Ambiguous Base Research Articles

Development and validation of the Kernis-Goldman authenticity inventory-short form (KGAI-SF)

Psychological authenticity has long been of interest to social thinkers, and empirical research on this topic has steadily increased since the 1970s. The present work contributes to this body of knowledge by describing the development of a short form for the Kernis-Goldman Authenticity Inventory (KGAI), a widely used self-report instrument. Thirteen of the 45 items from the original KGAI were removed on the basis of semantic ambiguity or redundancy, and the remaining 32-items were subjected to cross-validated ordinal confirmatory factor analysis (N = 1252) in an effort to identify psychometrically redundant or unreliable items. The resulting 20-item short-form (KGAI-SF) exhibited good reliability across the ranges of the four underlying dimensions of authenticity (awareness, unbiased processing, behavior, relational orientation), as well as good discriminant and convergent validity.

Self‐Governance in Latin America: To What Extent Can Citizens Make Policy via Direct Democracy?

In the past two decades, many Latin American countries incorporated direct‐democracy mechanisms (e.g. initiatives and referendums) into their constitutions. By expanding the room for citizens' political participation, direct democracy was meant to reduce the gap between citizens and government and create a more‐inclusive form of governing, but was it really the case? This article asks, to what extent can citizens use direct democracy to shape public policy in Latin America? It argues that constitutions in Latin America provide an ambiguous basis for the use of referendums and initiatives, which allows governments to shape and limit their use during the agenda‐setting stage. By specifying the limitations on the types of mechanisms used, the issues that cannot be decided via direct democracy, and the barriers to placing mechanisms on the ballot, governments can control the direct democracy process to a greater extent than has heretofore been acknowledged.

A MinION™-based pipeline for fast and cost-effective DNA barcoding.

DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory and is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrating that one flow cell can generate barcodes for ~500 specimens despite the high basecall error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. Consensus barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. They are addressed with an optional error correction pipeline that is based on conserved amino acid motifs from publicly available barcodes. The effectiveness of this pipeline is documented by analysing reads from three MinION™ runs that represent three different stages of MinION™ development. They generated data for (i) 511 specimens of a mixed Diptera sample, (ii) 575 specimens of ants and (iii) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION™ barcodes for 490 of the 511 specimens which were assessed against reference Sanger barcodes (N=471). Overall, the MinION™ barcodes have an accuracy of 99.3%-100% with the number of ambiguous bases after correction ranging from <0.01% to 1.5% depending on which correction pipeline is used. We demonstrate that it requires ~2hr of sequencing to gather all information needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1,000 barcodes can be generated in one flow cell and that the cost per barcode can be <USD 2.

Molecular identification of temperate Cricetidae and Muridae rodent species using fecal samples collected in a natural habitat

Molecular species identification from biological material collected at field sites has become an established ecological tool. However, extracting and amplifying DNA from degraded field samples, such as prey remains and feces that have been exposed to the elements, remains a challenge and costly. We collected 115 fecal samples of unknown small mammals, resembling fecal droppings of voles and mice (i.e., Cricetidae and Muridae), from a salt marsh in The Netherlands. We modified a previously published protocol into a relatively low-cost method with a PCR success of 95%. We demonstrate that species identification is possible for both Cricetidae and Muridae species using fecal samples of unknown age deposited in the field. For 90 samples, sequences of the variable control region in the mitochondrial genome were obtained and compared to published DNA sequences of small mammals occurring in north European salt marshes. A single sample, probably environmentally contaminated, appeared as Sus scrofa (n = 1). We positively identified house mouse Mus musculus, being the positive control (n = 1), and common vole Microtus arvalis (n = 88). In 81 sequences of 251 nt without ambiguous bases, ten haplotypes were present. These haplotypes, representing the central lineage of the western subspecies M. arvalis arvalis, were separated by 20 mutations from published control region haplotypes of the western European lineages sampled in France. Unlike earlier studies of cytochrome b variation in coastal European populations, we did not find indications of recent purging of genetic variation in our study area.

Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.

Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers. Based on a z-score threshold, Zseq sweeps through the sequences again and filters those with a z-score less than the user-defined threshold.Zseq algorithm is able to provide a better mapping rate; it reduces the number of ambiguous bases significantly in comparison with other methods. Evaluation of the filtered reads has been conducted by aligning the reads and assembling the transcripts using the reference genome as well as de novo assembly. The assembled transcripts show a better discriminative ability to separate cancer and normal samples in comparison with another state-of-the-art method. Moreover, de novo assembled transcripts from the reads filtered by Zseq have longer genomic sequences than other tested methods. Estimating the threshold of the cutoff point is introduced using labeling rules with optimistic results.

APPLICATION OF DISTRIBUTED ANTENNA SYSTEMS FOR DETERMINATION OF RADIATION SOURCE COORDINATES WITH USE OF PHASE METHOD IN FRESNEL ZONE

Background. Talking about evolution of passive radar systems and multifunction antenna systems, it is necessary to acknowledge that distributed antenna systems (DAS) are supposed to be widely spread in the very near future in many areas of human activity, such as organization of high-quality mobile communication in large offices, shopping centers, fitness buildings and so on. Structurally, DAS consist of different groups of antennas and base stations with active and passive repeaters of radio signals. Generally, mutual location of such antennas and base stations can be chosen experimentally according to the criterion of service area maximization. For the further quality of service improvement, it is necessary to use smart antennas in DAS as basic structure elements. The use of smart antennas will allow tracking the subscriber`s (or SOR – source of radiation) location by means of direction-finding (DF) and to increase radiation power of radio signal towards SOR thus decreasing interference to other subscribers. It is important to note that amplitude methods of DF are unacceptable in this case because base stations have antenna beam patterns which are rather wide. Use of phase methods for direction finding is actual but constrained because of electromagnetic waves (EMW) multipath propagation and large DF errors caused by the following reason – it happens that SOR is located in Fresnel zone of direction-finder antenna system. So, consideration of the phenomenon of EMW front curvature in DAS is very important in order to construct direction-finders. Objective. Consideration of EMW phase front sphericity (curvature) and its influence on the accuracy of SOR coordinates determination measured by DAS phase methods. Scheme technical decisions of phase direction-finders (PDF) based on this process are also represented. Methods. To study the effect of the EMW phase front curvature on the accuracy of determining the coordinates of the SOR analytical dependencies are synthesized. Calculations of the direction characteristics, errors in determining the phase shifts between the antenna elements of the phase direction-finder, as well as the error in determining the distance to SOR in the Fresnel zone as a function of the range to SOR and its bearing were made based on MathCad 14 program. Results. During the process of SOR angular coordinates determination in Fresnel zone with use of EMW phase front curvature оn the basis of planar antenna array, it is necessary to execute consistently two operations: 1) to define the fact of presence of EMW phase front curvature; 2) to switch PDF from the mode of bearing and tilt angles estimation (when it is in plane phase front) to the mode of bearing and tilt angles estimation (and also distance to SOR if needed) with phase front curvature of EMW. Taking into account the analysis relating to errors of bearing angle measurements in Fresnel zone (depending on the location of rough, but exact bases, for three-element sparse LAA) it is possible to conclude that their position doesn’t impact on exactness of bearing angle measuring in PDF. But to support more exact determination of SOR distance they must be placed in the center of exact, but ambiguous bases of PDF. Conclusions. Failure to take into account EMW phase front curvature from SOR harmonic signal leads to errors of SOR coordinate calculation under conditions of its location in Fresnel zone and absence of other SORs. Knowledge of distance to SOR can be used in passive radar systems, in radio monitoring systems of radio interference sources which have bearing angles equal with useful SOR ones, but located on different distances from useful SOR. This knowledge can also be used in mobile communication networks to strengthen signal level on certain distance with EMW energy focusing, in vehicle control systems on the basis of the satellite navigation systems etc.

Female-to-male sex reversal associated with unique Xp21.2 deletion disrupting genomic regulatory architecture of the dosage-sensitive sex reversal region

BackgroundThe XX male disorder of sex development (DSD) is a rare condition that is most commonly associated with the presence of the SRY gene on one of the X chromosomes...

Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections.

Chronic bacterial airway infections in people with cystic fibrosis (CF) are often caused by Pseudomonas aeruginosa, typically showing high phenotypic diversity amongst co-isolates from the same sputum sample. Whilst adaptive evolution during chronic infections has been reported, the genetic mechanisms underlying the observed rapid within-population diversification are not well understood. Two recent conflicting reports described very high and low rates of homologous recombination in two closely related P. aeruginosa populations from the lungs of different chronically infected CF patients. To investigate the underlying cause of these contrasting observations, we combined the short read datasets from both studies and applied a new comparative analysis. We inferred low rates of recombination in both populations. The discrepancy in the findings of the two previous studies can be explained by differences in the application of variant calling techniques. Two novel algorithms were developed that filter false-positive variants. The first algorithm filters variants on the basis of ambiguity within duplications in the reference genome. The second omits probable false-positive variants at regions of non-homology between reference and sample caused by structural rearrangements. As gains and losses of prophage or genomic islands are frequent causes of chromosomal rearrangements within microbial populations, this filter has broad appeal for mitigating false-positive variant calls. Both algorithms are available in a Python package.

Dancing around the pole: holarctic phylogeography of the Arctic fairy shrimp Branchinecta paludosa (Anostraca, Branchiopoda)

The distributional patterns of Arctic species are commonly affected by the recurring Pleistocene glaciations, which contributed to transient or permanent genetic isolation. Here we explore the phylogeography of the climate-sensitive Arctic fairy shrimp Branchinecta paludosa, which has a circumpolar range of distribution, with certain southern alpine outreaches. We sequenced the mitochondrial cytochrome oxidase I subunit from samples collected at ten Nearctic and nine Palaearctic sites, including southern alpine populations. A handful of ambiguous bases in certain sequences strongly suggested heteroplasmy, possibly being reported for the first time in anostracans. Evolutionary analysis of the sequence variations showed a temporal divergence coinciding with the flooding of the Beringia land bridge. Sequence alignment with outgroup taxa for phylogenetic analysis showed three distinct major clades, reflecting geographical isolation. The most divergent clade, from isolated alpine ponds in the Rocky Mountains, probably represents a different and undescribed species. Two other major clades corresponded to the geographical areas of Nearctic and Palaearctic. Finally, the southern Palaearctic outstretch showed genetic separation, most likely representing a geographical and climatic isolated relict population.

Continuously Ingesting Fructooligosaccharide Can't Maintain Rats’ GutBifidobacteriumat a High Level

Fructooligosaccharide (FOS) has been reported to increase Lactobacillus and Bifidobacterium populations in animal and human gut. Hence, it has been utilized to regulate the balance of gut microbiota. In this study, we compared the effects of high-FOS (HFOS) diet on normal and obese rats' gut Lactobacillus and Bifidobacterium, with high-soybean-fibers (HSF) diet as control. The results showed that the level of Bifidobacterium population substantially increased at week 4 in groups of rats fed the HFOS diet (P < 0.05), but significantly reduced to a small level at week 8 (P < 0.05); the abundance of Lactobacillus was increased in normal rats (P < 0.05), but decreased in obese rats (P < 0.05). The HSF diet did not promote the growth of Lactobacillus and Bifidobacterium in rats' gut. The findings suggested that Bifidobacterium population could not be maintained at a high level when the rats continuously ingested the HFOS diet for 8 wk; additionally, Lactobacillus population could adapt to a relatively stable level with the consumption of HFOS diet. Fructooligosaccharide (FOS) is one of the most popular prebiotics, and it is widely used in infant formulas, which is aiming to increase the growth of probiotics like Lactobacillus and Bifidobacterium. This study discovered new growth rhythm of Bifidobacterium based on a high-FOS diet. The growth of Bifidobacterium was first promoted but receded in the end. This finding is highly instructive and meaningful for the application of fructooligosaccharide in probiotic or prebiotic food.

Gene loss in keratinization programs accompanies adaptation of cetacean skin to aquatic lifestyle.

Gene loss in keratinization programs accompanies adaptation of cetacean skin to aquatic lifestyle.

Beyond the social embeddedness of economic activity: the quality-orientedness in coffee production of Timor-Leste and its implication for legal pluralism

Legal pluralism has argued that overlapping and ambiguous regulatory bases can be found in any social field. However, most legal pluralism scholars still deplore the fact that the dominant view of the legal mechanism assumes a unified legal system with stable legal hierarchies. Does this mean that the dominant legal philosophy has very effectively disguised those complicated legal-pluralist negotiations as a realm of fixity? This question may be connected with another important question of how multi-scale normative orders are represented in knowledge practices. Attempting to explicate these questions, I aim to illuminate the issue of multiscalarity through a rethinking of the social embeddedness of economic activity. While some critical discussions on the concept of social embeddedness by economic geographers tended to focus on the typology of embeddednesses for explaining the linkage between social factors and economic outcomes, this assumed linkage itself must be carefully examined. In this paper, it is argued that since the social is not inherently a spatial concept, a turn to the act of embedding is required, detaching the adjective social from the noun embeddedness. Indeed, spaces are defined and redefined by identifying the terms of incorporation into the multiscalarity in question, rather than by their spatial property per se. In parallel, the complementarity between vertical and horizontal networks as simple reflections of realities must be rejected, requiring a new point of departure for legal pluralism in the context of rural development.

Cross-cultural adaptation process of the "Conversation Analysis Profile for People with Aphasia" to the Portuguese language.

The Conversation Analysis Profile for People with Aphasia (CAPPA) provides specific information about strengths and weaknesses of the communication between people with aphasia and their family caregiver within a conversational context.ObjectiveThe aim of this paper was to present the results of the first stages of cross-cultural adaptation of the CAPPA for the European Portuguese language.MethodsThis methodology study describes the translation and back-translation processes, following the recommended steps to that end. In addition, following the consent of one of the original authors, the process of content validation of the CAPPA commenced. The instrument was submitted for assessment before a panel of experts in the area, who constituted the population of this study.ResultsAfter the translation and back-translation processes, a panel of experts was convened to adapt the Delphi technique. Some questions were excluded on the basis of ambiguity, relevance and potential repetition. Suggestions made by the expert panel were included in a revised version of the tool. 159 items obtained a 100% consensus in relevance, and 157 items were considered suitable by the expert panel, validating the content of the instrument.ConclusionThe final version will now be applied to the target population in order to carry out the psychometric validation.

Probing ambiguous base-pairs by genetic transformation with XNA templates.

The templating potential of anhydrohexitol oligonucleotides bearing ambiguous bases was studied in vivo, by using a selection screen for mosaic heteroduplex plasmids in Escherichia coli. 1,5-Anhydro-2,3-dideoxy-2-(5-nitroindazol-1-yl)-D-arabino-hexitol showed the greatest ambiguity among the three nucleosides tested. At most two successive ambiguous bases could be tolerated on hexitol templates read in bacterial cells. Hexitol nucleosides bearing simplified heterocycles thus stand as promising monomers for generating random DNA sequences in vivo from defined synthetic oligonucleotides.

A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation.

BackgroundMulti-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence.MethodsBoth MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay), HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM) diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region) or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region). Samples were classified as MAA positive (likely from individuals with recent HIV infection) if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1) the proportion of samples classified as MAA positive as a function of duration of infection, (2) the mean window period, (3) the shadow (the time period before sample collection that is being assessed by the MAA), and (4) the accuracy of cross-sectional incidence estimates for three cohort studies.ResultsThe proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were <1 year. Both MAAs provided cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion.ConclusionsMAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation.

‘Neither fish nor fowl’: an analysis of status ambiguity of the Houses of Chiefs in Ghana

This article sets out to explain the basis of status ambiguity of the Houses of Chiefs and Traditional Councils in Ghana and the implications of this ambiguity on the status of the administrative personnel working in them. The interest was necessitated by complaints from administrative personnel in the Houses of Chiefs who were excluded from the general salary enhancement to all civil servants in Ghana in 2007. Between 2007 and 2009, research was conducted in all the 10 Regional Houses of Chiefs, in the National House of Chiefs and at the Ministry of Chieftaincy and Culture (MCC). While interviews were the main methods used at the MCC, it was combined with observations at the Houses of Chiefs. Primary and secondary documents were also consulted in the process. Data revealed that the Houses of Chiefs serve as “customary” courts for chieftaincy disputes and over the years, have incorporated certain practices of the English common law into their proceedings. Thus, they are neither customary courts in the strictest sense, nor common law courts, which equally explains the difficulty in determining whether or not the administrative personnel in these Houses are civil servants.

Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system

Pyrosequencing of the 16S ribosomal RNA gene (16S) has become one of the most popular methods to assess microbial diversity. Pyrosequencing reads containing ambiguous bases (Ns) are generally discarded based on the assumptions of their non-sequence-dependent formation and high error rates. However, taxonomic composition differed by removal of reads with Ns. We determined whether Ns from pyrosequencing occur in a sequence-dependent manner. Our reads and the corresponding flow value data revealed occurrence of sequence-specific N errors with a common sequential pattern (a homopolymer + a few nucleotides with bases other than the homopolymer + N) and revealed that the nucleotide base of the homopolymer is the true base for the following N. Using an algorithm reflecting this sequence-dependent pattern, we corrected the Ns in the 16S (86.54%), bphD (81.37%) and nifH (81.55%) amplicon reads from a mock community with high precisions of 95.4, 96.9 and 100%, respectively. The new N correction method was applicable for determining most of Ns in amplicon reads from a soil sample, resulting in reducing taxonomic biases associated with N errors and in shotgun sequencing reads from public metagenome data. The method improves the accuracy and precision of microbial community analysis and genome sequencing using 454 pyrosequencing.

Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.

BackgroundGrowing interest in cellulolytic clostridia with potential for consolidated biofuels production is mitigated by low conversion of raw substrates to desired end products. Strategies to improve conversion are likely to benefit from emerging techniques to define molecular systems biology of these organisms. Clostridium stercorarium DSM8532T is an anaerobic thermophile with demonstrated high ethanol production on cellulose and hemicellulose. Although several lignocellulolytic enzymes in this organism have been well-characterized, details concerning carbohydrate transporters and central metabolism have not been described. Therefore, the goal of this study is to define an improved whole genome sequence (WGS) for this organism using in-depth molecular profiling by RNA-seq transcriptomics and tandem mass spectrometry-based proteomics.ResultsA paired-end Roche/454 WGS assembly was closed through application of an in silico algorithm designed to resolve repetitive sequence regions, resulting in a circular replicon with one gap and a region of 2 kilobases with 10 ambiguous bases. RNA-seq transcriptomics resulted in nearly complete coverage of the genome, identifying errors in homopolymer length attributable to 454 sequencing. Peptide sequences resulting from high-throughput tandem mass spectrometry of trypsin-digested protein extracts were mapped to 1,755 annotated proteins (68% of all protein-coding regions). Proteogenomic analysis confirmed the quality of annotation and improvement pipelines, identifying a missing gene and an alternative reading frame. Peptide coverage of genes hypothetically involved in substrate hydrolysis, transport and utilization confirmed multiple pathways for glycolysis, pyruvate conversion and recycling of intermediates. No sequences homologous to transaldolase, a central enzyme in the pentose phosphate pathway, were observed by any method, despite demonstrated growth of this organism on xylose and xylan hemicellulose.ConclusionsComplementary omics techniques confirm the quality of genome sequence assembly, annotation and error-reporting. Nearly complete genome coverage by RNA-seq likely indicates background DNA in RNA extracts, however these preps resulted in WGS enhancement and transcriptome profiling in a single Illumina run. No detection of transaldolase by any method despite xylose utilization by this organism indicates an alternative pathway for sedoheptulose-7-phosphate degradation. This report combines next-generation omics techniques to elucidate previously undefined features of substrate transport and central metabolism for this organism and its potential for consolidated biofuels production from lignocellulose.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-567) contains supplementary material, which is available to authorized users.

Genetic attributes of blood‐derived subtype‐C HIV‐1 tat and env in India and neurocognitive function

Genetic elements in HIV-1 subtype B tat and env are associated with neurotoxicity yet less is known about other subtypes. HIV-1 subtype C tat and env sequences were analyzed to determine viral genetic elements associated with neurocognitive impairment in a large Indian cohort. Population-based sequences of HIV-1 tat (exon 1) and env (C2-V3 coding region) were generated from blood plasma of HIV-infected patients in Pune, India. Participants were classified as cognitively normal or impaired based on neuropsychological assessment. Tests for signature residues, positive and negative selection, entropy, and ambiguous bases were performed using tools available through Los Alamos National Laboratory (http://www.hiv.lanl.gov) and Datamonkey (http://www.datamonkey.org). HIV-1 subtype C tat and env sequences were analyzed for 155 and 160 participants, of which 34-36% were impaired. Two signature residues were unique to impaired participants in exon 1 of tat at codons 29 (arginine) and 68 (proline). Positive selection was noted at codon 29 among normal participants and at codon 68 in both groups. The signature at codon 29 was also a signature for low CD4+ (<200 cells/mm(3)) counts but remained associated with impairment after exclusion of those with low CD4+ counts. No unique genetic signatures were noted in env. In conclusion, two signature residues were identified in exon 1 of HIV-1 subtype C tat that were associated with neurocognitive impairment in India and not completely accounted for by HIV disease progression. These signatures support a linkage between diversifying selection in HIV-1 subtype C tat and neurocognitive impairment.

English

&nbsp; Due to the difficulty in collecting specimens, the genus&nbsp;Squamigera&nbsp;(Insecta: Nicoletiidae: Cubacubaninae) remains one of the least studied groups of the American nicoletiid insects. before this investigation, only six specimens were available for study. Furthermore, previous assessments of its phylogenetic relationship within&nbsp;the Cubacubaninae used incomplete 16S rRNA sequences that had ambiguous bases from only a single&nbsp;Squamigera&nbsp;specimen, thus reducing the resolution. We describe here a new species of&nbsp;Squamigera&nbsp;and provide for future studies, a&nbsp;more complete&nbsp;16S rRNA&nbsp;sequence for&nbsp;the genus using this new species. &nbsp; Key words:&nbsp;Silverfish, bristletails, thysanura, morphology, molecular data.