because population maintenance then only relies on adult survival and low genetic diversity leads to decreased adaptive potential. We investigated the rare, southernmost populations of the mostly circumboreal twinflower Linnaea borealis, located in the Western Alps. Based on 105 AFLP markers and 118 leaf samples, including replicates, we estimated the genetic similarity threshold above which samples belong to a single clone. Although the species is known for extensive clonal propagation, we observed high genotypic diversity within the seven studied populations and almost all samples were genetically distinct. Nevertheless, some clonal samples were detected in two populations, separated by up to 180 m. We found a strong genetic differentiation among populations (overall Fst = 0.38), which was congruent with the previously documented high plastid diversity in the region. We therefore hypothesize that Alpine populations are relicts of the Quaternary glacial periods, when the species probably survived at these lower latitudes before colonizing Northern Europe. Regarding conservation, our results suggest that most extant plants result from sexual reproduction and that populations are not highly threatened. Nevertheless, since clones can be very long-lived and almost no seedlings were observed in recent years, events of sexual reproduction may be ancient. The current reproductive dynamics should therefore be studied to estimate e.g. pollinators activity, proportions of flowering plants, and seed set.

A biomechanical breast model evaluated with respect to MRI data collected in three different positions.

BACKGROUND: Mammography is a specific type of breast imaging that uses low-dose X-rays to detect cancer in early stage. During the exam, the women breast is compressed between two plates in order to even out the breast thickness and to spread out the soft tissues. This technique improves exam quality but can be uncomfortable for the patient. The perceived discomfort can be assessed by the means of a breast biomechanical model. Alternative breast compression techniques may be computationally investigated trough finite elements simulations. METHODS: The aim of this work is to develop and evaluate a new biomechanical Finite Element (FE) breast model. The complex breast anatomy is considered including adipose and glandular tissues, muscle, skin, suspensory ligaments and pectoral fascias. Material hyper-elasticity is modeled using the Neo-Hookean material models. The stress-free breast geometry and subject-specific constitutive models are derived using tissues deformations measurements from MR images. FINDINGS: The breast geometry in three breast configurations were computed using the breast stress-free geometry together with the estimated set of equivalent Young's modulus (Ebreastr = 0.3 kPa, Ebreastl = 0.2 kPa, Eskin = 4 kPa, Efascia = 120 kPa). The Hausdorff distance between estimated and measured breast geometries for prone, supine and supine tilted configurations is equal to 2.17 mm, 1.72 mm and 5.90 mm respectively. INTERPRETATION: A subject-specific breast model allows a better characterization of breast mechanics. However, the model presents some limitations when estimating the supine tilted breast configuration. The results show clearly the difficulties to characterize soft tissues mechanics at large strain ranges with Neo-Hookean material models.

The French Muséum national d'histoire naturelle vascular plant herbarium collection dataset.

We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d'histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.

Genetic structure of colline and montane populations of an endangered plant species.

Due to land-use intensification, lowland and colline populations of many plants of nutrient-poor grasslands have been strongly fragmented in the last decades, with potentially negative consequences for their genetic diversity and persistence. Populations in mountains might represent a genetic reservoir for grassland plants, because they have been less affected by land-use changes. We studied the genetic structure and diversity of colline and montane Vosges populations of the threatened perennial plant Arnica montana in western central Europe using AFLP markers. Our results indicate that in contrast to our expectation even strongly fragmented colline populations of A. montana have conserved a considerable amount of genetic diversity. However, mean seed mass increased with the proportion of polymorphic loci, suggesting inbreeding effects in low diversity populations. At a similar small geographical scale there was a clear IBD pattern for the montane Vosges but not for the colline populations. However, there was a strong IBD-pattern for the colline populations at a large geographical scale suggesting that this pattern is a legacy of historical gene flow, as most of the colline populations are today strongly isolated from each other. Genetic differentiation between colline and montane Vosges populations was strong. Moreover, results of a genome scan study indicated differences in loci under selection, suggesting that plants from montane Vosges populations might be maladapted to conditions at colline sites. Our results suggest caution in using material from montane populations of rare plants for the reinforcement of small genetically depauperate lowland populations.

Litter chemistry prevails over litter consumers in mediating effects of past steel industry activities on leaf litter decomposition.

Soil pollution has adverse effects on the performance and life history traits of microorganisms, plants, and animals, yet evidence indicates that even the most polluted sites can support structurally-complex and dynamic ecosystems. The present study aims at determining whether and how litter decomposition, one of the most important soil ecological processes leaf, is affected in a highly trace-metal polluted site. We postulated that past steel mill activities resulting in soil pollution and associated changes in soil characteristics would influence the rate of litter decomposition through two non-exclusive pathways: altered litter chemistry and responses of decomposers to lethal and sub-lethal toxic stress. We carried out a litter-bag experiment using Populus tremula L. leaf litter collected at, and allowed to decompose in, a trace metal polluted site and in three unpolluted sites used as controls. We designed a fully-factorial transplant experimental design to assess effects of litter origin and exposure site on the rate of litter decomposition. We further determined initial litter chemistry, fungal biomass, mesofauna abundance in litter bags, and the soil macrofauna community. Irrespective of the site of litter exposure, litter originating from the polluted site had a two-fold faster decomposition than litter from the unpolluted sites. Litter chemistry, notably the lignin content, seemed most important in explaining the degradation rate of the leaf litter. Abundance of meso and macro-detritivores was higher at the polluted site than at the unpolluted sites. However, litter decomposition proceeded at similar rates in polluted and unpolluted sites. Our results show that trace metal pollution and associated soil and litter changes do not necessarily weaken consumer control on litter decomposition through lethal and sub-lethal toxic stress.

Robot guidance of an ultrasound probe toward a 3D region of interest detected through X-ray mammography.

PURPOSE: This research is situated in the context of breast cancer detection where the standard procedure is the succession of an initial mammography (MX) examination and a supplementary ultrasound (US) scan. One major difficulty of this procedure results from the fact that breast geometry changes between both examinations due to different patient's positions. The proposed system facilitates this combined examination by keeping the breast geometry and by adding a US probe guidance robot to the mammography system. METHODS: A comanipulation system is set up where the robot and user simultaneously manipulate the probe toward the target previously localized in MX images. Calibration procedures and robot control are detailed. RESULTS: A test protocol was presented to conduct two tests that are both related to the medical application. The first tests aim at evaluating robot guidance for localizing a lesion which was previously defined in the X-ray images. The second tests aim at quantifying robot influence when scanning a target lesion. The studied task consists of a pointing/scanning exercise, where the US beam intersects a breast lesion. CONCLUSIONS: The experiments show a significant increase in examination quality when using robot guidance as compared to the nonassisted examination.

Soil genotoxicity assessment--results of an interlaboratory study on the Vicia micronucleus assay in the context of ISO standardization.

The Vicia micronucleus assay was standardized in an international protocol, ISO 29200, "Assessment of genotoxic effects on higher plants-Vicia faba micronucleus test," for soil or soil materials (e.g., compost, sludge, sediment, waste, and fertilizing materials). The aim of this interlaboratory study on the Vicia micronucleus assay was to investigate the robustness of this in vivo assay in terms of its applicability in different countries where each participant were asked to use their own seeds and reference soil, in agreement with the ISO 29200 standard. The ISO 29200 standard protocol was adopted for this study, and seven laboratories from three countries (France, Italy, and Brazil) participated in the study. Negative and positive controls were correctly evaluated by 100 % of the participants. In the solid-phase test, the micronucleus frequency (number of micronuclei/1,000 cells) varied from 0.0 to 1.8 for the negative control (i.e., Hoagland's solution) and from 5.8 to 85.7 for the positive control (i.e., maleic hydrazide), while these values varied from 0.0 to 1.7 for the negative control and from 14.3 to 97.7 for the positive control in the case of liquid-phase test. The variability in the data obtained does not adversely affect the robustness of the protocol assessed, on the condition that the methodology described in the standard ISO 29200 is strictly respected. Thus, the Vicia micronucleus test (ISO 29200) is appropriate for complementing prokaryotic or in vitro tests cited in legislation related to risk assessment of genotoxicity potential.

Spatio-temporal variability of faunal and floral assemblages in Mediterranean temporary wetlands.

Six temporary wetlands in the region of Sejenane (Mogods, NW Tunisia) were studied in order to characterize the aquatic flora and fauna and to quantify their spatio-temporal variability. Samplings of aquatic fauna, phytosociological relevés, and measurements of the physicochemical parameters of water were taken during four different field visits carried out during the four seasons of the year (November 2009-July 2010). Despite the strong anthropic pressures on them, these temporary wetlands are home to rich and diversified biodiversity, including rare and endangered species. Spatial and temporal variations affect fauna and flora differently, as temporal variability influences the fauna rather more than the plants, which are relatively more dependent on spatial factors. These results demonstrate the interest of small water bodies for maintaining biodiversity at the regional level, and thus underscore the conservation issues of Mediterranean temporary wetlands that are declining on an ongoing basis currently.

Effects of soil pH on the Vicia-micronucleus genotoxicity assay.

In the field of contaminated sites and soil management, chemical analyses only bring typological data about pollution. As far as bioavailability and effects on organisms are concerned, we need ecotoxicology tools. In this domain, among many existing tests, we chose to study genotoxicity because it is a short-term endpoint with long-term consequences. The aim of this study is to assess the effects of soil pH on the results of the Vicia faba root tip micronucleus test for the two following reasons: (i) to define the pH range within which the test can be performed without modifying the soil to be tested, within the framework of the ISO standard of the test and (ii) to provides information about the effects of the pH on the genotoxic potential of soils. In this context, we modified the pH of a standard soil with HCl or NaOH and we spiked the matrix with copper (2, 4 and 8 mmol kg(-1) dry soil) or with maleic hydrazide, an antigerminative chemical (5, 10 and 20 µmol kg(-1) dry soil). We concluded that the pH had no effect on the mitotic index or micronucleus frequency in the root cells of the negative controls: extreme pH values did not induce micronucleus formation in root cells. Moreover, according to our results, the Vicia-micronucleus test can be performed with pH values ranging between 3.2 and 9.0, but in the ISO 29200 "Soil quality--assessment of genotoxic effects on higher plants--V. faba micronucleus test" we recommended to use a control soil with a pH value ranging between 5 and 8 for a more accurate assessment of chemical genotoxicity. We also found that acid pH could increase the genotoxic potential of pollutants, especially heavy metals. With hydrazide maleic spiked soil, plants were placed in a situation of double stress, i.e. toxicity caused by extreme pH values and toxicity induced by the pollutant.

Soil phosphorus constrains biodiversity across European grasslands.

Nutrient pollution presents a serious threat to biodiversity conservation. In terrestrial ecosystems, the deleterious effects of nitrogen pollution are increasingly understood and several mitigating environmental policies have been developed. Compared to nitrogen, the effects of increased phosphorus have received far less attention, although some studies have indicated that phosphorus pollution may be detrimental for biodiversity as well. On the basis of a dataset covering 501 grassland plots throughout Europe, we demonstrate that, independent of the level of atmospheric nitrogen deposition and soil acidity, plant species richness was consistently negatively related to soil phosphorus. We also identified thresholds in soil phosphorus above which biodiversity appears to remain at a constant low level. Our results indicate that nutrient management policies biased toward reducing nitrogen pollution will fail to preserve biodiversity. As soil phosphorus is known to be extremely persistent and we found no evidence for a critical threshold below which no environmental harm is expected, we suggest that agro-environmental schemes should include grasslands that are permanently free from phosphorus fertilization.

Optimization of contrast-enhanced spectral mammography depending on clinical indication.

The objective is to optimize low-energy (LE) and high-energy (HE) exposure parameters of contrast-enhanced spectral mammography (CESM) examinations in four different clinical applications for which different levels of average glandular dose (AGD) and ratios between LE and total doses are required. The optimization was performed on a Senographe DS with a SenoBright® upgrade. Simulations were performed to find the optima by maximizing the contrast-to-noise ratio (CNR) on the recombined CESM image using different targeted doses and LE image quality. The linearity between iodine concentration and CNR as well as the minimal detectable iodine concentration was assessed. The image quality of the LE image was assessed on the CDMAM contrast-detail phantom. Experiments confirmed the optima found on simulation. The CNR was higher for each clinical indication than for SenoBright®, including the screening indication for which the total AGD was 22% lower. Minimal iodine concentrations detectable in the case of a 3-mm-diameter round tumor were 12.5% lower than those obtained for the same dose in the clinical routine. LE image quality satisfied EUREF acceptable limits for threshold contrast. This newly optimized set of acquisition parameters allows increased contrast detectability compared to parameters currently used without a significant loss in LE image quality.