Bioinspired Quantum Oracle Circuits for Biomolecular Solutions of the Maximum Cut Problem.

Given an undirected, unweighted graph with n vertices and m edges, the maximum cut problem is to find a partition of the n vertices into disjoint subsets V1 and V2 such that the number of edges between them is as large as possible. Classically, it is an NP-complete problem, which has potential applications ranging from circuit layout design, statistical physics, computer vision, machine learning and network science to clustering. In this paper, we propose a biomolecular and a quantum algorithm to solve the maximum cut problem for any graph G. The quantum algorithm is inspired by the biomolecular algorithm and has a quadratic speedup over its classical counterparts, where the temporal and spatial complexities are reduced to, respectively, [Formula: see text] and [Formula: see text]. With respect to oracle-related quantum algorithms for NP-complete problems, we identify our algorithm as optimal. Furthermore, to justify the feasibility of the proposed algorithm, we successfully solve a typical maximum cut problem for a graph with three vertices and two edges by carrying out experiments on IBM's quantum simulator.

Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae).

BACKGROUND: The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. RESULTS: These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599-31,486 bp) separated by a large single-copy region (LSC: 82,048-94,046 bp) and a small single-copy region (SSC: 16,343-17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL-accD, ycf4-cemA, petA-psbJ, ycf1-ndhF, ndhF-rpl32 and ycf1, and it was found that ndhF-rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. CONCLUSION: The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF-rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.

Biomolecular and quantum algorithms for the dominating set problem in arbitrary networks.

A dominating set of a graph [Formula: see text] is a subset U of its vertices V, such that any vertex of G is either in U, or has a neighbor in U. The dominating-set problem is to find a minimum dominating set in G. Dominating sets are of critical importance for various types of networks/graphs, and find therefore potential applications in many fields. Particularly, in the area of communication, dominating sets are prominently used in the efficient organization of large-scale wireless ad hoc and sensor networks. However, the dominating set problem is also a hard optimization problem and thus currently is not efficiently solvable on classical computers. Here, we propose a biomolecular and a quantum algorithm for this problem, where the quantum algorithm provides a quadratic speedup over any classical algorithm. We show that the dominating set problem can be solved in [Formula: see text] queries by our proposed quantum algorithm, where n is the number of vertices in G. We also demonstrate that our quantum algorithm is the best known procedure to date for this problem. We confirm the correctness of our algorithm by executing it on IBM Quantum's qasm simulator and the Brooklyn superconducting quantum device. And lastly, we show that molecular solutions obtained from solving the dominating set problem are represented in terms of a unit vector in a finite-dimensional Hilbert space.

[Protective effect of vitrification and controlled slow freezing on immature testicular tissue].

OBJECTIVE: To explore and compare the current mainstream testicular tissue freezing methods, namely vitrification and controlled slow freezing, and optimize the best testicular tissue freezing methods. METHODS: Testicular tissues of 3-week-old mice and <2-year old prepubertal cynomophage monkeys were collected and cut to 6-26 mm3, and divided into three groups: Fresh group, vitrification group and controlled slow freezing group were resuscitated after 5-7 days of freezing. HE staining, immunofluorescence staining, TUNEL staining and Western blot were used to evaluate the frozen-thawed testicular tissue. RESULTS: 1. In the testes of C57BL6/J mice, the expression level of spermatogonial stem cell marker UCHL1 in the controlled slow freezing group was higher than that in the vitrification group, and the content of apoptotic cells (TUNEL+ cells) was lower than that in the vitrification group. 2. In the testicular tissue of cynomolgus monkeys, the expression levels of spermatogonial stem cell markers UCHL1 and cell proliferation marker PCNA in the CSF group were higher than those in the vitrification group. CONCLUSION: Both vitrification and CSF can successfully preserve the testes of immature mice and cynomolgus monkeys before puberty. However, in the vitrification, there are more frozen damaged areas in the testicular tissue with the frozen volume of 6-26mm3, which may affect the cryopreservation of spermatogonial stem cells in the testicular tissue.

Quantum Speedup for Inferring the Value of Each Bit of a Solution State in Unsorted Databases Using a Bio-Molecular Algorithm on IBM Quantum's Computers.

In this paper, we propose a bio-molecular algorithm with O( n 2) biological operations, O( 2n-1 ) DNA strands, O( n ) tubes and the longest DNA strand, O( n ), for inferring the value of a bit from the only output satisfying any given condition in an unsorted database with 2n items of n bits. We show that the value of each bit of the outcome is determined by executing our bio-molecular algorithm n times. Then, we show how to view a bio-molecular solution space with 2n-1 DNA strands as an eigenvector and how to find the corresponding unitary operator and eigenvalues for inferring the value of a bit in the output. We also show that using an extension of the quantum phase estimation and quantum counting algorithms computes its unitary operator and eigenvalues from bio-molecular solution space with 2n-1 DNA strands. Next, we demonstrate that the value of each bit of the output solution can be determined by executing the proposed extended quantum algorithms n times. To verify our theorem, we find the maximum-sized clique to a graph with two vertices and one edge and the solution b that satisfies b2 ≡ 1 (mod 15) and using IBM Quantum's backend.

Quantum Speedup and Mathematical Solutions of Implementing Bio-Molecular Solutions for the Independent Set Problem on IBM Quantum Computers.

In this paper, we propose a bio-molecular algorithm with O( n2 + m ) biological operations, O( 2n ) DNA strands, O( n ) tubes and the longest DNA strand, O( n ), for solving the independent-set problem for any graph G with m edges and n vertices. Next, we show that a new kind of the straightforward Boolean circuit yielded from the bio-molecular solutions with m NAND gates, ( m +n × ( n + 1 )) AND gates and (( n × ( n + 1 ))/2) NOT gates can find the maximal independent-set(s) to the independent-set problem for any graph G with m edges and n vertices. We show that a new kind of the proposed quantum-molecular algorithm can find the maximal independent set(s) with the lower bound Ω ( 2n/2 ) queries and the upper bound O( 2n/2 ) queries. This work offers an obvious evidence for that to solve the independent-set problem in any graph G with m edges and n vertices, bio-molecular computers are able to generate a new kind of the straightforward Boolean circuit such that by means of implementing it quantum computers can give a quadratic speed-up. This work also offers one obvious evidence that quantum computers can significantly accelerate the speed and enhance the scalability of bio-molecular computers. Next, the element distinctness problem with input of n bits is to determine whether the given 2n real numbers are distinct or not. The quantum lower bound of solving the element distinctness problem is Ω ( 2n×(2/3) ) queries in the case of a quantum walk algorithm. We further show that the proposed quantum-molecular algorithm reduces the quantum lower bound to Ω (( 2n/2 )/( [Formula: see text]) queries. Furthermore, to justify the feasibility of the proposed quantum-molecular algorithm, we successfully solve a typical independent set problem for a graph G with two vertices and one edge by carrying out experiments on the backend ibmqx4 with five quantum bits and the backend simulator with 32 quantum bits on IBM's quantum computer.

Quantum Speedup for Protein Structure Prediction.

Protein structure prediction (PSP) predicts the native conformation for a given protein sequence. Classically, the problem has been shown to belong to the NP-complete complexity class. Its applications range from physics, through bioinformatics to medicine and quantum biology. It is possible however to speed it up with quantum computational methods, as we show in this paper. Here we develop a fast quantum algorithm for PSP in three-dimensional hydrophobic-hydrophilic model on body-centered cubic lattice with quadratic speedup over its classical counterparts. Given a protein sequence of n amino acids, our algorithm reduces the temporal and spatial complexities to, respectively, [Formula: see text] and O(n2 logn) . With respect to oracle-related quantum algorithms for the NP-complete problems, we identify our algorithm as optimal. To justify the feasibility of the proposed algorithm we successfully solve the problem on IBM quantum simulator involving 21 and 25 qubits. We confirm the experimentally obtained high probability of success in finding the desired conformation by calculating the theoretical probability estimations.

[The Molecular Switches and Atomic Biological Mechanisms Underlying the Physiological and Pathophysio-logical Effects of Hydrogen Sulfide to Regulate Its "Receptors"].

Hydrogen sulfide (H2S)has emerged as pivotal signaling molecules since it is recognized as the third gasotransmitter together with nitric oxide and carbon monoxide. The development of detecting technologies contributed to the research in H2S biology.H2S plays significant roles in human body systems, such as the cardiovascular system, nervous system, respiratory system etc.. Alterations of H2S concentrations have been connected with many diseases. Hypertension, atherosclerosis, neurodegenerative disorder, asthma and many other diseases are found to be related with abnormal H2S metabolism. It has become a potential drug for therapeutic purposes. Understanding the mechanism of H2S biology, including a molecular switch contained in its "receptor", has deepened the research on how small molecules regulate big molecules, as well as providing new strategy for the therapeutic approaches for varies of diseases.

[Dispute for Japanese(wild) honeysuckle flower based on supermolecular imprinting templates].

More and more disputes have happened to confront us continuously since the separation of Japanese(wild) honeysuckle flower in Chinese Pharmacopoeia in 2005. The state pharmacopeia committee decided to separate Japanese(wild) honeysuckle flower into two species for japanese(wild) honeysuckle flower, but didn't define their the convincing reasons still did not provide to us as a result that two medicines are not described the differences in natural properties, efficiency and indication, usage and dosage, as well as not given a resolving methodand specific solution. It was known for us that in the history of traditional Chinese medicine（TCM）, the phenomenenphenomena of the "one drug from multi-species" and "one species for multi-drug" are very ordinary thingswere ubiquitous. Whether separation of the drug species are separated shall be decided to by clinical efficiency. Through Chinese pharmacopoeia (2015 edition) issue of Chinese Pharmacopoeia the 2015 issue of the Chinese Pharmacopoeia, we still cannot find a scientific solution for the dispute of for Japanese (wild) honeysuckle flower, perhaps because of insufficient reorganization of TCM clinical medication regularities, such as "treatment of different diseases with same drug", " treatment of the same disease with different drugs" and "treatment of the same syndrome with multi-prescriptions", and "one prescription treating multiple syndromes"; lack of in-depth analysis for multi-component TCM compounds and autonomisation of "supermolecular template" for organs and meridians; less attention to the advance of efficacy and safety evaluation technologies for multi-component TCM compounds; impacts from the medication mode of "one ingredient-one composition-one effect"; as well as insufficient research methods for bioequivalent evaluation in preclinic and clinic studies . The dispute for species combination or separation for Japanese(wild) honeysuckle flower was apparently caused by regional economy, drug biological equivalent of efficacy and safety, but arising from clinical principles for systematical syndrome treatment with TCM, or concepts in the treatment of diseases with TCM or western medicines. This paper focused on current studies on Japanese(wild) honeysuckle flower in the combination with TCM clinical medication regularities, such as "treatment of different diseases with same drug", "treatment of the same disease with different drugs" and "treatment of the same syndrome with multi-prescriptions", and "one prescription treating multiple syndromes", expounded the specific pharmacological regularity of "heterogeneous equivalence" of Japanese (wild) honeysuckle flower, and put forward methods for studying bioequivalence of Japanese(wild) honeysuckle flower, in order to solve the combination and separation of Japanese(wild) honeysuckle flower and lay a foundation for promoting the development of Chinese herbal medicine industry.

Dispute for Japanese(wild) honeysuckle flower based on supermolecular imprinting templates / 中国中药杂志

More and more disputes have happened to confront us continuously since the separation of Japanese(wild) honeysuckle flower in Chinese Pharmacopoeia in 2005. The state pharmacopeia committee decided to separate Japanese(wild) honeysuckle flower into two species for japanese(wild) honeysuckle flower, but didn't define their the convincing reasons still did not provide to us as a result that two medicines are not described the differences in natural properties, efficiency and indication, usage and dosage, as well as not given a resolving methodand specific solution. It was known for us that in the history of traditional Chinese medicine（TCM）, the phenomenenphenomena of the "one drug from multi-species" and "one species for multi-drug" are very ordinary thingswere ubiquitous. Whether separation of the drug species are separated shall be decided to by clinical efficiency. Through Chinese pharmacopoeia (2015 edition) issue of Chinese Pharmacopoeia the 2015 issue of the Chinese Pharmacopoeia, we still cannot find a scientific solution for the dispute of for Japanese (wild) honeysuckle flower, perhaps because of insufficient reorganization of TCM clinical medication regularities, such as "treatment of different diseases with same drug", " treatment of the same disease with different drugs" and "treatment of the same syndrome with multi-prescriptions", and "one prescription treating multiple syndromes"; lack of in-depth analysis for multi-component TCM compounds and autonomisation of "supermolecular template" for organs and meridians; less attention to the advance of efficacy and safety evaluation technologies for multi-component TCM compounds; impacts from the medication mode of "one ingredient-one composition-one effect"; as well as insufficient research methods for bioequivalent evaluation in preclinic and clinic studies . The dispute for species combination or separation for Japanese(wild) honeysuckle flower was apparently caused by regional economy, drug biological equivalent of efficacy and safety, but arising from clinical principles for systematical syndrome treatment with TCM, or concepts in the treatment of diseases with TCM or western medicines. This paper focused on current studies on Japanese(wild) honeysuckle flower in the combination with TCM clinical medication regularities, such as "treatment of different diseases with same drug", "treatment of the same disease with different drugs" and "treatment of the same syndrome with multi-prescriptions", and "one prescription treating multiple syndromes", expounded the specific pharmacological regularity of "heterogeneous equivalence" of Japanese (wild) honeysuckle flower, and put forward methods for studying bioequivalence of Japanese(wild) honeysuckle flower, in order to solve the combination and separation of Japanese(wild) honeysuckle flower and lay a foundation for promoting the development of Chinese herbal medicine industry.

The DNA-Based Algorithms of Implementing Arithmetical Operations of Complex Vectors on a Biological Computer.

Here we show that arithmetical operations of complex vectors can be implemented by means of the proposed DNA-based algorithms.

DNA algorithms of implementing biomolecular databases on a biological computer.

In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases.

Quantum algorithms and mathematical formulations of biomolecular solutions of the vertex cover problem in the finite-dimensional hilbert space.

In this paper, it is shown that the proposed quantum algorithm for implementing Boolean circuits generated from the DNA-based algorithm solving the vertex-cover problem of any graph G with m edges and n vertices is the optimal quantum algorithm. Next, it is also demonstrated that mathematical solutions of the same biomolecular solutions are represented in terms of a unit vector in the finite-dimensional Hilbert space. Furthermore, for testing our theory, a nuclear magnetic resonance (NMR) experiment of three quantum bits to solve the simplest vertex-cover problem is completed.

[Current state of studies on screening method for sensitinogens in injections for traditional Chinese medicine and synthetic immunity method].

Injections for traditional Chinese medicine have over 60 years of history of development and application. In recent years, however, their adverse reactions have been reported one after another. Consequently, studies on screening sensitinogens (sensibiligens) from injections for traditional Chinese medicine have drawn people's attention and become a tough problem all over the world. This essay analyzes the current state of studies on screening techniques of sensitinogens in injections for traditional Chinese medicine according their mechanism of immunotoxicity, and then proposes to adopt the synthetic immunoassay combining immunity bottle chip, immunity cover chip and immunity chromatographic fingerprint to screen sensitinogens from injections for traditional Chinese medicine, in order to build a safety evaluation barrier for development and clinical application of injections for traditional Chinese medicine.

[Current development of rapid high-throughout determination technology for total components of traditional Chinese medicines and formula and synthetic immunity chip method].

The qualitative and quantitative analysis on traditional Chinese medicine and formula components can be made by chemical and instrumental analysis methods. Of both, the instrumental analysis methods play a dominant role, including HPLC, HPLC-MS, HPLC-NMR, GC, GC-MS, biochemical and biological effect. But because traditional Chinese medicines and formula have complicated components, chemical methods are so unspecific that they shall be used less or with caution. While instrumental analysis methods are so specific that they are appropriate for analyzing complicated single component. The analysis techniques for multiple components of traditional Chinese medicines and formula focus on fingerprints, but all of these analysis techniques are limited by the pre-requisite of separation and the lack of general-purpose detectors and therefore being hard to realize the determination of all components of traditional Chinese medicines and formula. In the natural world, however, organisms identify native and alien components through specificity and non-specificity of clusters decided by antigens and antibodies. For example, components of traditional Chinese medicines are directly or indirectly synthesized into antigens and injected into animals, in order to generate specific antibodies and then collect cross reaction information of these components to specific antibodies. As for components without cross reaction, their contents shall be directly read out on the basis of the inhibition rate curve of competitive reaction for specificity of antigens and antibodies. Besides, a cross inhibition rate matrix shall be established first, and them a multiple regression linear equation between cross component concentration or concentration logarithm and inhibition rate by labeling the immunity competitive reaction between antibodies and haptens of traditional Chinese medicine and compound components, and then solved to obtain concentration of each component. The two results are combined to establish the synthetic immunity chip method for traditional Chinese medicine and formula components.

Fast parallel DNA-based algorithms for molecular computation: quadratic congruence and factoring integers.

Assume that n is a positive integer. If there is an integer such that M (2) ≡ C (mod n), i.e., the congruence has a solution, then C is said to be a quadratic congruence (mod n). If the congruence does not have a solution, then C is said to be a quadratic noncongruence (mod n). The task of solving the problem is central to many important applications, the most obvious being cryptography. In this article, we describe a DNA-based algorithm for solving quadratic congruence and factoring integers. In additional to this novel contribution, we also show the utility of our encoding scheme, and of the algorithm's submodules. We demonstrate how a variety of arithmetic, shifted and comparative operations, namely bitwise and full addition, subtraction, left shifter and comparison perhaps are performed using strands of DNA.

Current state of studies on screening method for sensitinogens in injections for traditional Chinese medicine and synthetic immunity method / 中国中药杂志

Injections for traditional Chinese medicine have over 60 years of history of development and application. In recent years, however, their adverse reactions have been reported one after another. Consequently, studies on screening sensitinogens (sensibiligens) from injections for traditional Chinese medicine have drawn people's attention and become a tough problem all over the world. This essay analyzes the current state of studies on screening techniques of sensitinogens in injections for traditional Chinese medicine according their mechanism of immunotoxicity, and then proposes to adopt the synthetic immunoassay combining immunity bottle chip, immunity cover chip and immunity chromatographic fingerprint to screen sensitinogens from injections for traditional Chinese medicine, in order to build a safety evaluation barrier for development and clinical application of injections for traditional Chinese medicine.

Current development of rapid high-throughout determination technology for total components of traditional Chinese medicines and formula and synthetic immunity chip method / 中国中药杂志

The qualitative and quantitative analysis on traditional Chinese medicine and formula components can be made by chemical and instrumental analysis methods. Of both, the instrumental analysis methods play a dominant role, including HPLC, HPLC-MS, HPLC-NMR, GC, GC-MS, biochemical and biological effect. But because traditional Chinese medicines and formula have complicated components, chemical methods are so unspecific that they shall be used less or with caution. While instrumental analysis methods are so specific that they are appropriate for analyzing complicated single component. The analysis techniques for multiple components of traditional Chinese medicines and formula focus on fingerprints, but all of these analysis techniques are limited by the pre-requisite of separation and the lack of general-purpose detectors and therefore being hard to realize the determination of all components of traditional Chinese medicines and formula. In the natural world, however, organisms identify native and alien components through specificity and non-specificity of clusters decided by antigens and antibodies. For example, components of traditional Chinese medicines are directly or indirectly synthesized into antigens and injected into animals, in order to generate specific antibodies and then collect cross reaction information of these components to specific antibodies. As for components without cross reaction, their contents shall be directly read out on the basis of the inhibition rate curve of competitive reaction for specificity of antigens and antibodies. Besides, a cross inhibition rate matrix shall be established first, and them a multiple regression linear equation between cross component concentration or concentration logarithm and inhibition rate by labeling the immunity competitive reaction between antibodies and haptens of traditional Chinese medicine and compound components, and then solved to obtain concentration of each component. The two results are combined to establish the synthetic immunity chip method for traditional Chinese medicine and formula components.

A broadly flavivirus cross-neutralizing monoclonal antibody that recognizes a novel epitope within the fusion loop of E protein.

Flaviviruses are a group of human pathogenic, enveloped RNA viruses that includes dengue (DENV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses. Cross-reactive antibodies against Flavivirus have been described, but most of them are generally weakly neutralizing. In this study, a novel monoclonal antibody, designated mAb 2A10G6, was determined to have broad cross-reactivity with DENV 1-4, YFV, WNV, JEV, and TBEV. Phage-display biopanning and structure modeling mapped 2A10G6 to a new epitope within the highly conserved flavivirus fusion loop peptide, the (98)DRXW(101) motif. Moreover, in vitro and in vivo experiments demonstrated that 2A10G6 potently neutralizes DENV 1-4, YFV, and WNV and confers protection from lethal challenge with DENV 1-4 and WNV in murine model. Furthermore, functional studies revealed that 2A10G6 blocks infection at a step after viral attachment. These results define a novel broadly flavivirus cross-reactive mAb with highly neutralizing activity that can be further developed as a therapeutic agent against severe flavivirus infections in humans.

Searching for disease modifiers-PKC activation and HDAC inhibition - a dual drug approach to Alzheimer's disease that decreases Abeta production while blocking oxidative stress.

A series of benzolactam compounds were synthesized, some of which caused a concentration-dependent increase in sAPPalpha and decrease in Abeta production in the concentration range of 0.1-10 microM. Moreover, some compounds showed neuroprotective effects in the 10-20 microM range in the HCA cortical neuron model of oxidative stress and no toxicity in measurements of neuron viability by MTT assay, even at the highest concentrations tested (20 microM). Alzheimer's disease (AD) is a well-studied neurodegenerative process characterized by the presence of amyloid plaques and neurofibrillary tangles. In this study, a series of protein kinase C (PKC) activators were investigated, some of which also exhibit histone deacetylase (HDAC) inhibitory activity, under the hypothesis that such compounds might provide a new path forward in the discovery of drugs for the treatment of AD. The PKC-activating properties of these drugs were expected to enhance the alpha-secretase pathway in the processing of amyloid precursor protein (APP), while their HDAC inhibition was anticipated to confer neuroprotective activity. We found that benzolactams 9 and 11-14 caused a concentration-dependent increase in sAPPalpha and decrease in beta-amyloid (Abeta) production in the concentration range of 0.1-10 microM, consistent with a shift of APP metabolism toward the alpha-secretase-processing pathway. Moreover, compounds 9-14 showed neuroprotective effects in the 10-20 microM range in the homocysteate (HCA) cortical neuron model of oxidative stress. In parallel, we found that the most neuroprotective compounds caused increased levels of histone acetylation (H4), thus indicating their likely ability to inhibit HDAC activity. As the majority of the compounds studied also show nanomolar binding affinities for PKC, we conclude that it is possible to design, de novo, agents that combine both PKC-activating properties along with HDAC inhibitory properties. Such agents would be capable of modulating amyloid processing while showing neuroprotection. These findings may offer a new approach to therapies that exhibit disease-modifying effects, as opposed to symptomatic relief, in the treatment of AD.