PCR-based generation of shRNA libraries from cDNAs

BACKGROUND: The use of small interfering RNAs (siRNAs) to silence target gene expression has greatly facilitated mammalian genetic analysis by generating loss-of-function mutants. In recent years, high-throughput, genome-wide screening of siRNA libraries has emerged as a viable approach. Two different methods have been used to generate short hairpin RNA (shRNA) libraries; one is to use chemically synthesized oligonucleotides, and the other is to convert complementary DNAs (cDNAs) into shRNA cassettes enzymatically. The high cost of chemical synthesis and the low efficiency of the enzymatic approach have hampered the widespread use of screening with shRNA libraries. RESULTS: We report here an improved method for constructing genome-wide shRNA libraries enzymatically. The method includes steps of cDNA fragmentation and endonuclease MmeI digestion to generate 19-bp fragments, capping the 19-bp cDNA fragments with a hairpin oligonucleotide, and amplification of the hairpin structures by PCR. The PCR step converts hairpins into double-stranded DNAs that contain head-to-head cDNA fragments that can be cloned into a vector downstream of a Pol III promoter. CONCLUSION: This method can readily be used to generate shRNA libraries from a small amount of mRNA and thus can be used to create cell- or tissue-specific libraries

Rotational Differential-Linear Distinguishers of ARX Ciphers with Arbitrary Output Linear Masks

The rotational differential-linear attacks, proposed at EUROCRYPT 2021, is a generalization of differential-linear attacks by replacing the differential part of the attacks with rotational differentials. At EUROCRYPT 2021, Liu et al. presented a method based on Morawiecki et al.’s technique (FSE 2013) for evaluating the rotational differential-linear correlations for the special cases where the output linear masks are unit vectors. With this method, some powerful (rotational) differential-linear distinguishers with output linear masks being unit vectors against Friet, Xoodoo, and Alzette were discovered. However, how to compute the rotational differential-linear correlations for arbitrary output masks was left open. In this work, we partially solve this open problem by presenting an efficient algorithm for computing the (rotational) differential-linear correlation of modulo additions for arbitrary output linear masks, based on which a technique for evaluating the (rotational) differential-linear correlation of ARX ciphers is derived. We apply the technique to Alzette, Siphash, Chacha, and Speck. As a result, significantly improved (rotational) differential-linear distinguishers including deterministic ones are identified. All results of this work are practical and experimentally verified to confirm the validity of our methods. In addition, we try to explain the experimental distinguishers employed in FSE 2008, FSE 2016, and CRYPTO 2020 against Chacha. The predicted correlations are close to the experimental ones

Signature of the coexistence of ferromagnetism and superconductivity at KTaO3_3 heterointerfaces

The coexistence of superconductivity and ferromagnetism is a long-standing issue in the realm of unconventional superconductivity due to the antagonistic nature of these two ordered states. Experimentally identifying and characterizing novel heterointerface superconductors that coexist with magnetism is challenging. Here, we report the experimental observation of long-range ferromagnetic order at the verge of two-dimensional superconductivity at KTaO$_3$ heterointerfaces. Remarkably, we observe in-plane magnetization hysteresis loop persisting up to room temperature with direct current superconducting quantum interference device measurements. Furthermore, first-principles calculations suggest that the observed robust ferromagnetism is attributed to the presence of oxygen vacancies that localize electrons in nearby Ta 5$d$ states. Our findings not only indicate KTaO$_3$ heterointerfaces as unconventional superconductors with time-reversal symmetry breaking, but also inject a new momentum to the study of the delicate interplay between superconductivity and magnetism boosted by strong spin-orbit coupling inherent to the heavy Ta in 5$d$ orbitals of KTaO$_3$ heterointerfaces.Comment: 7 pages, 3 figure

A Note on the Bias of Rotational Differential-Linear Distinguishers

This note solves the open problem of finding a closed formula for the bias of a rotational differential-linear distinguisher proposed in IACR ePrint 2021/189 (EUROCRYPT 2021), completely generalizing the results on ordinary differential-linear distinguishers due to Blondeau, Leander, and Nyberg (JoC 2017) to the case of rotational differential-linear distinguishers

High-Speed Modular Multipliers for Isogeny-Based Post-Quantum Cryptography

As one of the post-quantum protocol candidates, the supersingular isogeny key encapsulation (SIKE) protocol delivers promising public and secret key sizes over other candidates. Nevertheless, the considerable computations form the bottleneck and limit its practical applications. The modular multiplication operations occupy a large proportion of the overall computations required by the SIKE protocol. The VLSI implementation of the high-speed modular multiplier remains a big challenge. In this paper, we propose three improved modular multiplication algorithms based on an unconventional radix for this protocol, all of which cost about 20% fewer computations than the prior art. Besides, a multi-precision scheme is also introduced for the proposed algorithms to improve the scalability in hardware implementation, resulting in three new algorithms. We then present very efficient high-speed modular multiplier architectures for the six algorithms. It is shown that these new architectures can be highly optimized and extensively pipelined to obtain high throughput thanks to the adopted overlapping processing scheme. The FPGA implementation results show the proposed multipliers without the multi-precision scheme all achieve about 60 times higher throughput than the state-of-the-art design (the FFM2 multiplier), and those with the multi-precision scheme all acquire almost 10 times higher throughput than this work. Meanwhile, each of the multi-precision based designs has almost the same resource consumptions as the FFM2 does

Quantum metallic state in the titanium sesquioxide heterointerface superconductor

The emergence of the quantum metallic state marked by a saturating finite electrical resistance in the zero-temperature limit in a variety of two-dimensional superconductors injects a new momentum to the realm of unconventional superconductivity. Despite much research efforts over last few decades, there is not yet a general consensus on the nature of this unexpected quantum metal. Here, we report the unique quantum metallic state within the hallmark of Bose-metal characterized by the saturated resistance and simultaneously vanished Hall resistance in the titanium sesquioxide heterointerface superconductor Ti$_2$O$_3$/GaN. Strikingly, the quantum bosonic metallic state proximate to the two-dimensional superconductivity-metal transition tuned by magnetic fields persists in the normal phase, suggesting that the existence of composite bosons formed by electron Cooper pairs survives even in the normal phase. Our work marks the observation of the preformed electron Cooper pairs in heterointerface superconductor and sheds new light on understanding the underlying pairing mechanism of unconventional superconductivity.Comment: 6 pages, 4 figure

High-Speed Low-Power Viterbi Decoder Design for TCM Decoders

High-speed, low-power design of Viterbi decoders for trellis coded modulation (TCM) systems is presented in this paper. It is well known that the Viterbi decoder (VD) is the dominant module determining the overall power consumption of TCM decoders. We propose a pre-computation architecture incorporated with T-algorithm for VD, which can effectively reduce the power consumption without degrading the decoding speed much. A general solution to derive the optimal pre-computation steps is also given in the paper. Implementation result of a VD for a rate-3/4 convolutional code used in a TCM system shows that compared with the full trellis VD, the pre-computation architecture reduces the power consumption by as much as 70% without performance loss, while the degradation in clock speed is negligible.This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by IEEE and can be found at: http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=6257480. ©2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.Keywords: Trellis coded modulation (TCM), Viterbi decoder, VLS

Efficient Software Implementation of the SIKE Protocol Using a New Data Representation

Thanks to relatively small public and secret keys, the Supersingular Isogeny Key Encapsulation (SIKE) protocol made it into the third evaluation round of the post-quantum standardization project of the National Institute of Standards and Technology (NIST). Even though a large body of research has been devoted to the efficient implementation of SIKE, its latency is still undesirably long for many real-world applications. Most existing implementations of the SIKE protocol use the Montgomery representation for the underlying field arithmetic since the corresponding reduction algorithm is considered the fastest method for performing multiple-precision modular reduction. In this paper, we propose a new data representation for supersingular isogeny-based Elliptic-Curve Cryptography (ECC), of which SIKE is a sub-class. This new representation enables significantly faster implementations of modular reduction than the Montgomery reduction, and also other finite-field arithmetic operations used in ECC can benefit from our data representation. We implemented all arithmetic operations in C using the proposed representation such that they have constant execution time and integrated them to the latest version of the SIKE software library. Using four different parameters sets, we benchmarked our design and the optimized generic implementation on a 2.6 GHz Intel Xeon E5-2690 processor. Our results show that, for the prime of SIKEp751, the proposed reduction algorithm is approximately 2.61 times faster than the currently best implementation of Montgomery reduction, and our representation also enables significantly better timings for other finite-field operations. Due to these improvements, we were able to achieve a speed-up by a factor of about 1.65, 2.03, 1.61, and 1.48 for SIKEp751, SIKEp610, SIKEp503, and SIKEp434, respectively, compared to state-of-the-art generic implementations.IKEp751, SIKEp610, SIKEp503, and SIKEp434, respectively, compared to state-of-the-art generic implementations

Middle Jurassic terrestrial environmental and floral changes linked to volcanism: Evidence from the Qinghai Tibet Plateau, China

The breakup of Pangaea and the rapid opening of the Ligurian and Central Atlantic oceans during the Middle Jurassic resulted in widespread volcanism accompanied by significant shifts in global environments, climates, and floras. Although major volcanism is a plausible driver of such global changes, linking these phenomena in the Middle Jurassic is hindered by a lack of detailed sedimentary records from which to evaluate cause and effect. Here, we link Middle Jurassic environmental, climatic, and floral changes with volcanism using records from the Dameigou section of the Qaidam Basin on the Qinghai-Tibet Plateau. High-resolution chemostratigraphic (δ13Corg patterns) and biostratigraphic (palynological fossils) data reveal three negative organic carbon isotope excursions (NCIE) at the Aalenian-Bajocian boundary, the Bajocian-Bathonian boundary, and in the middle of the Callovian, respectively. The first two NCIEs (NCIE-I and NCIE-II) were accompanied by relatively warm and humid climatic conditions and coal accumulation. In contrast, the third NCIE (NCIE-III) was accompanied by warm but dry climatic conditions, a decrease in coal accumulation, a decline in plant diversity, the significant decline in fern spore diversity and abundance, and a rapid increase in the abundance of Classopollis pollen (based on petrological, palynological, PCA, Hydrophyte/Xerophyte ratio, and nMDS data). Four sedimentary mercury anomalies (Hg/Al spikes) have temporal coincidence with the three NCIEs and climate warming events, suggesting a volcanic origin for these. We suggest that volcanism was a key driver of Middle Jurassic change, with major pulses releasing large amounts of CO2 and Hg into the atmosphere, resulting in Hg loading, NCIEs, climatic warming, and floral changes in terrestrial strata. Our multi-proxy study provides new insights into the links between volcanism and terrestrial environmental, climatic, and floral changes during the Middle Jurassic

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1H NMR-based metabolic profiling combined with multivariate data analysis was used to explore the metabolic phenotype of functional dyspepsia (FD) in stressed rats and evaluate the intervention effects of the Chinese medicine Weikangning (WKN). After a 7-day period of model establishment, a 14-day drug administration schedule was conducted in a WKN-treated group of rats, with the model and normal control groups serving as negative controls. Based on 1H NMR spectra of urine and serum from rats, PCA, PLS-DA, and OPLS-DA were performed to identify changing metabolic profiles. According to the key metabolites determined by OPLS-DA, alterations in energy metabolism, stress-related metabolism, and gut microbiota were found in FD model rats after stress stimulation, and these alterations were restored to normal after WKN administration. This study may provide new insights into the relationship between FD and psychological stress and assist in research into the metabolic mechanisms involved in Chinese medicine