Pre and Post-hoc Diagnosis and Interpretation of Malignancy from Breast DCE-MRI

We propose a new method for breast cancer screening from DCE-MRI based on a post-hoc approach that is trained using weakly annotated data (i.e., labels are available only at the image level without any lesion delineation). Our proposed post-hoc method automatically diagnosis the whole volume and, for positive cases, it localizes the malignant lesions that led to such diagnosis. Conversely, traditional approaches follow a pre-hoc approach that initially localises suspicious areas that are subsequently classified to establish the breast malignancy -- this approach is trained using strongly annotated data (i.e., it needs a delineation and classification of all lesions in an image). Another goal of this paper is to establish the advantages and disadvantages of both approaches when applied to breast screening from DCE-MRI. Relying on experiments on a breast DCE-MRI dataset that contains scans of 117 patients, our results show that the post-hoc method is more accurate for diagnosing the whole volume per patient, achieving an AUC of 0.91, while the pre-hoc method achieves an AUC of 0.81. However, the performance for localising the malignant lesions remains challenging for the post-hoc method due to the weakly labelled dataset employed during training.Comment: Submitted to Medical Image Analysi

Formal institutions and opportunity entrepreneurship. The contingent role of informal institutions

This paper analyzes opportunity entrepreneurship through the interplay between formal and informal institutions. It seems evident that not all entrepreneurial initiatives have the same quality, thus the goal of a society should be to encourage the activities that best contribute to innovation and value generation. We theorize that informal institutions are contingent to the formal institutional environment where the new ventures operate. Our empirical results, using GEM data, confirm that, in countries with a more individualistic orientation, the relationship between formal institutions and opportunity entrepreneurship is more intense, as happens in societies with lower levels of uncertainty avoidance

Training Medical Image Analysis Systems like Radiologists

The training of medical image analysis systems using machine learning approaches follows a common script: collect and annotate a large dataset, train the classifier on the training set, and test it on a hold-out test set. This process bears no direct resemblance with radiologist training, which is based on solving a series of tasks of increasing difficulty, where each task involves the use of significantly smaller datasets than those used in machine learning. In this paper, we propose a novel training approach inspired by how radiologists are trained. In particular, we explore the use of meta-training that models a classifier based on a series of tasks. Tasks are selected using teacher-student curriculum learning, where each task consists of simple classification problems containing small training sets. We hypothesize that our proposed meta-training approach can be used to pre-train medical image analysis models. This hypothesis is tested on the automatic breast screening classification from DCE-MRI trained with weakly labeled datasets. The classification performance achieved by our approach is shown to be the best in the field for that application, compared to state of art baseline approaches: DenseNet, multiple instance learning and multi-task learning.Comment: Oral Presentation at MICCAI 201

Multi Scale Curriculum CNN for Context-Aware Breast MRI Malignancy Classification

Classification of malignancy for breast cancer and other cancer types is usually tackled as an object detection problem: Individual lesions are first localized and then classified with respect to malignancy. However, the drawback of this approach is that abstract features incorporating several lesions and areas that are not labelled as a lesion but contain global medically relevant information are thus disregarded: especially for dynamic contrast-enhanced breast MRI, criteria such as background parenchymal enhancement and location within the breast are important for diagnosis and cannot be captured by object detection approaches properly. In this work, we propose a 3D CNN and a multi scale curriculum learning strategy to classify malignancy globally based on an MRI of the whole breast. Thus, the global context of the whole breast rather than individual lesions is taken into account. Our proposed approach does not rely on lesion segmentations, which renders the annotation of training data much more effective than in current object detection approaches. Achieving an AUROC of 0.89, we compare the performance of our approach to Mask R-CNN and Retina U-Net as well as a radiologist. Our performance is on par with approaches that, in contrast to our method, rely on pixelwise segmentations of lesions.Comment: Accepted to MICCAI 201

Fertility of fresh and frozen sex-sorted semen in dairy cows and heifers in seasonal-calving pasture-based herds

peer-reviewedOur objective in this study was to evaluate the reproductive performance of dairy heifers and cows inseminated with fresh or frozen sex-sorted semen (SS) in seasonal-calving pasture-based dairy herds. Ejaculates of 10 Holstein-Friesian bulls were split and processed to provide (1) fresh conventional semen at 3 × 106 sperm per straw (CONV); (2) fresh SS at 1 × 106 sperm per straw (SS-1M); (3) fresh SS semen at 2 × 106 sperm per straw (SS-2M); and (4) frozen SS at 2 × 106 sperm per straw (SS-FRZ). Generalized linear mixed models were used to evaluate the effect of semen treatment and other explanatory variables on pregnancy per artificial insemination (P/AI) in heifers (n = 3,214) and lactating cows (n = 5,457). In heifers, P/AI was greater for inseminations with CONV (60.9%) than with SS-FRZ (52.8%) but did not differ from SS-1M (54.2%) or SS-2M (53.5%). Cows inseminated with CONV had greater P/AI (48.0%) than cows inseminated with SS, irrespective of treatment (SS-1M, SS-2M, and S-FROZEN; 37.6, 38.9, and 40.6%, respectively). None of the SS treatments differed from each other with regard to P/AI in either heifers or cows. The relative performance of SS compared with CONV was also examined [i.e., relative P/AI = (SS P/AI)/(CONV P/AI) × 100]. Frozen SS achieved relative P/AI >84%. Bull affected P/AI in both heifers and cows, but no bull by semen treatment interaction was observed. In heifers, P/AI increased with increasing Predicted Transmitting Ability for milk protein percentage. In cows, P/AI increased with increasing Economic Breeding Index (EBI) and with days in milk (DIM) at AI but decreased with increasing EBI milk subindex, parity and with DIM2. Cows in parity ≥5 had the lowest P/AI and differed from cows in parities 1, 2, or 3. Dispatch-to-AI interval of fresh semen did not affect P/AI in lactating cows, but a dispatch-to-AI interval by bull interaction was detected whereby P/AI was constant for most bulls but increased with greater dispatch-to-AI intervals for 2 bulls. In conclusion, frozen SS achieved greater P/AI relative to conventional semen than was previously reported in lactating cows. Fresh SS did not achieve greater P/AI than frozen SS, regardless of whether the sperm dose per straw was 1 × 106 or 2 × 106. A bull effect for all semen treatments, as well as a dispatch-to-AI interval by bull interaction for fresh semen, highlights the importance of using a large team of bulls for breeding management

Characteristics of offspring derived from conventional and X-sorted bovine sperm

peer-reviewedThe objective of this retrospective study was to compare survival during the first year of life and adult performance of offspring derived from artificial insemination (AI) with X-sorted or conventional sperm processed from the same ejaculates. We analyzed a data set that included AI of dairy heifers and lactating cows with fresh conventional sperm (3 × 106 sperm per straw), fresh X-sorted sperm (1 or 2 × 106 sperm per straw), or frozen X-sorted sperm (2 × 106 sperm per straw). The data set contained records of 5,179 offspring born on 396 farms. Offspring were classified as born from conventional sperm (CONV) if they were the product of an insemination with fresh conventional sperm, or born from X-sorted sperm (SS) if they were product of any of the 3 X-sorted sperm treatments. Generalized linear mixed models were used to evaluate the effect of sperm treatment on (1) survival during the first year of life; (2) reproductive performance, lactation performance, and survival of female offspring; and (3) slaughter characteristics of male offspring. Stillbirth rates and mortality rates during the first 2 mo of life were greater for male calves (2.8 and 5.0%, respectively) than for female calves (1.6 and 2.0%, respectively). No differences between offspring derived from SS and CONV were detected for incidences of stillbirth or mortality during the first 12 mo of life within sex of calf. Reproductive performance, milk volume, milk fat, milk protein yields during first; second; and third lactations, and survival to third lactation did not differ between female offspring derived from CONV and SS. Across all age groups, CONV steers had heavier carcasses than SS steers (325.3 vs. 318.3 kg), but there were no differences in weight between CONV and SS steers within any of the age groups (≤24, 25–27, 28–30, and >30 mo of age). The distribution of slaughter age did not differ between CONV and SS steers when the analysis was restricted to herds that reared steers derived from both types of sperm. Carcass conformation and fat scores of steers were not affected by sperm treatment. There was no difference in carcass weight between young bulls (≤2 yr) derived from CONV or SS. In conclusion, the results provide no evidence of differences in survival during the first year of life between offspring derived from CONV or SS, or for any of the reproductive and lactation performance characteristics studied between female offspring derived from CONV or SS. Modest differences in carcass weight between CONV and SS steers were detected, but this may reflect differences in management and husbandry in the rearing herds rather than the sex-sorting process. A controlled study using steers derived from conventional or X-sorted sperm from split ejaculates and reared under the same husbandry conditions is needed to clarify whether there is a true difference in body weight gain due to the sex-sorting process

Enhanced Exchange And Reduced Magnetization of Gd in an Fe/Gd/Fe Trilayer

The exchange interaction of Gd adjacent to Fe has been characterized by transport measurements on a double spin valve with a Fe/Gd/Fe trilayer as the middle layer. Our measurements show that the ferromagnetism of the Gd is enhanced by the presence of the Fe, and it remains ferromagnetic over its Curie temperature up to a thickness no smaller than 1 nm adjacent to the Fe. This thickness is more than double what has been reported before. Additionally, the saturation magnetization of the thin Gd layer sandwiched in Fe was found to be half of its bulk value. This reduced magnetization does not seem to be related to the proximity of Fe but rather to the incomplete saturation of Gd even for very high field