Validation, Optimization, and Application of the Zebrafish Developmental Toxicity Assay for Pharmaceuticals Under the ICH S5(R3) Guideline

The zebrafish as an alternative animal model for developmental toxicity testing has been extensively investigated, but its assay protocol was not harmonized yet. This study has validated and optimized the zebrafish developmental toxicity assay previously reported by multiple inter-laboratory studies in the United States and Europe. In this study, using this classical protocol, of 31 ICH-positive compounds, 23 compounds (74.2%) were teratogenic in zebrafish, five had false-negative results, and three were neither teratogenic nor non-teratogenic according to the protocol standard; of 14 ICH-negative compounds, 12 compounds (85.7%) were non-teratogenic in zebrafish and two had false-positive results. After we added an additional TI value in the zebrafish treated with testing compounds at 2 dpf along with the original 5 dpf, proposed a new category as the uncategorized compounds for those TI values smaller than the cutoff both at 2 dpf and 5 dpf but inducing toxic phenotypes, refined the testing concentration ranges, and optimized the TI cut-off value from ≥ 10 to ≥ 3 for compounds with refined testing concentrations, this optimized zebrafish developmental assay reached 90.3% sensitivity (28/31 positive compounds were teratogenic in zebrafish) and 88.9% (40/45) overall predictability. Our results from this study strongly support the use of zebrafish as an alternative in vivo method for screening and assessing the teratogenicity of candidate drugs for regulatory acceptance.

The role of localizable concurrence in quantum teleportation protocols

Teleporting an unknown qubit state is a paradigmatic quantum information processing task revealing the advantage of quantum communication protocols over their classical counterpart. For a teleportation protocol using a Bell state as quantum channel, the resource has been identified to be the concurrence. However, for mixed multipartite states the lack of computable entanglement measures has made the identification of the quantum resource responsible for this advantage more challenging. Here, by building on previous results showing that localizable concurrence is the necessary resource for controlled quantum teleportation, we show that any teleportation protocol using an arbitrary multipartite state, that includes a Bell measurement, requires a nonvanishing localizable concurrence between two of its parties to perform better than the classical protocol. By first analyzing Greenberger–Horne–Zeilinger (GHZ) channel and GHZ measurement teleportation protocol, in the presence of GHZ-symmetric-preserving noise, we compare different multipartite entanglement measures with the fidelity of teleportation, and we find that the protocol performs better than the classical protocol when all multipartite entanglement measures vanish, except for the localizable concurrence. Finally, we extend our proof to an arbitrary teleportation protocol with an arbitrary multipartite entangled channel.

Cultivation of a lytic double-stranded RNA bacteriophage infecting Microvirgula aerodenitrificans reveals a mutualistic parasitic lifestyle

Bacteriophages are considered the most abundant entities on earth. However, there are merely seven sequenced double-stranded (ds)RNA phages compared with thousands of dsDNA phages. Interestingly, dsRNA viruses are quite common in fungi and usually have a lifestyle of commensalism or mutualism. Thus, the classical protocol of using double-layer agar plates to characterize phage plaques might be significantly biased in the isolation of dsRNA phages beyond strictly lytic lifestyles. Thus, we applied the protocol of isolating fungal viruses to identify RNA phages in bacteria and successfully isolated a novel dsRNA phage, phiNY, from Microvirgula aerodenitrificans . phiNY has a genome of three dsRNA segments, and its genome sequence has no nucleotide sequence similarity with any other phage. Although phiNY encodes a lytic protein of glycoside hydrolase and phage particles are consistently released during bacterial growth, phiNY replication did not block bacteria growth, nor did it form any plaque on agar plates. More strikingly, the phiNY-infected strain grew faster than the phiNY-negative strain, indicating a mutualistic parasitic lifestyle. Thus, this study not only reveals a new mutualistic parasitic dsRNA phage but also implies that other virus isolation methods would be valuable to identify phages with other lifestyles. Importance Viruses with dsRNA genomes are quite diverse and infect organisms in all three domains of life. Though dsRNA viruses infecting humans, plants and fungi are quite common, dsRNA viruses infecting bacteria, known as bacteriophages, are quite understudied and only seven dsRNA phages have been sequenced so far. One possible explanation for the rare isolation of dsRNA phages might be the protocols of double-layer agar plates assay. Phages beyond strictly lytic lifestyles might not form plaques. Thus, we applied the protocol of isolating fungal viruses to identify RNA phages inside bacteria and successfully isolated a novel dsRNA phage phiNY with a mutualistic parasitic lifestyle. This study implies dsRNA phages beyond strictly lytic lifestyle might be common in nature and deserves more investigations.

Complementary methods for SARS-CoV-2 diagnosis in times of material shortage

The pandemic caused by SARS-CoV-2 resulted in increasing demands for diagnostic tests, leading to a shortage of recommended testing materials and reagents. This study reports on the performance of self-sampled alternative swabbing material (ordinary Q-tips tested against flocked swab and rayon swab), of reagents for classical RNA extraction (phenol/guanidine-based protocol against a commercial kit), and of intercalating dye-based one-step quantitative reverse transcription real-time PCRs (RT-qPCR) compared against the gold standard hydrolysis probe-based assays for SARS-CoV-2 detection. The study found sampling with Q-tips, RNA extraction with classical protocol and intercalating dye-based RT-qPCR as a reliable and comparably sensitive strategy for detection of SARS-CoV-2—particularly valuable in the current period with a resurgent and dramatic increase in SARS-CoV-2 infections and growing shortage of diagnostic materials especially for regions limited in resources.

An Extensive Formal Analysis of Multi-factor Authentication Protocols

Passwords are still the most widespread means for authenticating users, even though they have been shown to create huge security problems. This motivated the use of additional authentication mechanisms in so-called multi-factor authentication protocols. In this article, we define a detailed threat model for this kind of protocol: While in classical protocol analysis attackers control the communication network, we take into account that many communications are performed over TLS channels, that computers may be infected by different kinds of malware, that attackers could perform phishing, and that humans may omit some actions. We formalize this model in the applied pi calculus and perform an extensive analysis and comparison of several widely used protocols—variants of Google 2-step and FIDO’s U2F (Yubico’s Security Key token). The analysis is completely automated, generating systematically all combinations of threat scenarios for each of the protocols and using the P ROVERIF tool for automated protocol analysis. To validate our model and attacks, we demonstrate their feasibility in practice, even though our experiments are run in a laboratory environment. Our analysis highlights weaknesses and strengths of the different protocols. It allows us to suggest several small modifications of the existing protocols that are easy to implement, as well as an extension of Google 2-step that improves security in several threat scenarios.

Diagnosis of SARS-CoV-2 infections in times of material shortage

The pandemic caused by SARS-CoV-2 resulted in increasing demands for diagnostic tests, leading to a shortage of recommended testing materials and reagents. This study reports on the performance of self-sampled alternative swabbing material (ordinary Q-tips tested against flocked swab and rayon swab), of reagents for classical RNA extraction (phenol/guanidine-based protocol against a commercial kit), and of intercalating dye-based one-step quantitative reverse transcription real-time PCRs (RT-qPCR) compared against the gold standard hydrolysis probe-based assays for SARS-CoV-2 detection. The study found sampling with Q-tips, RNA extraction with classical protocol and intercalating dye-based RT-qPCR as a reliable and comparably sensitive strategy for detection of SARS-CoV-2 - particularly valuable in the current period with a resurgent and dramatic increase in SARS-CoV-2 infections and growing shortage of diagnostic materials as well for regions limited in resources.

Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages

ABSTRACT As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is less expensive and can be as efficient as the classical protocol, which involves column purification of the viral RNA. In addition, it bypasses the need for swab sampling, decreases the risk of the health care personnel involved in the testing process, and accelerates the diagnostic procedure.

Saliva sampling is an excellent option to increase the number of SARS CoV2 diagnostic tests in settings with supply shortages

As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for SARS CoV-2. Detection of the viral genome through RT-qPCR is the golden standard for this test, however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR test has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is cheaper and can be as efficient as the classical protocol that involves column purification of the viral RNA. In addition, it surpasses the need for swab sampling, decreases the risk of the healthcare personnel involved in this process, and accelerates the diagnostic procedure.

Experimental demonstration of quantum advantage for one-way communication complexity surpassing best-known classical protocol

Demonstrating a quantum advantage with currently available experimental systems is of utmost importance in quantum information science. While this remains elusive for quantum computation, the field of communication complexity offers the possibility to already explore and showcase this advantage for useful tasks. Here, we define such a task, the Sampling Matching problem, which is inspired by the Hidden Matching problem and features an exponential gap between quantum and classical protocols in the one-way communication model. Our problem allows by its conception a photonic implementation based on encoding in the phase of coherent states of light, the use of a fixed size linear optic circuit, and single-photon detection. This enables us to demonstrate in a proof-of-principle experiment an advantage in the transmitted information resource over the best known classical protocol, something impossible to reach for the original Hidden Matching problem. Our demonstration has implications in quantum verification and cryptographic settings.