Miracle-dz/UniFAR-FTUs huggingface dataset:
CPU to FPGA Power Covert Channel in FPGA-SoCs

FPGA-SoCs are a popular platform for accelerating a wide range of applications due to their performance and flexibility. From a security point of view, these systems have been shown to be vulnerable to various attacks, especially side-channel attacks where an attacker can obtain the secret key of a cryptographic algorithm via laboratory measurement equipment or even remotely with sensors implemented inside the FPGA logic itself. Fortunately, a variety of countermeasures on the algorithmic level have been proposed to mitigate this threat. Beyond side-channel attacks, covert channels constitute another threat which enables communication through a hidden channel. In this work, we demonstrate the possibility of implementing a covert channel between the CPU and an FPGA by modulating the usage of the Power Distribution Network. We show that this resource is especially vulnerable since it can be easily controlled and observed, resulting in a stealthy communication and a high transmission data rate. The power usage is modulated using simple and inconspicuous instructions executed on the CPU. Additionally, we use Time-to-Digital Converter sensors to observe these power variations. The sensor circuits are programmed into the FPGA fabric using only standard logic components. Our covert channel achieves a transmission rate of up to 16.7 kbit/s combined with an error rate of 2.3%. Besides a good transmission quality, our covert channel is also stealthy and can be used as an activation function for a hardware trojan.
Prime Match: A Privacy-Preserving Inventory Matching System

Inventory matching is a standard mechanism/auction for trading financial stocks by which buyers and sellers can be paired. In the financial world, banks often undertake the task of finding such matches between their clients. The related stocks can be traded without adversely impacting the market price for either client. If matches between clients are found, the bank can offer the trade at advantageous rates. If no match is found, the parties have to buy or sell the stock in the public market, which introduces additional costs. A problem with the process as it is presently conducted is that the involved parties must share their order to buy or sell a particular stock, along with the intended quantity (number of shares), to the bank. Clients worry that if this information were to leak somehow, then other market participants would become aware of their intentions and thus cause the price to move adversely against them before their transaction finalizes. We provide a solution, Prime Match, that enables clients to match their orders efficiently with reduced market impact while maintaining privacy. In the case where there are no matches, no information is revealed. Our main cryptographic innovation is a two-round secure linear comparison protocol for computing the minimum between two quantities without preprocessing and with malicious security, which can be of independent interest. We report benchmarks of our Prime Match system, which runs in production and is adopted by J.P. Morgan. The system is designed utilizing a star topology network, which provides clients with a centralized node (the bank) as an alternative to the idealized assumption of point-to-point connections, which would be impractical and undesired for the clients to implement in reality. Prime Match is the first secure multiparty computation solution running live in the traditional financial world.
Broadband nearfield acoustical holography for vibrating cylinders

Generalized nearfield acoustical holography (GENAH), a noncontact technique to measure the vibration and radiation from vibrating cylinders, has been applied in the past to study submerged cylinders excited into vibration at a single frequency. The technique has been expanded to broadband excitation, so that from a single experiment several octaves of acoustic data can be provided. With this new capability GENAH reaches its full power as an experimental technique for studying the complete acoustics of a vibrating, fluid‐loaded cylinder. GENAH is used to reconstruct the radial velocity on the surface of a capped cylinder driven into vibration with a miniature shaker. Important validation of this reconstruction is provided by an accelerometer attached to the surface, which is compared to the reconstructed velocity. Agreement between them over the band of measurement (2.0–8.0 kHz) is better than 2 dB.
High Throughput Lattice-Based Signatures on GPUs: Comparing Falcon and Mitaka

The US National Institute of Standards and Technology initiated a standardization process for post-quantum cryptography in 2017, with the aim of selecting key encapsulation mechanisms and signature schemes that can withstand the threat from emerging quantum computers. In 2022, Falcon was selected as one of the standard signature schemes, eventually attracting effort to optimize the implementation of Falcon on various hardware architectures for practical applications. Recently, Mitaka was proposed as an alternative to Falcon, allowing parallel execution of most of its operations. These recent advancements motivate us to develop high throughput implementations of Falcon and Mitaka signature schemes on Graphics Processing Units (GPUs), a massively parallel architecture widely available on cloud service platforms. In this article, we propose the first parallel implementation of Falcon on various GPUs. We develop an iterative version of the sampling process in Falcon, which is also the most time-consuming Falcon operation. This allows us to implement Falcon signature generation without relying on expensive recursive function calls on GPUs. In addition, we propose a parallel random samples generation approach to accelerate the performance of Mitaka on GPUs. We evaluate our implementation techniques on state-of-the-art GPU architectures (RTX 3080, A100, T4 and V100). Experimental results show that our Falcon-512 implementation achieves 58,595 signatures/second and 2,721,562 verifications/second on an A100 GPU, which is <inline-formula><tex-math notation="LaTeX">$20.03\times$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>20</mml:mn><mml:mo>. </mml:mo><mml:mn>03</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="hwang-ieq1-3367319.gif"/></alternatives></inline-formula> and <inline-formula><tex-math notation="LaTeX">$29.51\times$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>29</mml:mn><mml:mo>. </mml:mo><mml:mn>51</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="hwang-ieq2-3367319.gif"/></alternatives></inline-formula> faster than the highly optimized AVX2 implementation on CPU. Our Mitaka implementation achieves 161,985 signatures/second and 1,421,046 verifications/second on the same GPU. Due to the adoption of a parallelizable sampling process, Mitaka signature generation enjoys <inline-formula><tex-math notation="LaTeX">$\approx 2$</tex-math><alternatives><mml:math><mml:mrow><mml:mo>≈</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:math><inline-graphic xlink:href="hwang-ieq3-3367319.gif"/></alternatives></inline-formula>–<inline-formula><tex-math notation="LaTeX">$20 \times$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>20</mml:mn><mml:mo>×</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="hwang-ieq4-3367319.gif"/></alternatives></inline-formula> higher throughput than Falcon on various GPUs. The high throughput signature generation and verification achieved by this work can be very useful in various emerging applications, including the Internet of Things.
Emergence of Bow-tie Architecture in Evolving Feedforward Networks

Bow-tie architecture is a layered network structure that has a narrow middle layer with multiple inputs and outputs. Such structures are widely seen in the molecular networks in cells, suggesting that a universal evolutionary mechanism underlies the emergence of bow-tie architecture. The previous theoretical studies have implemented evolutionary simulations of the feedforward network to satisfy a given input–output goal, and proposed that the bow-tie architecture emerges when the ideal input– output relation is given as a rank-deficient matrix with mutations in network link strength in a multiplicative manner. Here, we report that the bow-tie network inevitably appears when the link intensities representing molecular interactions are small at the initial condition of the evolutionary simulation, regardless of the rank of the goal matrix. Our dynamical system analysis clarifies the mechanisms underlying the emergence of the bow-tie structure. Further, we demonstrate that the increase in the input–output matrix facilitates the emergence of bow-tie architecture even when starting from strong network links. Our data suggest that bow-tie architecture emerges as a side effect of evolution rather than as a result of evolutionary adaptation. Author Summary Many biological networks including gene regulatory networks, metabolic networks, and signaling networks, show a characteristic hierarchical structure known as the bow-tie architecture. This architecture consists of a narrow middle layer with multiple inputs and outputs. Understanding why bow-tie architecture has universally appeared through evolution may provide insight into the design principle of a network within a cell. The universality of the bow-tie structure has so far been explained by the adaptive advantages such as high evolvability and capability to classify the inputs. However, our computer simulation demonstrates that the bow-tie structure inevitably emerges even without functional advantages when the molecular interactions within the network are weak at the initial condition of the evolution. We also demonstrate that an increase in the number of inputs (i.e., receptors) and outputs (i.e., downstream genes) leads to the emergence of bow-tie architecture, even when evolution starts from a strong molecular interaction. Although many previous studies have discussed the adaptive properties of bow-tie architecture, our findings suggest that bow-tie architecture is a byproduct of evolution rather than a result of evolutionary adaptation.
Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killifish karyotypes

Repetitive DNA may have significant impact on genome evolution. African annual killifishes of the genus Nothobranchius (Teleostei: Nothobranchiidae), which has adapted to temporary water pools in African savannahs, possess genomes with high repeat content. They are also characterized by rapid karyotype and sex chromosome evolution but the role of genome repeats in these processes remains largely unknown. Here, we analyzed the distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (isolated formerly from N. furzeri) by fluorescence in situ hybridization in representatives across the Nothobranchius phylogeny (15 species), and with Fundulosoma thierryi as an outgroup. All analyzed taxa shared the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes (from small clusters scattered genome-wide, to large localized accumulations, or a combined pattern). Nfu-SatC landscape was similar in conspecific populations of N. guentheri and N. melanospilus but slightly-to-moderately differed between populations of N. pienaari, and between closely related N. kuhntae and N. orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and N. krysanovi, including distinct segments present often in heterozygous condition. We revealed mostly no sex-linked patterns of studied repeat’s distribution in any of the sampled species including those with known sex chromosomes. Only in N. brieni (having an X1X2Y multiple sex chromosome system), Nfu-SatC probe covered substantial portion of the Y chromosome, similarly as formerly found in N. furzeri and N. kadleci (XY sex chromosomes), sister species not closely related to N. brieni. All studied species further shared patterns of telomeric FISH, with expected signals at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed i) the presence of conserved satDNA class in Nothobranchius clade (a rare pattern among ray-finned fishes), ii) independent trajectories of Nothobranchius sex chromosome diferentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species, and iii) genus-wide shared propensity to loss of telomeric repeats during the mechanism of interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.
Delta-dependent Notch activation closes the early neuroblast temporal program to promote lineage progression and neurogenesis termination in Drosophila

Neuroblasts in Drosophila divide asymmetrically, sequentially expressing a series of intrinsic factors to generate a diversity of neuron types. These intrinsic factors known as temporal factors dictate timing of neuroblast transitions in response to steroid hormone signaling and specify early versus late temporal fates in neuroblast neuron progeny. After completing their temporal programs, neuroblasts differentiate or die, finalizing both neuron number and type within each neuroblast lineage. From a screen aimed at identifying genes required to terminate neuroblast divisions, we identified Notch and Notch pathway components. When Notch is knocked down, neuroblasts maintain early temporal factor expression longer, delay late temporal factor expression, and continue dividing into adulthood. We find that Delta, expressed in cortex glia, neuroblasts, and after division, their GMC progeny, regulates neuroblast Notch activity. We also find that Delta in neuroblasts is expressed high early, low late, and is controlled by the intrinsic temporal program: early factor Imp promotes Delta, late factors Syp/E93 reduce Delta. Thus, in addition to systemic steroid hormone cues, forward lineage progression is controlled by local cell-cell signaling between neuroblasts and their cortex glia/GMC neighbors: Delta transactivates Notch in neuroblasts bringing the early temporal program and early temporal factor expression to a close.
SQ3370, the first clinical click chemistry-activated cancer therapeutic, shows safety in humans and translatability across species

Background SQ3370 is the first demonstration of the Click Activated Protodrugs Against Cancer (CAPAC™) platform that uses click chemistry to activate drugs directly at tumor sites, maximizing therapeutic exposure. SQ3370 consists of a tumor-localizing biopolymer (SQL70) and a chemically-attenuated doxorubicin (Dox) protodrug SQP33; the protodrug is activated upon clicking with the biopolymer at tumor sites. Here, we present data from preclinical studies and a Phase 1 dose-escalation clinical trial in adult patients with advanced solid tumors (NCT04106492) demonstrating SQ3370’s activation at tumor sites, safety, systemic pharmacokinetics (PK), and immunological activity. Methods Treatment cycles consisting of an intratumoral or subcutaneous injection of SQL70 biopolymer followed by 5 daily intravenous doses of SQP33 protodrug were evaluated in tumor-bearing mice, healthy dogs, and adult patients with solid tumors. Results SQL70 effectively activated SQP33 at tumor sites, resulting in high Dox concentrations that were well tolerated and unachievable by conventional treatment. SQ3370 was safely administered at 8.9x the veterinary Dox dose in dogs and 12x the conventional Dox dose in patients, with no dose-limiting toxicity reported to date. SQ3370’s safety, toxicology, and PK profiles were highly translatable across species. SQ3370 increased cytotoxic CD3+ and CD8+ T-cells in patient tumors indicating T-cell-dependent immune activation in the tumor microenvironment. Conclusions SQ3370, the initial demonstration of click chemistry in humans, enhances the safety of Dox at unprecedented doses and has the potential to increase therapeutic index. Consistent safety, toxicology, PK, and immune activation results observed with SQ3370 across species highlight the translatability of the click chemistry approach in drug development. Trial registration NCT04106492; 7 September 2019
Molecular Evidence of Internal Carbon-Driven Partial Denitrification Annamox (PdNA) in a mainstream Pilot A-B System Coupled with Side-stream EBPR treating municipal wastewater

Achieving mainstream short-cut nitrogen removal via nitrite has been a carbon and energy-efficient goal which wastewater engineers are dedicated to explore. This study applied a novel pilot-scale A-B-S2EBPR system process integrated with sidestream enhanced biological phosphorus removal) to achieve the nitrite accumulation and downstream anammox for treating municipal wastewater. Nitrite accumulated to 5.5 ± 0.3 mg N/L in the intermittently aerated tanks of B-stage with the nitrite accumulation ratio (NAR) of 79.1 ± 6.5%. The final effluent concentration and removal efficiency of total inorganic nitrogen (TIN) were 4.6 ± 1.8 mg N/L and 84.9 ± 5.6%, respectively. Batch nitrification/denitrification activity tests and functional gene abundance of ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) suggested that the nitrite accumulation was mostly caused by partial denitrification without NOB- selection. The unique features of S2EBPR (longer anaerobic HRT/SRT, lower ORPs, high and more complex VFAs etc.) seemed to impact the nitrogen microbial communities: the conventional AOB kept at a very low level of 0.13 ± 0.13% during the operation period, and the dominant candidate internal carbon-accumulating heterotrophic genera of Acinetobacter (17.8 ± 15.5)% and Comamonadaceae (6.7 ± 3.4%) were highly enriched. Furthermore, the single-cell Raman spectroscopy-based intracellular polymer analysis revealed the dominate microorganisms that could utilize polyhydroxyalkanoates (PHA) as the potential internal carbon source to drive partial denitrification. This study provides insights and a new direction for implementing the mainstream PdNA short-cut nitrogen removal via incorporating S2EBPR into sustainable A-B process.
Methylglyoxal is the main culprit to impairing neuronal function: mediated through tryptophan depletion

Depression is a common and prevalent illness and the exact cause of major depressive disorder is not known. Here, we investigated how methylglyoxal (MGO) stress induces depression and unveiled the potential molecular mechanism. Our in vivo results suggested that MGO caused depression in mice, confirmed by several behavioral tests. Interestingly, it halted the mice’s brain’s tryptophan levels and its related neurotransmitters. In addition, MGO induced a reduction in the number of cells in different hippocampal regions. Moreover, it decreased tryptophan hydroxylase 1 (TPH1) and tryptophan hydroxylase 1 (TPH2) levels in the brain and large intestine. Surprisingly, MGO showed the highest affinity and trapping ability toward tryptophan. Most importantly, combined treatment with MGO-tryptophan displayed similar effects as those exhibited by the tryptophan-null treatment in neuronal cells, which included neuronal apoptosis, decrease TPH1 and TPH2 levels, and inhibition of neuronal outgrowth. However, tryptophan treatment improved MGO induced depression-like behavior of mice and recovered the loss of neuronal and hippocampal cells. Subsequently, it also induced MGO detoxifying factors, tryptophan levels, and reduces inflammation in the intestine. Collectively, our data revealed that MGO induced depression facilitated by neuronal and synaptic dysfunction is mediated through the disturbance of tryptophan metabolism in the brain and intestine.
Ramen: Souper Fast Three-Party Computation for RAM Programs

Secure RAM computation allows a number of parties to evaluate a function represented as a random-access machine (RAM) program in a way that reveals nothing about the private inputs of the parties except from what is already revealed by the function output itself. In this work we present Ramen, which is a new protocol for computing RAM programs securely among three parties, tolerating up to one passive corruption. Ramen provides reasonable asymptotic guarantees and is concretely efficient at the same time. We have implemented our protocol and provide extensive benchmarks for various settings. Asymptotically, our protocol requires a constant number of rounds and an amortized sublinear amount of communication and computation per memory access. In terms of concrete efficiency, our protocol outperforms previous solutions. For a memory of size 226 our memory accesses are 25x faster in the LAN and 8x faster in the WAN setting, when compared to the previously fastest, and concurrent, solution by Vadapalli, Henry, and Goldberg (USENIX Security 2023). Due to our superior asymptotic guarantees, the efficiency gap is only widening as the memory gets larger and for this reason Ramen provides the currently most scalable concretely efficient solution for securely computing RAM programs.
The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature

Sour cherry (Prunus cerasus L.) is an economically important allotetraploid cherry species believed to have evolved in the Caspian Sea and Black Sea regions. How, when and where exactly the evolution of this species took place is unclear. It resulted from a hybridization of the tetraploid ground cherry (Prunus fruticosa Pall.) and an unreduced (2n) pollen of the diploid ancestor sweet cherry (P. avium L.). Some indications implement that the genome of sour cherry is segmental allopolyploid, but how it is structured and to what extent is unknown. To get an insight, the genome of the sour cherry cultivar ‘Schattenmorelle’ was sequenced at ~400x using Illumina NovaSeqTM short-read and Oxford Nanopore long-read technologies (ONT R9.4.1 PromethION). Additionally, the transcriptome of ‘Schattenmorelle’ was sequenced using PacBio Sequel II SMRT cell sequencing at ~300x. The final assembly resulted in a ~629 Mbp long pseudomolecule reference genome, which could be separated into two subgenomes each split into eight chromosomes. Subgenome PceS_a which originates from P. avium has a length of 269 Mbp, whereas subgenome PceS_f which originates from P. fruticosa has a length of 299.5 Mbp. The length of unassembled contigs was 60 Mbp. The genome of the sour cherry shows a size-reduction compared to the genomes of its ancestral species. It also shows traces of homoeologous sequence exchanges throughout the genome. Comparative positional sequence and protein analyses provided evidence that the genome of sour cherry is segmental allotetraploid and that it has evolved in a very recent event in the past.