HE-MAN -- Homomorphically Encrypted MAchine learning with oNnx models

Machine learning (ML) algorithms are increasingly important for the success of products and services, especially considering the growing amount and availability of data. This also holds for areas handling sensitive data, e.g. applications processing medical data or facial images. However, people are reluctant to pass their personal sensitive data to a ML service provider. At the same time, service providers have a strong interest in protecting their intellectual property and therefore refrain from publicly sharing their ML model. Fully homomorphic encryption (FHE) is a promising technique to enable individuals using ML services without giving up privacy and protecting the ML model of service providers at the same time. Despite steady improvements, FHE is still hardly integrated in today's ML applications. We introduce HE-MAN, an open-source two-party machine learning toolset for privacy preserving inference with ONNX models and homomorphically encrypted data. Both the model and the input data do not have to be disclosed. HE-MAN abstracts cryptographic details away from the users, thus expertise in FHE is not required for either party. HE-MAN 's security relies on its underlying FHE schemes. For now, we integrate two different homomorphic encryption schemes, namely Concrete and TenSEAL. Compared to prior work, HE-MAN supports a broad range of ML models in ONNX format out of the box without sacrificing accuracy. We evaluate the performance of our implementation on different network architectures classifying handwritten digits and performing face recognition and report accuracy and latency of the homomorphically encrypted inference. Cryptographic parameters are automatically derived by the tools. We show that the accuracy of HE-MAN is on par with models using plaintext input while inference latency is several orders of magnitude higher compared to the plaintext case

The proteasome cap RPT5/Rpt5p subunit prevents aggregation of unfolded ricin A chain

The plant cytotoxin ricin enters mammalian cells by receptor-mediated endocytosis, undergoing retrograde transport to the endoplasmic reticulum (ER) where its catalytic A chain (RTA) is reductively separated from the holotoxin to enter the cytosol and inactivate ribosomes. The currently accepted model is that the bulk of ER-dislocated RTA is degraded by proteasomes. We show here that the proteasome has a more complex role in ricin intoxication than previously recognised, that the previously reported increase in sensitivity of mammalian cells to ricin in the presence of proteasome inhibitors simply reflects toxicity of the inhibitors themselves, and that RTA is a very poor substrate for proteasomal degradation. Denatured RTA and casein compete for a binding site on the regulatory particle of the 26S proteasome, but their fates differ. Casein is degraded, but the mammalian 26S proteasome AAA-ATPase subunit RPT5 acts as a chaperone that prevents aggregation of denatured RTA and stimulates recovery of catalytic RTA activity in vitro. Furthermore, in vivo, the ATPase activity of Rpt5p is required for maximal toxicity of RTA dislocated from the Saccharomyces cerevisiae ER. Our results implicate RPT5/Rpt5p in the triage of substrates in which either activation (folding) or inactivation (degradation) pathways may be initiated

The hrp23 Protein in the Balbiani Ring Pre-mRNP Particles Is Released Just before or at the Binding of the Particles to the Nuclear Pore Complex

Balbiani ring (BR) pre-mRNP particles reside in the nuclei of salivary glands of the dipteran Chironomus tentans and carry the message for giant-sized salivary proteins. In the present study, we identify and characterize a new protein component in the BR ribonucleoprotein (RNP) particles, designated hrp23. The protein with a molecular mass of 20 kD has a single RNA-binding domain and a glycine-arginine-serine–rich auxiliary domain. As shown by immunoelectron microscopy, the hrp23 protein is added to the BR transcript concomitant with transcription, is still present in the BR particles in the nucleoplasm, but is absent from the BR particles that are bound to the nuclear pore complex or are translocating through the central channel of the complex. Thus, hrp23 is released just before or at the binding of the particles to the nuclear pore complex. It is noted that hrp23 behaves differently from two other BR RNP proteins earlier studied: hrp36 and hrp45. These proteins both reach the nuclear pore complex, and hrp36 even accompanies the RNA into the cytoplasm. It is concluded that each BR RNA-binding protein seems to have a specific flow pattern, probably related to the particular role of the protein in gene expression

Combined systems approaches reveal highly plastic responses to antimicrobial peptide challenge in Escherichia coli

Obtaining an in-depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics. We investigated whether a whole organism view of antimicrobial peptide (AMP) challenge on Escherichia coli would provide a suitably sophisticated bacterial perspective on AMP mechanism of action. Selecting structurally and physically related AMPs but with expected differences in bactericidal strategy, we monitored changes in bacterial metabolomes, morphological features and gene expression following AMP challenge at sub-lethal concentrations. For each technique, the vast majority of changes were specific to each AMP, with such a plastic response indicating E. coli is highly capable of discriminating between specific antibiotic challenges. Analysis of the ontological profiles generated from the transcriptomic analyses suggests this approach can accurately predict the antibacterial mode of action, providing a fresh, novel perspective for previous functional and biophysical studies

A novel cultivation-based approach for understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from sedimentary ecosystems

The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth's subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both cultivation and molecular techniques, including a pre-PCR propidium monoazide treatment, to investigate viable members of the MCG in vitro. Enrichment cultures prepared from estuarine sediment were provided with one of a variety of carbon substrates or cultivation conditions and incubated for 3 weeks. Compared with the samples from time zero, there was an order-of-magnitude increase in the number of MCG 16S rRNA genes in almost all cultures, indicating that MCG archaea are amenable to in vitro cultivation. None of the tested substrates or conditions significantly stimulated growth of MCG archaea more than the basal medium alone; however, glycerol (0.02%) had a significantly inhibitory effect (P < 0.05). Diversity analysis of populations resulting from four culture treatments (basal medium, addition of amino acids, H2-CO2 as the gas phase, or initial aerobic conditions) revealed that the majority of viable MCG archaea were affiliated with the MCG-8 and MCG-4 clusters. There were no significant differences in MCG diversity between these treatments, also indicating that some members of MCG-4 and MCG-8 are tolerant of initially oxic conditions. The methods outlined here will be useful for further investigation of MCG archaea and comparison of substrates and cultivation conditions that influence their growth in vitro

Prognostic value at 5 years of microvascular obstruction after acute myocardial infarction assessed by cardiovascular magnetic resonance

<p>Abstract</p> <p>Background</p> <p>Early and late microvascular obstruction (MVO) assessed by cardiovascular magnetic resonance (CMR) are prognostic markers for short-term clinical endpoints after acute ST-elevation myocardial infarction (STEMI). However, there is a lack of studies with long-term follow-up periods (>24 months).</p> <p>Methods</p> <p>STEMI patients reperfused by primary angioplasty (n = 129) underwent MRI at a median of 2 days after the index event. Early MVO was determined on dynamic Gd first-pass images directly after the administration of 0.1 mmol/kg bodyweight Gd-based contrast agent. Furthermore, ejection fraction (EF, %), left ventricular myocardial mass (LVMM) and total infarct size (% of LVMM) were determined with CMR. Clinical follow-up was conducted after a median of 52 months. The primary endpoint was defined as a composite of death, myocardial re-infarction, stroke, repeat revascularization, recurrence of ischemic symptoms, atrial fibrillation, congestive heart failure and hospitalization.</p> <p>Results</p> <p>Follow-up was completed by 107 patients. 63 pre-defined events occurred during follow-up. Initially, 74 patients showed early MVO. Patients with early MVO had larger infarcts (mean: 24.9 g <it>vs.</it> 15.5 g, p = 0.002) and a lower EF (mean: 39% <it>vs.</it> 46%, p = 0.006). The primary endpoint occurred in 66.2% of patients with MVO and in 42.4% of patients without MVO (p < 0.05). The presence of early MVO was associated with a reduced event-free survival (log-rank p < 0.05). Early MVO was identified as the strongest independent predictor for the occurrence of the primary endpoint in the multivariable Cox regression analysis adjusting for age, ejection fraction and infarct size (hazard ratio: 2.79, 95%-CI 1.25-6.25, p = 0.012).</p> <p>Conclusion</p> <p>Early MVO, as assessed by first-pass CMR, is an independent long-term prognosticator for morbidity after AMI.</p

Fatigue Strength Analysis of a Prototype Francis Turbine in a Multilevel Lifetime Assessment Procedure Part II: Method Application and Numerical Investigation

Part I of the publication series addressed the fundamentals of lifetime assessment of prototype Francis turbines. This paper (Part II) focuses on the numerical part of the procedure. The essential steps and requirements shall be presented (background). The starting points for the numerical considerations are the pressure fields of the transient CFD simulations, which are exported per time step and applied to the existing structure via a fluid–structure interaction. That enables a transient mechanical stress calculation to be conducted, resulting in the fatigue analysis of the component to estimate the remaining lifetime. The individual model requirements should be represented accordingly and applied to the prototype facility (method). The results obtained from this application should be discussed and evaluated. It has to be mentioned that the validation of the numerical results will be performed at Part IV of this publication series (results). The present paper will end up discussing the results and conclusions about further data processing (Conclusion)