Ambiguous Sequences Research Articles

Earley Parsers with Contributive Paths

This paper proposed two contributive paths based on the probabilistic Earley algorithm. We argue that these paths contribute better to the grammaticality of the input sentence than the Viterbi path, and hence are more capable of parsing structurally ambiguous sequences. An exponentially weighted combination of the parsing results from the contributive and the Viterbi paths achieved promising performances on the parsing task of CIPS ParsEval-2009. Besides, our experiment results on a set of 1200 ambiguous Chinese sentences also showed that the Earley parser with contributive paths outperformed both the Viterbi Earley and the Berkley parser significantly.

Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region

The palindromic nucleotide substitutions (PNS) at the three variable loci (V1, V2 and V3) in the 5′-untranslated region (UTR) of the Pestivirus genome have been considered for taxonomical segregation of the species, through the evaluation of 534 strains. On the basis of qualitative and quantitative secondary structure characteristics, species have been identified within the genus, determining genetic distances between species isolates, clarifying borderline and multirelated sequences, and characterizing and clustering the Pestivirus strains showing unexpected genomic sequences. Nine genomic groups have been identified: the species Bovine viral diarrhea virus 1 (BVDV-1), Bovine viral diarrhea virus 2 (BVDV-2), Border disease virus (BDV) and Classical swine fever virus (CSFV) and the tentative species Pronghorn, Giraffe, Bovine viral diarrhea virus 3 (BVDV-3) (HoBi group), Border disease virus 2 (BDV-2) (Italian small ruminant isolates) and Bungowannah.Palindromic positions have been characterized according to changes in nucleotide base-pairs identifying low variable positions (LVP) including base-pairs present in less than 80% of the genus. The determination of divergence between single strain sequences or genetic groups was obtained easily by comparing base-pairing combinations from aligned secondary structures. This provided clear information such as the level of heterogeneity within a species, the relatedness between species, or facilitating the characterization and clustering of specific strains. The BVDV-1 and BDV species resulted heterogeneous, showing isolates located on a borderline in the species. Within the BVDV-2 species, two main genogroups were identified, with strains showing common sequence characteristics to both groups (multirelated strains). They could be allocated correctly by quantitative analysis. Similarly, the relation between CSFV and BDV species appeared very clearly. Also in this case, ambiguous strain sequences could be clustered in the species showing the lowest divergence values.In conclusion, the proposed taxonomical procedure is based on the evaluation of only the strategic and highly conserved genome regions in the 5′-UTR. Furthermore, the application of quantitative analytical procedure allowed for a better determination of relation among species.

Diversity gradients and phylogeographic patterns in Santiria trimera (Burseraceae), a widespread African tree typical of mature rainforests

New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations. Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of São Tomé, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogooué River, suggesting refuges on both sides of the river bed. The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity.

Flexible taxonomic assignment of ambiguous sequencing reads.

BackgroundTo characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it.ResultsWe present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed.ConclusionsThe assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

Involvement of entrained neural oscillations in the perception of ambiguous sound sequences

Event Abstract Back to Event Involvement of entrained neural oscillations in the perception of ambiguous sound sequences Jordi Costa-Faidella1*, Elyse S. Sussman2 and Carles Escera1 1 University of Barcelona, Spain 2 Albert Einstein College of Medicine, United States The auditory system is constantly parsing the acoustic input into meaningful units (i.e. streams) to which behavior can be directed. This phenomenon is referred to as auditory scene analysis (ASA), and although extensively described, its underlying neural mechanisms are poorly understood. One hypothesis states that sounds activating distinct neural populations are heard as separate streams. However, there is increasing support for the role of temporal coherence in perceptual grouping and segregation. Here we aim to provide evidence for the entrainment of brain oscillations to temporally coherent acoustic patterns as one plausible neural mechanism of ASA. EEG data was recorded from 12 healthy participants while performing two tasks promoting two different perceptual organizations of the same sound sequence. Tone duration and intensity variations following different but temporally coherent patterns served as anchoring points to integrate or segregate sounds in different streams. Subjects performed at ceiling level in both tasks. A significant increase of phase-locking factor (PLF) was found in the frequency band corresponding to the stimulus presentation rate in both conditions, together with a specific increase corresponding to the timing of the perceived sound organization. Increments of induced power were observed in the theta range (4-7 Hz) at fronto-temporal sites in the grouping condition, and in the alpha range (8-12 Hz) at parietal sites in the segregation condition. Our results suggest that brain oscillations entrained to the temporal coherence of acoustic stimuli play a critical role in binding or segregating them in streams, and that whereas theta rhythms might serve stimulus integration, alpha rhythms might be involved in the suppression of irrelevant stimuli. Keywords: EEG, Perception Conference: XI International Conference on Cognitive Neuroscience (ICON XI), Palma, Mallorca, Spain, 25 Sep - 29 Sep, 2011. Presentation Type: Poster Presentation Topic: Poster Sessions: Neurophysiology of Sensation and Perception Citation: Costa-Faidella J, Sussman ES and Escera C (2011). Involvement of entrained neural oscillations in the perception of ambiguous sound sequences. Conference Abstract: XI International Conference on Cognitive Neuroscience (ICON XI). doi: 10.3389/conf.fnhum.2011.207.00351 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 23 Nov 2011; Published Online: 28 Nov 2011. * Correspondence: Dr. Jordi Costa-Faidella, University of Barcelona, Barcelona, Spain, jcostafaidella@ub.edu Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Jordi Costa-Faidella Elyse S Sussman Carles Escera Google Jordi Costa-Faidella Elyse S Sussman Carles Escera Google Scholar Jordi Costa-Faidella Elyse S Sussman Carles Escera PubMed Jordi Costa-Faidella Elyse S Sussman Carles Escera Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Contrastive breathiness on consonants and vowels.

While numerous languages exhibit contrastive breathy phonation either on consonants (e.g., Indic languages) or on vowels (e.g., Zapotec languages); very few languages preserve this contrast across both consonants and vowels. Two such languages are Gujarati and White Hmong. Given that breathiness on consonants is typically realized as a breathy-voiced release into the following vowel, how are the two types of breathiness distinguished in CV sequences, if at all? We examine acoustic and electroglottographic data collected from speakers of Gujarati and White Hmong to determine what properties reliably distinguish breathy and modal voice in potentially ambiguous CV sequences, and to explore the phonetic and phonological properties shared between these two genetically unrelated languages. Preliminary results from both languages are strikingly similar; modal vowels adjacent to breathy consonant releases strongly resemble phonemically breathy vowels, and only the exact timing and magnitude of the acoustic reflexes of breathiness phonetically distinguish the two sequences. Phonological evidence in the form of distributional constraints, however, can aid listeners of both languages in determining the source of breathiness: both languages prohibit the co-occurrence of breathy consonants and breathy vowels, and in White Hmong, tonal cues can also reveal the underlying phonation of an ambiguous CV sequence.

A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags

Motivation: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is widely used in biological research. ChIP-seq experiments yield many ambiguous tags that can be mapped with equal probability to multiple genomic sites. Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information.Results: We have developed a Gibbs sampling-based algorithm for the genomic mapping of ambiguous sequence tags. Our algorithm relies on the local genomic tag context to guide the mapping of ambiguous tags. The Gibbs sampling procedure we use simultaneously maps ambiguous tags and updates the probabilities used to infer correct tag map positions. We show that our algorithm is able to correctly map more ambiguous tags than existing mapping methods. Our approach is also able to uncover mapped genomic sites from highly repetitive sequences that can not be detected based on unique tags alone, including transposable elements, segmental duplications and peri-centromeric regions. This mapping approach should prove to be useful for increasing biological knowledge on the too often neglected repetitive genomic regions.Availability: http://esbg.gatech.edu/jordan/software/mapContact: king.jordan@biology.gatech.eduSupplementary Information: Supplementary data are available at Bioinformatics online.

Strain identification of commercial influenza vaccines by mass spectrometry

Current influenza vaccine manufacturing and testing timelines require that the constituent hemagglutinin (HA) and neuraminidase (NA) strains be selected each year approximately 10 months before the vaccine becomes available. The threat of a pandemic influenza outbreak requires that more rapid testing methods be found. We have developed a specialized on-filter sample preparation method that uses both trypsin and chymotrypsin to enzymatically digest peptide- N-glycosidase F (PNGase F)-deglycosylated proteins in vaccines. In tandem with replicate liquid chromatography–mass spectrometry (LC–MS) analyses, this approach yields sufficient protein sequencing data (>85% sequence coverage on average) for strain identification of HA and NA components. This has allowed the confirmation, and in some cases the correction, of the identity of the influenza strains in recent commercial vaccines as well as the correction of some ambiguous HA sequence annotations in available databases. This method also allows the identification of low-level contaminant egg proteins produced during the manufacturing process.

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

BackgroundSequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences from the datasets. The sequenced reads can contain deletions or insertions due to sequencing limitations, and the primer sequence may contain ambiguous bases. Furthermore, the tag sequence may be unavailable or incorrectly reported. Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data.ResultsTagCleaner is a web application developed to automatically identify and remove known or unknown tag sequences allowing insertions and deletions in the dataset. TagCleaner is designed to filter the trimmed reads for duplicates, short reads, and reads with high rates of ambiguous sequences. An additional screening for and splitting of fragment-to-fragment concatenations that gave rise to artificial concatenated sequences can increase the quality of the dataset. Users may modify the different filter parameters according to their own preferences.ConclusionsTagCleaner is a publicly available web application that is able to automatically detect and efficiently remove tag sequences from metagenomic datasets. It is easily configurable and provides a user-friendly interface. The interactive web interface facilitates export functionality for subsequent data processing, and is available at http://edwards.sdsu.edu/tagcleaner.

Novel Protein–Protein Contacts Facilitate mRNA 3′-Processing Signal Recognition by Rna15 and Hrp1

Precise 3′-end processing of mRNA is essential for correct gene expression, yet in yeast, 3′-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3′-processing and are recognized by the RNA-binding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein–protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3′-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.

Word segmentation of American English /s/ in semi‐spontaneous speech.

To comprehend spoken language, listeners need to find words from a continuous stream of speech sounds. Little work has explored whether there are reliable acoustic cues to word boundaries in conversational speech, which is highly reduced and under‐articulated, potentially creating ambiguities at word boundaries. Segmentation may be even more difficult when the same segment repeats at a word boundary, ending the preceding word and beginning the following word (e.g., gas station). Segmentation in this environment was investigated by examining the production and perception of fricative /s/ in semi‐spontaneous speech. Twenty talkers produced sentences containing ambiguous two‐word sequences with /s/ between the two words. All sequences are interpretable in three ways (e.g., grow snails, gross snails, and gross nails) depending on how the frication is segmented. Acoustic analyses of the production data examined whether there are acoustic cues distinguishing the three versions of the ambiguous sequences. Listening experiments using the talkers’ productions as stimuli evaluated the degree of ambiguity in the tokens and identified acoustic cues that listeners use to segment the two words. Results will be discussed in the context of theories of speech perception and word segmentation.

Known knowns, known unknowns, unknown unknowns and the propagation of scientific enquiry

In February 2002, Donald Rumsfeld, the then US Secretary of State for Defence, stated at a Defence Department briefing: ‘There are known knowns. There are things we know that we know. There are known unknowns. That is to say, there are things that we now know we don’t know. But there are also unknown unknowns. There are things we do not know we don’t know.’ As a result, he was almost universally lampooned since many people initially thought the statement was nonsense. However, careful examination of the statement reveals that it does make sense, indeed the concept of the unknown unknown existed long before Donald Rumsfeld gave it a new audience. Much scientific research is based on investigating known unknowns. In other words, scientists develop a hypothesis to be tested, and then in an ideal situation experiments are best designed to test the null hypothesis. At the outset the researcher does not know whether or not the results will support the null hypothesis. However, it is common for the researcher to believe that the result that will be obtained will be within a range of known possibilities. Occasionally, however, the result is completely unexpected—it was an unknown unknown. There are many known knowns of intracellular protein targeting and, as with many fields of research, it seems that the number of known unknowns increase in parallel. The key determinants for targeting to mitochondria have been determined, and there are at least four subclasses of mitochondrial-targeted proteins containing different targeting signals that are directed to different sites within the mitochondrion (outer membrane, inter-membrane space, inner membrane, and matrix) by different mechanisms (Bolender et al., 2008; Whelan and Glaser, 2007) (Fig. 1). However, much remains unknown, especially in plants. For example, there are now a number of known unknowns resulting from a previously unknown unknown: the existence of proteins dually targeted to both plastids and mitochondria (Peeters and Small, 2001; Ma and Taylor, 2002; Whelan and Glaser, 2007). We now know that dual targeting to plastids and mitochondria occurs as a result of ambiguous signal sequences, but we do not know how these signals are recognized by both organelles, when other proteins are only recognized by one (Whelan and Glaser, 2007). The paper by Chatre et al. (2009) in this issue is an excellent example of research uncovering unknown unknowns. Typically, investigations into the mechanics of intracellular protein targeting have been performed using protein biochemistry, but the investigation by Chatre et al. (2009) is not typical. If the study had simply been investigating mitochondrial targeting using in vitro translation of various proteins with altered targeting signals, detected by protein electrophoresis and immunoblotting, the results would have been a combination of ‘yes, the construct targets to mitochondria’ and ‘no, the construct does not target to mitochondria’. However, because a cell biological approach was taken, so much more information was garnered; that is the power of using fluorescent protein fusions in vivo. By means of a bioinformatics screen, Chatre et al. (2009) identified nucleus-encoded proteins that were predicted, based on the presence of a coiled-coil domain, to be targeted to the secretory pathway. However, one of the proteins identified, and named MITS1, was targeted to mitochondria when a full-length protein fusion was made to the N-terminus of YFP (Fig. 2A). MITS1, a putative actinbinding protein, was also correctly predicted, by various

Becker muscular dystrophy caused by an intronic mutation reducing the efficiency of the splice donor site of intron 26 of the dystrophin gene

We describe an 11-year-old boy with dystrophinopathy who presented with a history of progressive proximal muscle weakness and elevated serum creatine kinase levels at age 6. Sequence analysis of the dystrophin ( DMD) gene did not identify a mutation in the coding regions but revealed a nucleotide substitution in intron 26 (c.3603+3A>T). Since computer algorithms did not conclusively indicate that this sequence variant inactivated the splice site, we analyzed the DMD mRNA from a muscle biopsy of the patient to determine its functional significance. PCR and sequence analysis of the cDNA demonstrated that the mutation reduced the efficiency of the donor splice site and caused activation of a cryptic donor site 113 bp downstream. Activation of the cryptic donor site led to inclusion of 116 bp of intronic sequence containing a stop codon producing a truncated dystrophin protein. Residual wild-type splicing was also detected, which would explain the milder Becker rather than Duchenne phenotype in this patient. We highlight the importance of mRNA analysis for determination of pathogenicity in patients with ambiguous sequence variants in the DMD gene.

Syntactic complexity and ambiguity resolution in a free word order language: Behavioral and electrophysiological evidences from Basque

In natural languages some syntactic structures are simpler than others. Syntactically complex structures require further computation that is not required by syntactically simple structures. In particular, canonical, basic word order represents the simplest sentence-structure. Natural languages have different canonical word orders, and they vary in the degree of word order freedom they allow. In the case of free word order, whether canonical word order plays any role in processing is still unclear. In this paper, we present behavioral and electrophysiological evidence that simpler, canonical word order preference is found even in a free word order language. Canonical and derived structures were compared in two self-paced reading and one ERPs experiment. Non-canonical sentences required further syntactic computation in Basque, they showed longer reading times and a modulation of anterior negativities and P600 components providing evidence that even in free word order, case-marking grammars, underlying canonical word order can play a relevant role in sentence processing. These findings could signal universal processing mechanisms because similar processing patterns are found in typologically very distant grammars. We also provide evidence from syntactically fully ambiguous sequences. Our results on ambiguity resolution showed that fully ambiguous sequences were processed as canonical sentences. Moreover, when fully ambiguous sequences were forced to complex interpretation by means of the world knowledge of the participants, a frontal negativity distinguished simple and complex ambiguous sequences. Thus the preference of simple structures is presumably a universal design property for language processing, despite differences on parametric variation of a given grammar.

Ten‐month‐old infants use prior information to identify an actor's goal

For adults, prior information about an individual's likely goals, preferences or dispositions plays a powerful role in interpreting ambiguous behavior and predicting and interpreting behavior in novel contexts. Across two studies, we investigated whether 10-month-old infants' ability to identify the goal of an ambiguous action sequence was facilitated by seeing prior instances in which the actor directly pursued and obtained her goal, and whether infants could use this prior information to understand the actor's behavior in a new context. Experiment 1 demonstrated that the goal preview impacted infants' subsequent action understanding, but only if the preview was delivered in the same room as the subsequent action sequence. Experiment 2 demonstrated that infants' failure to transfer prior goal information across situations arose from a change in the room per se and not other features of the task. Our results suggest that infants may use their understanding of simple actions as a leverage point for understanding novel or ambiguous actions, but that their ability to do so is limited to certain types of contextual changes.

Processing reduced word-forms in speech perception using probabilistic knowledge about speech production.

Two experiments examined how Dutch listeners deal with the effects of connected-speech processes, specifically those arising from word-final /t/ reduction (e.g., whether Dutch [tas] is tas, bag, or a reduced-/t/ version of tast, touch). Eye movements of Dutch participants were tracked as they looked at arrays containing 4 printed words, each associated with a geometrical shape. Minimal pairs (e.g., tas/tast) were either both above (boven) or both next to (naast) different shapes. Spoken instructions (e.g., "Klik op het woordje tas boven de ster," [Click on the word bag above the star]) thus became unambiguous only on their final words. Prior to disambiguation, listeners' fixations were drawn to /t/-final words more when boven than when naast followed the ambiguous sequences. This behavior reflects Dutch speech-production data: /t/ is reduced more before /b/ than before /n/. We thus argue that probabilistic knowledge about the effect of following context in speech production is used prelexically in perception to help resolve lexical ambiguities caused by continuous-speech processes.

From protein interactions to functional annotation: graph alignment in Herpes

BackgroundSequence alignment is a prolific basis of functional annotation, but remains a challenging problem in the 'twilight zone' of high sequence divergence or short gene length. Here we demonstrate how information on gene interactions can help to resolve ambiguous sequence alignments. We compare two distant Herpes viruses by constructing a graph alignment, which is based jointly on the similarity of their protein interaction networks and on sequence similarity. This hybrid method provides functional associations between proteins of the two organisms that cannot be obtained from sequence or interaction data alone.ResultsWe find proteins where interaction similarity and sequence similarity are individually weak, but together provide significant evidence of orthology. There are also proteins with high interaction similarity but without any detectable sequence similarity, providing evidence of functional association beyond sequence homology. The functional predictions derived from our alignment are consistent with genomic position and gene expression data.ConclusionOur approach shows that evolutionary conservation is a powerful filter to make protein interaction data informative about functional similarities between the interacting proteins, and it establishes graph alignment as a powerful tool for the comparative analysis of data from highly diverged species.

A multilevel and cross-modal approach towards neuronal mechanisms of auditory streaming

We report first results of a multilevel, cross-modal study on the neuronal mechanisms underlying auditory sequential streaming, with the focus on the impact of visual sequences on perceptually ambiguous tone sequences which can either be perceived as two separate streams or one alternating stream. We combined two psychophysical experiments performed on humans and monkeys with two human brain imaging experiments which allow to obtain complementary information on brain activation with high spatial (fMRI) and high temporal (MEG) resolution. The same acoustic paradigm based on the pairing of tone sequences with visual stimuli was used in all human studies and, in an adapted version, in the psychophysical study on monkeys. Our multilevel approach provides experimental evidence that the pairing of auditory and visual stimuli can reliably introduce a bias towards either an integrated or a segregated perception of ambiguous sequences. Thus, comparable to an explicit instruction, this approach can be used to control the subject's perceptual organization of an ambiguous sound sequence without the need for the subject to directly report it. This finding is of particular importance for animal studies because it allows to compare electrophysiological responses of auditory cortex neurons to the same acoustic stimulus sequence eliciting either a segregated or integrated percept.

Spetses 1943-1944: Occupation, Resistance, and Terror in Reality and Fiction

This paper is a local study of the widespread civil conflict that took place in the last year of the German occupation of Greece. In it I focus on the events in Spetses, from March to June 1944, in which a number of kidnappings and executions by the communist-led resistance were followed by massive collaboration of the locals with the Germans in their subsequent anti-resistance operations. Drawing on primary sources such as trial transcripts, unpublished reports, and interviews, I describe a morally ambiguous sequence of events, in which communist violence against perceived local opponents was avenged by collaboration with the Germans, inspired and led by the victims' relatives. I also discuss the fictionalized version of these wartime events in John Fowles's novel The Magus and argue that this version is based on misleading information transmitted to the author during his stay in Spetses.

Defeatingnumts: Semi-pure mitochondrial DNA from eggs and simple purification methods for field-collected wildlife tissues

Mitochondrial DNA (mtDNA) continues to play a pivotal role in phylogeographic, phylogenetic, and population genetic studies. PCR amplification with mitochondrial primers often yields ambiguous sequences, in part because of the co-amplification of nuclear copies of mitochondrial genes (numts) and true mitochondrial heteroplasmy arising from mutations, hybridization with paternal leakage, gene duplications, and recombination. Failing to detect numts or to distinguish the origin of such homologous sequences results in the incorrect interpretation of data. However, few studies obtain purified mtDNA to confirm the mitochondrial origin of the first reference sequences for a species. Here, we demonstrate the importance and ease of obtaining semi-pure mtDNA from wildlife tissues, preserved under various typical field conditions, and investigate the success of 3 commercial extraction kits, cesium-chloride gradient mtDNA purification, long-template PCR amplification, cloning, and more species-specific degenerate primers. Using more detailed avian examples, we illustrate that unfertilized or undeveloped eggs provide the purest sources of mtDNA; that kits provide an alternative to cesium-chloride gradient methods; and that long-template PCR, cloning, and degenerate primers cannot be used to produce reliable mitochondrial reference sequences, but can be powerful tools when used in conjunction with purified mtDNA stocks to distinguish numts from true heteroplasmy.