Interfacing external quantum devices to a universal quantum computer

We present a scheme to use external quantum devices using the universal quantum computer previously constructed. We thereby show how the universal quantum computer can utilize networked quantum information resources to carry out local computations. Such information may come from specialized quantum devices or even from remote universal quantum computers. We show how to accomplish this by devising universal quantum computer programs that implement well known oracle based quantum algorithms, namely the Deutsch, Deutsch-Jozsa, and the Grover algorithms using external black-box quantum oracle devices. In the process, we demonstrate a method to map existing quantum algorithms onto the universal quantum computer.     

Demonstration of a universal surface DNA computer

A fundamental concept in computer science is that of the universal Turing machine, which is an abstract definition of a general purpose computer. A general purpose (universal) computer is defined as one which can compute anything that is computable. It has been shown that any computer which is able to simulate Boolean logic circuits of any complexity is such a general purpose computer. The field of DNA computing was founded in 1994 by Adleman's solution of a 7-bit instance of the Hamiltonian path problem. This work, as well as most of the subsequent experimental and theoretical investigations in the area, focused primarily upon the solution of NP-complete problems, which are a subset of the larger universal class of problems. In the present work a surface DNA computer capable of simulating Boolean logic circuits is demonstrated. This was done by constructing NOR and OR gates and combining them into a simple logic circuit. The NOR gate is one of the universal gates in Boolean logic, meaning that any other logic gate can be built from it alone. The circuit was solved using DNA-based operations, demonstrating the universal nature of this surface DNA computing model.     

Identification of PDZ5, a candidate universal minicircle sequence binding protein of Trypanosoma cruzi

The dodecamer universal minicircle sequence is a conserved sequence present in minicircles of trypanosomatid kinetoplast DNA studied so far. This sequence is recognised by a protein named universal minicircle sequence binding protein, described for Crithidia fasciculata, involved in minicircle DNA replication. We have identified a Trypanosoma cruzi gene homologue of the Crithidia fasciculata universal minicircle sequence binding protein. Similar to the Crithidia fasciculata universal minicircle sequence binding protein, the Trypanosoma cruzi protein, named PDZ5, contains five zinc finger motifs. Pulsed field gel electrophoresis indicated that the pdz5 gene is located in the chromosomal band XX of the Trypanosoma cruzi genome. The predicted amino acid sequence of PDZ5 shows a high degree of similarity with several trypanosomatid zinc finger proteins. Specific antibody raised against Crithidia fasciculata universal minicircle sequence binding protein recognises both the recombinant and endogenous PDZ5. The complete pdz5 coding sequence cloned in bacteria expresses a recombinant PDZ5 protein that binds specifically to the universal minicircle sequence dodecamer. These data strongly suggest that PDZ5 represents a Trypanosoma cruzi universal minicircle sequence binding protein.     

Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution

Sequence saturation mutagenesis (SeSaM) is a conceptually novel and practically simple method that truly randomizes a target sequence at every single nucleotide position. A SeSaM experiment can be accomplished within 2–3 days and comprises four steps: generating a pool of DNA fragments with random length, ‘tailing’ the DNA fragments with universal base using terminal transferase at 3′-termini, elongating DNA fragments in a PCR to the full-length genes using a single-stranded template and replacing the universal bases by standard nucleotides. Random mutations are created at universal sites due to the promiscuous base-pairing property of universal bases. Using enhanced green fluorescence protein as the model system and deoxyinosine as the universal base, we proved by sequencing 100 genes the concept of the SeSaM method and achieved a random distribution of mutations with the mutational bias expected for deoxyinosine.     

Towards a unified system for detecting waterborne pathogens

Currently, there is no single method to collect, process, and analyze a water sample for all pathogenic microorganisms of interest. Some of the difficulties in developing a universal method include the physical differences between the major pathogen groups (viruses, bacteria, protozoa), efficiently concentrating large volume water samples to detect low target concentrations of certain pathogen groups, removing co-concentrated inhibitors from the sample, and standardizing a culture-independent endpoint detection method. Integrating the disparate technologies into a single, universal, simple method and detection system would represent a significant advance in public health and microbiological water quality analysis. Recent advances in sample collection, on-line sample processing and purification, and DNA microarray technologies may form the basis of a universal method to detect known and emerging waterborne pathogens. This review discusses some of the challenges in developing a universal pathogen detection method, current technology that may be employed to overcome these challenges, and the remaining needs for developing an integrated pathogen detection and monitoring system for source or finished water.     

Full-length cDNA cloning utilizing the polymerase chain reaction, a degenerate oligonucleotide sequence and a universal mRNA primer.

A full-length cDNA was selectively amplified by the polymerase chain reaction (PCR) utilizing a primer pair consisting of a "universal" 21-base synthetic deoxyoligonucleotide (oligo dT 17GGCC) and a specific degenerate deoxyoligonucleotide sequence (DOS) derived from the N-terminal amino acid sequence. This double-stranded amplified cDNA was uni-directionally cloned into M13mp19 utilizing two restriction sites that had been previously incorporated into the termini of the universal and specific DOS primers. Cloning of the specific cDNA via this PCR amplification with the universal/specific DOS primer pair approach was confirmed by screening with a second DOS contiguous with the DOS employed to prime second (sense)-strand cDNA synthesis. This technique allows for the selective full-length cDNA cloning of low-abundance mRNAs from a single-protein sequence determination.     

Sequence-specific detection using a universal probe system based on the formation of a four-way junction structure

We have developed a novel hybridization detection system using a universal probe based on the formation of a four-way junction (4WJ) structure. This methodology employs a combination of two sequence-specific probes and a universal quenching probe, and the same universal probe can be used for any target gene, allowing cost-effective assays. This 4WJ detection is ideal for extensive parallel identification of nucleic acids such as in multiplex polymerase chain reaction (PCR) systems. Compared with gel electrophoresis, this detection procedure is not only sensitive and rapid but also free of hazardous chemicals such as ethidium bromide. In addition, the 4WJ hybridization technology is more specific as an identifier than the size of a band on an agarose gel. We used a model multiplex PCR method that detected eight different virulence genes in Escherichia coli isolates, demonstrating that our 4WJ detection system is rapid, sensitive, and specific.     

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (±20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.     

Development of a universal gap repair vector for yeast-based screening of knockout rodents

Recently, we reported the production of the first knockout rats by combining N-ethyl-N-nitrosourea (ENU)-induced mutagenesis with a yeast-based truncation screening method. To make this new knockout technology more applicable for other laboratories and for high-throughput applications, we have developed a universal gap repair vector that is ready for use in screening for gene knockouts without additional engineering. The universal gap repair vector was validated for its application in both cDNA- and genomic DNA-based yeast truncation mutation assays. Breast cancer genes Brca1, Brca2, and Adenomatosis polyposis coli (Apc) genes from N2 rats of Brca1 and Brca2 knockouts and (Atm x ApcMin/+)F1 mice were examined, respectively. The results indicate that the universal gap repair vector we developed, using randomly selected codons as a universal cassette, is equally efficient at identifying truncation mutations as are those gap repair vectors designed specifically for Brca1 and Brca2. The availability of a universal gap repair vector should facilitate the broader screening of knockouts of most genes of many species using the combined approach of ENU-induced mutagenesis and yeast truncation assay.     

Depolarization of the Client's Moral Position as a Method of Psychological Consultation

In an earlier article we attempted to construct a universal psychotherapeutic theory. On the basis of an analysis of the works of Freud (1923), Carl Rogers (1965), and V. Frankel (1990), we distinguished some universal principles in explaining the mechanisms of formation of neurotic symptoms and formulated, in a more general way, the principal goal of psychotherapy of neuroses (Kapustin, 1993). We also showed that these principles can be used to explain the mechanisms of a broader range of clients' problems in psychological consultation (Kapustin, 1994). We regarded the purpose of a psychological consultation for this range of problems as a somewhat universal one, independent of the content of the problems or of the symptoms accompanying their mental disorders. Further development of our theory will inevitably require the development of a technique of consultation that fits the language and the concepts of the given theory.     

Noncongenital dominant universal alopecia in a family

An apparently hitherto undescribed noncongenital universal alopecia, due to an autosomal dominant gene with variable expressivity, is described.     

Development of multiplex DNA electronic microarrays using a universal adaptor system for detection of single nucleotide polymorphisms

The NanoChip electronic microarray is designed for the rapid detection of genetic variation in research and clinical diagnosis. We have developed a multiplex electronic microarray assay, specific for single nucleotide polymorphism (SNP) genotyping and mutation detection, using universal adaptor sequences tailed to the 5' end of PCR primers specific to each target. PCR products, amplified by primers directed to the universal adaptor sequence, are immobilized on the microarray either directly or via capture oligonucleotides complementary to the universal adaptor sequence. This simple modification results in a significant increase in fidelity with improved specificity and accuracy. In addition, the multiplexing of genetic variant detection allows increased throughput and significantly reduced cost per assay. This general schema can also be applied to other microarray and macroarray formats.     

快速检查寡聚DNA片段序列的方法

以质粒为模板,用待测寡聚DNA片段和通用测序引物进行PCR（聚合酶链式反应）,PCR片段经纯化后插入到pUC－18或pUC－19的多克隆位点中,然后用通用测序引物测定重组质粒上待测寡聚DNA片段,即可清晰、正确地知道它的序列．     

Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex

Background

The H1N1 pandemic in 2009 and the H5N1 pandemic in 2005 demonstrated that the drugs approved to treat influenza A viruses have low efficacy. This provided a stimulus for new studies of influenza A viruses in the context of the methods used in drug design developed over the past 100 years. Finding new universal drugs is the ultimate goal but its long time horizon is incompatible with emergency situations created by reoccurring influenza outbreaks. Therefore, we propose a computer-aided method for finding efficacious drugs and drug complexes based on the use of the DrugBank database.

Methods

(1) We start by assembling a panel of target proteins. (2) We then assemble a panel of drugs. (3) This is followed by a selection of benchmark binding pockets based on the panel of target proteins and the panel of drugs. (4) We generate a set of computational features, which measure the efficacy of a drug. (5) We propose a universal program to search for drugs and drug complexes. (6) A case study we report here illustrates how to use this universal program for finding an optimal drug and a drug complex for a given target. (7) Validation of the Azirchromycin and Aspirin complex is provided mathematically. (8) Finally, we propose a simple strategy to validate our computational prediction that the Azirchromycin and Aspirin complex should prove clinically effective.

Result

A set of computable features are mined and then based on these features, a universal program for finding the potential drug &drug complexes is proposed. Using this universal program, the Azirchromycin and Aspirin complex is selected and its efficacy is predicted mathematically. For clinical validation of this finding, future work is still required.     

Evolutionary precursors of social norms in chimpanzees: a new approach

Moral behaviour, based on social norms, is commonly regarded as a hallmark of humans. Hitherto, humans are perceived to be the only species possessing social norms and to engage in moral behaviour. There is anecdotal evidence suggesting their presence in chimpanzees, but systematic studies are lacking. Here, we examine the evolution of human social norms and their underlying psychological mechanisms. For this, we distinguish between conventions, cultural social norms and universal social norms. We aim at exploring whether chimpanzees possess evolutionary precursors of universal social norms seen in humans. Chimpanzees exhibit important preconditions for their presence and enforcement: tolerant societies, well-developed social-cognitive skills and empathetic competence. Here, we develop a theoretical framework for recognizing different functional levels of social norms and distinguish them from mere statistical behavioural regularities. Quasi social norms are found where animals behave functionally moral without having moral emotions. In proto social norms, moral emotions might be present but cannot be collectivized due to the absence of a uniquely human psychological trait, i.e. shared intentionality. Human social norms, whether they are universal or cultural, involve moral emotions and are collectivized. We will discuss behaviours in chimpanzees that represent potential evolutionary precursors of human universal social norms, with special focus on social interactions involving infants. We argue that chimpanzee infants occupy a special status within their communities and propose that tolerance towards them might represent a proto social norm. Finally, we discuss possible ways to test this theoretical framework.     

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

The deep sequencing of 16S rRNA genes amplified by universal primers has revolutionized our understanding of microbial communities by allowing the characterization of the diversity of the uncultured majority. However, some universal primers also amplify eukaryotic rRNA genes, leading to a decrease in the efficiency of sequencing of prokaryotic 16S rRNA genes with possible mischaracterization of the diversity in the microbial community. In this study, we compared 16S rRNA gene sequences from genome-sequenced strains and identified candidates for non-degenerate universal primers that could be used for the amplification of prokaryotic 16S rRNA genes. The 50 identified candidates were investigated to calculate their coverage for prokaryotic and eukaryotic rRNA genes, including those from uncultured taxa and eukaryotic organelles, and a novel universal primer set, 342F-806R, covering many prokaryotic, but not eukaryotic, rRNA genes was identified. This primer set was validated by the amplification of 16S rRNA genes from a soil metagenomic sample and subsequent pyrosequencing using the Roche 454 platform. The same sample was also used for pyrosequencing of the amplicons by employing a commonly used primer set, 338F-533R, and for shotgun metagenomic sequencing using the Illumina platform. Our comparison of the taxonomic compositions inferred by the three sequencing experiments indicated that the non-degenerate 342F-806R primer set can characterize the taxonomic composition of the microbial community without substantial bias, and is highly expected to be applicable to the analysis of a wide variety of microbial communities.     

Evaluation of a universal template for single-platform absolute T-lymphocyte subset enumeration

The single-platform absolute T-lymphocyte subset analysis was evaluated utilizing a universal protocol in a Canadian multicenter study with the collaboration of the members of the Canadian HIV Trials Network (CTN). Participants used flow cytometers and reagents of their choice for labeling and lysing whole blood. Over a 2-year period, CTN laboratories performed single-platform absolute T-lymphocyte subset enumerations on fresh and commercial stabilized blood products using commercially available microfluorospheres TruCount and Flow-Count. This multicenter evaluation demonstrated that the application of a universal template for single-platform analysis provides a generic approach that embraces a wide array of immunophenotyping settings available in clinical laboratory.     

pHLIP and acidity as a universal biomarker for cancer

Of great importance to clinical cancer diagnosis is the use of organic biomarkers. The detection of RNA, DNA, and protein antigen are all established methods for identifying specific cancer types and instrumental in promoting greater survivorship of the patient. Despite many decades of intense cancer research, we have yet to identify a "universal" protein or nucleic acid that allows us to diagnose more than a small subset of cancers at a time. In this review, we examine the use of localized cellular acidity as a universal marker for solid tumors, outlining some successes with a small peptide we call pHLIP, a pH-sensitive biosensor that allows us to label tumor tissue in live mice.     

Radiostereometric analysis using clinical radiographic views: Development of a universal calibration object

Radiostereometric analysis (RSA) is a highly accurate technique used to provide three-dimensional (3D) measurements of orthopaedic implant migration for clinical research applications, yet its implementation in routine clinical examinations has been limited. Previous studies have introduced a modified RSA procedure that separates the calibration examinations from the patient examinations, allowing routine clinical radiographs to be analyzed using RSA. However, in order to calibrate the wide range of clinical views, a new calibration object is required. In this study, a universal, isotropic calibration object was designed to calibrate any pair of radiographic views used in the clinic for RSA. A numerical simulation technique was used to design the calibration object, followed by a phantom validation test of a prototype to verify the performance of the novel object, and to compare the measurement reliability to the conventional calibration cage. The 3D bias for the modified calibration method using the new calibration object was 0.032 ± 0.006 mm, the 3D repeatability standard deviation was 0.015 mm, and the 3D repeatability limit was 0.042 mm. Although statistical differences were present between the universal calibration object and the conventional cage, the differences were considered to be not clinically meaningful. The 3D bias and repeatability values obtained using the universal calibration object were well under the threshold acceptable for RSA, therefore it was successfully validated. The universal calibration object will help further the adoption of RSA into a more routine practice, providing the opportunity to generate quantitative databases on joint replacement performance.