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  1. Abstract

    NAKED ENDOSPERM1 (NKD1), NKD2, and OPAQUE2 (O2) are transcription factors important for cell patterning and nutrient storage in maize (Zea mays) endosperm. To study the complex regulatory interrelationships among these 3 factors in coregulating gene networks, we developed a set of nkd1, nkd2, and o2 homozygous lines, including all combinations of mutant and wild-type genes. Among the 8 genotypes tested, we observed diverse phenotypes and gene interactions affecting cell patterning, starch content, and storage proteins. From ∼8 to ∼16 d after pollination, maize endosperm undergoes a transition from cellular development to nutrient accumulation for grain filling. Gene network analysis showed that NKD1, NKD2, and O2 dynamically regulate a hierarchical gene network during this period, directing cellular development early and then transitioning to constrain cellular development while promoting the biosynthesis and storage of starch, proteins, and lipids. Genetic interactions regulating this network are also dynamic. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) showed that O2 influences the global regulatory landscape, decreasing NKD1 and NKD2 target site accessibility, while NKD1 and NKD2 increase O2 target site accessibility. In summary, interactions of NKD1, NKD2, and O2 dynamically affect the hierarchical gene network and regulatory landscape during the transition from cellular development to grain filling in maize endosperm.

     
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  2. Abstract

    In recent years, deep learning gained proliferating popularity in the cybersecurity application domain, since when being compared to traditional machine learning methods, it usually involves less human efforts, produces better results, and provides better generalizability. However, the imbalanced data issue is very common in cybersecurity, which can substantially deteriorate the performance of the deep learning models. This paper introduces a transfer learning based method to tackle the imbalanced data issue in cybersecurity using return-oriented programming payload detection as a case study. We achieved 0.0290 average false positive rate, 0.9705 average F1 score and 0.9521 average detection rate on 3 different target domain programs using 2 different source domain programs, with 0 benign training data sample in the target domain. The performance improvement compared to the baseline is a trade-off between false positive rate and detection rate. Using our approach, the total number of false positives is reduced by 23.16%, and as a trade-off, the number of detected malicious samples decreases by 0.68%.

     
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  3. Free, publicly-accessible full text available April 1, 2024
  4. Abstract

    We developed intramolecular carboxyamidations of alkyne‐tetheredO‐acylhydroxamates followed by either thermally induced spontaneous or 4‐(dimethylamino)pyridine‐catalyzed O→O or O→N acyl group migration. Under iron‐catalyzed conditions, the carboxyamidation products were generated in high yield from bothZ‐alkene and arene‐tethered substrates. DFT calculations indicate that the iron‐catalyzed carboxyamidation proceeds via a stepwise mechanism involving iron‐imidyl radical cyclization followed by intramolecular acyloxy transfer from the iron center to the alkenyl radical center to furnish thecis‐carboxyamidation product. Upon treatment with 4‐(dimethylamino)pyridine, theZ‐alkene‐tethered carboxyamidation products underwent selective O→O acyl migration to generate 2‐acyloxy‐5‐acyl pyrroles. Thermal O→N acyl migration occurs during carboxyamidation if theZ‐alkene linker contains an alkyl or an aryl substituent at the β‐position of the carbonyl group. On the other hand, the arene linker‐containing compounds selectively undergo O→N acyl migration to generateN‐acyl‐3‐acylisoindolinones, and the corresponding O→O acyl migration forming isoindole derivatives was not observed.

     
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  5. Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation. 
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  6. With the rapid expansion of the Internet of Things, a vast number of microcontroller-based IoT devices are now susceptible to attacks through the Internet. Vulnerabilities within the firmware are one of the most important attack surfaces. Fuzzing has emerged as one of the most effective techniques for identifying such vulnerabilities. However, when applied to IoT firmware, several challenges arise, including: (1) the inability of firmware to execute properly in the absence of peripherals, (2) the lack of support for exploring input spaces of multiple peripherals, (3) difficulties in instrumenting and gathering feedback, and (4) the absence of a fault detection mechanism. To address these challenges, we have developed and implemented an innovative peripheral-independent hybrid fuzzing tool called . This tool enables testing of microcontroller-based firmware without reliance on specific peripheral hardware. First, a unified virtual peripheral was integrated to model the behaviors of various peripherals, thus enabling the physical devices-agnostic firmware execution. Then, a hybrid event generation approach was used to generate inputs for different peripheral accesses. Furthermore, two-level coverage feedback was collected to optimize the testcase generation. Finally, a plugin-based fault detection mechanism was implemented to identify typical memory corruption vulnerabilities. A Large-scale experimental evaluation has been performed to show ’s effectiveness and efficiency. 
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  7. Although the importance of using static taint analysis to detect taint-style vulnerabilities in Linux-based embedded firmware is widely recognized, existing approaches are plagued by following major limitations: (a) Existing works cannot properly handle indirect call on the path from attacker-controlled sources to security-sensitive sinks, resulting in lots of false negatives. (b) They employ heuristics to identify mediate taint source and it is not accurate enough, which leads to high false positives. To address issues, we propose EmTaint, a novel static approach for accurate and fast detection of taint-style vulnerabilities in Linux-based embedded firmware. In EmTaint, we first design a structured symbolic expression-based (SSE-based) on-demand alias analysis technique. Based on it, we come up with indirect call resolution and accurate taint analysis scheme. Combined with sanitization rule checking, EmTaint can eventually discovers a large number of taint-style vulnerabilities accurately within a limited time. We evaluated EmTaint against 35 real-world embedded firmware samples from six popular vendors. The result shows EmTaint discovered at least 192 vulnerabilities, including 41 n-day vulnerabilities and 151 0-day vulnerabilities. At least 115 CVE/PSV numbers have been allocated from a subset of the reported vulnerabilities at the time of writing. Compared with state-of-the-art tools such as KARONTE and SaTC, EmTaint found significantly more vulnerabilities on the same dataset in less time. 
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  8. Abstract

    Methods that can simultaneously install multiple different functional groups to heteroarenes via C−H functionalizations are valuable for complex molecule synthesis, which, however, remain challenging to realize. Here we report the development of vicinal di‐carbo‐functionalization of indoles in a site‐ and regioselective manner, enabled by the palladium/norbornene (Pd/NBE) cooperative catalysis. The reaction is initiated by the Pd(II)‐mediated C3‐metalation and specifically promoted by the C1‐substituted NBEs. The mild, scalable, and robust reaction conditions allow for a good substrate scope and excellent functional group tolerance. The resulting C2‐arylated C3‐alkenylated indoles can be converted to diverse synthetically useful scaffolds. The combined experimental and computational mechanistic study reveals the unique role of the C1‐substituted NBE in accelerating the turnover‐limiting oxidative addition step.

     
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