NeRN -- Learning Neural Representations for Neural Networks

Neural Representations have recently been shown to effectively reconstruct a wide range of signals from 3D meshes and shapes to images and videos. We show that, when adapted correctly, neural representations can be used to directly represent the weights of a pre-trained convolutional neural network, resulting in a Neural Representation for Neural Networks (NeRN). Inspired by coordinate inputs of previous neural representation methods, we assign a coordinate to each convolutional kernel in our network based on its position in the architecture, and optimize a predictor network to map coordinates to their corresponding weights. Similarly to the spatial smoothness of visual scenes, we show that incorporating a smoothness constraint over the original network's weights aids NeRN towards a better reconstruction. In addition, since slight perturbations in pre-trained model weights can result in a considerable accuracy loss, we employ techniques from the field of knowledge distillation to stabilize the learning process. We demonstrate the effectiveness of NeRN in reconstructing widely used architectures on CIFAR-10, CIFAR-100, and ImageNet. Finally, we present two applications using NeRN, demonstrating the capabilities of the learned representations

Metabolic networking in Brunfelsia calycina petals after flower opening

Brunfelsia calycina flowers change colour from purple to white due to anthocyanin degradation, parallel to an increase in fragrance and petal size. Here it was tested whether the production of the fragrant benzenoids is dependent on induction of the shikimate pathway, or if they are formed from the anthocyanin degradation products. An extensive characterization of the events taking place in Brunfelsia flowers is presented. Anthocyanin characterization was performed using ultraperfomance liquid chromatography–quadrupole time of flight–tandem mass specrometry (UPLC-QTOF-MS/MS). Volatiles emitted were identified by headspace solid phase microextraction–gas chromatography–mass spectrometry (HS-SPME-GC-MS). Accumulated proteins were identified by 2D gel electrophoresis. Transcription profiles were characterized by cross-species hybridization of Brunfelsia cDNAs to potato cDNA microarrays. Identification of accumulated metabolites was performed by UPLC-QTOF-MS non-targeted metabolite analysis. The results include characterization of the nine main anthocyanins in Brunfelsia flowers. In addition, 146 up-regulated genes, 19 volatiles, seven proteins, and 17 metabolites that increased during anthocyanin degradation were identified. A multilevel analysis suggests induction of the shikimate pathway. This pathway is the most probable source of the phenolic acids, which in turn are precursors of both the benzenoid and lignin production pathways. The knowledge obtained is valuable for future studies on degradation of anthocyanins, formation of volatiles, and the network of secondary metabolism in Brunfelsia and related species

Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance for all participants. Methods CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes (path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with polypectomy when polyps were identified. Comparison was made with a retrospective cohort reported by the International Mismatch Repair Consortium (IMRC). This comprised confirmed and inferred path_MMR carriers who were first- or second-degree relatives of Lynch syndrome probands. Results In the PLSD, 8,153 subjects had follow-up colonoscopy surveillance for a total of 67,604 years and 578 carriers had CRC diagnosed. Average cumulative incidences of CRC in path_MLH1 carriers at 70 years of age were 52% in males and 41% in females; for path_MSH2 50% and 39%; for path_MSH6 13% and 17% and for path_PMS2 11% and 8%. In contrast, in the IMRC cohort, corresponding cumulative incidences were 40% and 27%; 34% and 23%; 16% and 8% and 7% and 6%. Comparing just the European carriers in the two series gave similar findings. Numbers in the PLSD series did not allow comparisons of carriers from other continents separately. Cumulative incidences at 25 years were < 1% in all retrospective groups. Conclusions Prospectively observed CRC incidences (PLSD) in path_MLH1 and path_MSH2 carriers undergoing colonoscopy surveillance and polypectomy were higher than in the retrospective (IMRC) series, and were not reduced in path_MSH6 carriers. These findings were the opposite to those expected. CRC point incidence before 50 years of age was reduced in path_PMS2 carriers subjected to colonoscopy, but not significantly so

Colorectal cancer incidences in Lynch syndrome : a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

Objective: To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance for all participants. Methods: CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes (path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with polypectomy when polyps were identified. Comparison was made with a retrospective cohort reported by the International Mismatch Repair Consortium (IMRC). This comprised confirmed and inferred path_MMR carriers who were first- or second-degree relatives of Lynch syndrome probands. Results: In the PLSD, 8,153 subjects had follow-up colonoscopy surveillance for a total of 67,604 years and 578 carriers had CRC diagnosed. Average cumulative incidences of CRC in path_MLH1 carriers at 70 years of age were 52% in males and 41% in females; for path_MSH2 50% and 39%; for path_MSH6 13% and 17% and for path_PMS2 11% and 8%. In contrast, in the IMRC cohort, corresponding cumulative incidences were 40% and 27%; 34% and 23%; 16% and 8% and 7% and 6%. Comparing just the European carriers in the two series gave similar findings. Numbers in the PLSD series did not allow comparisons of carriers from other continents separately. Cumulative incidences at 25 years were < 1% in all retrospective groups. Conclusions: Prospectively observed CRC incidences (PLSD) in path_MLH1 and path_MSH2 carriers undergoing colonoscopy surveillance and polypectomy were higher than in the retrospective (IMRC) series, and were not reduced in path_MSH6 carriers. These findings were the opposite to those expected. CRC point incidence before 50 years of age was reduced in path_PMS2 carriers subjected to colonoscopy, but not significantly so.publishedVersionPeer reviewe

Dominantly inherited micro-satellite instable cancer – the four Lynch syndromes - an EHTG, PLSD position statement

The recognition of dominantly inherited micro-satellite instable (MSI) cancers caused by pathogenic variants in one of the four mismatch repair (MMR) genes MSH2, MLH1, MSH6 and PMS2 has modified our understanding of carcinogenesis. Inherited loss of function variants in each of these MMR genes cause four dominantly inherited cancer syndromes with different penetrance and expressivities: the four Lynch syndromes. No person has an “average sex “or a pathogenic variant in an “average Lynch syndrome gene” and results that are not stratified by gene and sex will be valid for no one. Carcinogenesis may be a linear process from increased cellular division to localized cancer to metastasis. In addition, in the Lynch syndromes (LS) we now recognize a dynamic balance between two stochastic processes: MSI producing abnormal cells, and the host’s adaptive immune system’s ability to remove them. The latter may explain why colonoscopy surveillance does not reduce the incidence of colorectal cancer in LS, while it may improve the prognosis. Most early onset colon, endometrial and ovarian cancers in LS are now cured and most cancer related deaths are after subsequent cancers in other organs. Aspirin reduces the incidence of colorectal and other cancers in LS. Immunotherapy increases the host immune system’s capability to destroy MSI cancers. Colonoscopy surveillance, aspirin prevention and immunotherapy represent major steps forward in personalized precision medicine to prevent and cure inherited MSI cancer

Association between Chronic Exposure to Ambient Air Pollutants, Demography, Vaccination Level, and the Spread of COVID-19 during 2021 Delta Variant Morbidity Wave

Studies conducted in the early COVID-19 pandemic stages showed positive associations between chronic exposure to ambient air pollution and COVID-19 morbidity. Here, we examined the associations between populations’ chronic exposure to air pollutants (NO2, CO, PM10, PM2.5, and SO2), demographics, and vaccination rates, to COVID-19 morbidity rates in 280 Israeli municipalities during the Delta-variant-dominated morbidity wave of summer 2021. We found that COVID-19 morbidity was positively associated with chronic exposure to air pollutants, the municipality’s population density, total population size, and the rate of elderly people. Multivariate linear regression models showed similar trends: positive associations between COVID-19 rates and density, ratio of elderly people, and most air pollutants, and a non-significant link to COVID-19 vaccine second dose ratio. Our results emphasized the effects of chronic air pollution exposure on the spread of the pandemic and strengthen the urgent need for uncompromising policy for a dramatic reduction in air pollution. They also highlighted the vulnerable populations (elderly, densely populated municipalities) during the Delta morbidity wave. These findings could assist policy makers to better inform the public and manage health policies in future COVID-19 waves, hopefully leading to a reduced impact on health

Association between Chronic Exposure to Ambient Air Pollutants, Demography, Vaccination Level, and the Spread of COVID-19 during 2021 Delta Variant Morbidity Wave

Studies conducted in the early COVID-19 pandemic stages showed positive associations between chronic exposure to ambient air pollution and COVID-19 morbidity. Here, we examined the associations between populations&rsquo; chronic exposure to air pollutants (NO2, CO, PM10, PM2.5, and SO2), demographics, and vaccination rates, to COVID-19 morbidity rates in 280 Israeli municipalities during the Delta-variant-dominated morbidity wave of summer 2021. We found that COVID-19 morbidity was positively associated with chronic exposure to air pollutants, the municipality&rsquo;s population density, total population size, and the rate of elderly people. Multivariate linear regression models showed similar trends: positive associations between COVID-19 rates and density, ratio of elderly people, and most air pollutants, and a non-significant link to COVID-19 vaccine second dose ratio. Our results emphasized the effects of chronic air pollution exposure on the spread of the pandemic and strengthen the urgent need for uncompromising policy for a dramatic reduction in air pollution. They also highlighted the vulnerable populations (elderly, densely populated municipalities) during the Delta morbidity wave. These findings could assist policy makers to better inform the public and manage health policies in future COVID-19 waves, hopefully leading to a reduced impact on health