bluuebunny/crossref_metadata_2025_split huggingface dataset:
Normogram of Middle Cerebral Artery Doppler Indexes and Cerebroplacental Ratio at 12 to 14 Weeks in an Unselected Pregnancy Population
Authors: Ziade M. , Ghosn Ibrahim , Helou Nabil , Abu-Rustum Reem 
Published: July 2018

Objective The aim of this study is to assess the feasibility of visualizing the middle cerebral artery (MCA), establishing the normogram for MCA pulsatility index (PI) and peak systolic velocity (PSV), and calculating cerebroplacental ratio (CPR) at 12 to 14 weeks.
Study Design Prospective cross-sectional study on 186 gravidas presenting for nuchal translucency (NT) assessment. Maternal body mass index (BMI), fetal crown-rump length (CRL), biparietal diameter (BPD), and NT were obtained. Color Doppler was utilized to visualize the MCA and measure PI, PSV, and umbilical artery PI. Normograms for MCA PI and PSV, and for CPR, were constructed. Regression analysis was used for the reference range of MCA PI and CPR according to CRL and BPD. Chi-square and t-test were utilized. p-Value of < 0.05 was considered significant.
Results MCA was successfully visualized in 176/186 (94.6%), PI and PSV measured on 148/186 (79.6%) and 145/186 (78.0%), respectively, and CPR calculated in 133/186 (71.5%). There was no significant effect of BMI, CRL, or BPD on successful assessment of MCA or CPR. Normograms for MCA PI and CPR revealed no significant relation with CRL or BPD.
Conclusion MCA and CPR assessment is feasible at 12 to 14 weeks. A reference range for MCA Doppler indexes and CPR at 12 to 14 weeks has been established. This may prove helpful in the early evaluation of fetuses identified as at-risk for adverse neonatal outcome.
Identity and metapragmatic acts in a student forum discussion thread
Authors: Tanskanen Sanna-Kaisa 
Published: July 2018

Abstract
Starting with the idea that identity is dynamic, interactive and contextualised, the present study offers a close reading of a discussion thread from an online student discussion forum. During the discussion, the interactants both construct identity with language and use identity in order to frame and evaluate their own and others’ contributions. The discussion turns into a metapragmatic debate in which the interactants move away from the topic of the discussion to talk about who is allowed to say what on the topic. The analysis shows how a participant whose identity is flexible is challenged by the other participants, for whom her identity is defined from the beginning, as she self-positions as an outsider. Her contributions are evaluated against this positioning, and for the others her identity resists change.
Codex Argenteusin the light of science and technology
Authors: Munkhammar Lars 
Published: July 2018

AbstractTheCodex Argenteusin Uppsala is the most comprehensive Gothic document still extant. Over the years, its various symbolic values have inspired several investigations and experiments, not only in the humanities, but also in the field of science and technology ranging from deciphering and reproducing the worn and corrupted script to solving riddles in the field of book history by analysing the materials that make up the codex. At the same time, new advanced techniques have been put to the test: woodcut carving, photography, spectral analysis, C-14 analysis and DNA testing. This paper provides a historical survey of techniques, investigations and even manipulations to which theCodex Argenteushas been subjected in the course of the last four centuries.
The phonology and morphology of foreign words in Gothic revisited
Authors: Snædal Magnús 
Published: July 2018

Abstract
The present paper focuses on foreign names and loan words in the Gothic text corpus. The names are mostly Hebrew in origin but were
transferred to Gothic through Greek. Their phonetic, phonological and graphemic adaption will be discussed in light of the close connection
between the Wulfilian and Greek alphabets. In addition, we will raise the question and discuss whether some names are not fully adapted to
the Gothic inflection but remain Greek in form, as well as why foreign words are sometimes not assigned to the inflectional class which
would appear to be the most natural one.
Another hypothesis concerning the grammar and meaning ofInter eils goticum
Authors: Kleiner Yuri 
Published: July 2018

AbstractIn the Germanic part of the epigram, Intereilsgoticumscapia matzia ia drincan, preserved in Codex Salmasianus, it seems most reasonable to isolatescapiaand gloss it as the 1st person sg. of the verb corresponding to Gothicskapjan‘make’.Intereilsgoticumscapiamatzia iadrincanNon audet quisquam dignos edicere uersus.Calliope madido trepidat se iungere Baccho,Ne pedibus non stet ebria Musa suis.Anthologia Latina285(Riese 1869: 187)1
Prosody, genres and evidentiality in Spanish
Authors: Cabedo Nebot Adrián 
Published: July 2018

Abstract
The aim of this paper is to present a prosodic analysis of the evidential discourse marker por lo visto (‘apparently’) in six oral discourse genres: everyday conversation, discussion, sociolinguistic interviews, TV talks, parliamentary interventions, and news. The multimedia material used for this study comes from real samples of spontaneous speech; among the sources used are linguistic corpora (Valesco, CORLEC) and TV websites, or the Spanish government’s official site. In the experimental design, 29 records were analysed statistically according to different variables, mainly phonic (TOBI accents, pitch, intensity, speech rate and so on). The results showed that (a) the tonal accent L + H * is predominant in news, political discourse and sociolectal interviews; (b) only the political discourse and sociolectal interview showed examples of por lo visto as an independent intonational phrase; and (c) prosody seemed to differentiate the pragmatic and the core meanings of the evidential por lo visto in genres in which both possibilities coexist (excluding genres in which the examples are only oriented towards the core evidential pole (news) or towards the pragmatic pole (political speech).
‘No sé’
Authors: González Montserrat 
Published: July 2018

Abstract
The aim of this paper1 is to analyze and discuss the semantic-pragmatic scope that epistemic phrases such as Spanish ‘no sé’ (I don’t know) play in oral opinion reports, a genre that implies a strong presence of value judgements and engagement on the part of the speaker.
The stance frame that such epistemic phrases provide as fixed epistemic formulas has been pointed out by several authors that work in the interactional epistemic domain (Kärkkäinen 2003, 2007; Scheibman 2000, 2001; Thompson 2002), exploring whether the scope of these formulas (I think, I don’t know, I guess, I thought and I remember) extends over something that has yet to be verbalized (forward scope) or over something that has already been verbalized in the preceding turn (backward scope). The working hypothesis is that, contrary to conversational genre, where such fixed formulas tend to provide a forward scope, in opinion reports the scope is twofold, with a stronger presence of backward scope, in the case of ‘no sé’. Findings suggest: (i) strong presence of the epistemic phrasal form (‘no sé’), rather than the predicative one, in the genre analyzed; (ii) predominant role of ‘no sé’ as attitude marker, to convey affect (to construe emotional responses), judgement (to convey moral evaluations) and appreciation (to construe the value of things).
Tenses in interaction
Authors: Rodríguez Rosique Susana 
Published: July 2018

Abstract
This chapter analyzes the discursive functions performed by the future in Spanish. In order to do so, it departs from a definition of the future based on the deictic ‘distance forward’ instruction, which may be projected along a subjectivity axle and cross different levels of meaning. When distance is projected upon the utterance, the future plays several discursive roles and traverses a variety of categories that go beyond evidentiality. More specifically, the future in Spanish can be a powerful tool to persuade and convince (persuasive future); it can also help control disagreement as part of a counter-argumentation strategy (concessive future); or it can participate in an assessment process (mirative future). Information occurring in the future must have been previously activated for these values to arise, which naturally happens in the context of interaction.
Positioning of self in interaction
Authors: Aijmer Karin 
Published: July 2018

Abstract

Look, listen, come on, excuse me are examples of imperatives of verbs which have developed into discourse markers with an attention-getting function. It is shown that the functional markers are used by adolescents to position themselves in relation to what is said and other participants in the conversation in order to mark their disalignment with the norms of adult society. In the adolescents’ world impoliteness is the norm associated with creating a positive self-image of the speakers. Attention-getters are also an important part of how adolescents perform as tellers of narratives or anecdotes. Adolescents use attention-getters for irony and ‘mock politeness’ and in joking competitive exchanges.
Reformulating prior speaker’s turn in Finnish
Authors: Sorjonen Marja-Leena 
Published: July 2018

Abstract
This chapter examines the Finnish particles siis,
eli(kkä) and nii(n) et(tä)
when they occupy the turn-initial position. The chapter focuses on
the use of these particles when they preface a single type of
action, a reformulation of the prior speaker’s turn or more extended
stretch of talk. In contrast to reformulations without a prefacing
particle, the particles are used for contextualizing the turn by
displaying their speaker’s stance vis-à-vis the action being done.
It will be shown that while the prefaces share a range of
characteristics, most importantly making an explicit link to the
prior talk and projecting a reformulation to come, each of them
displays a distinctive epistemic stance (e.g. degree of certainty;
basis of the reformulation). The chapter sets the turn-initial use
of the particles in relation to their other types of usages and
etymology.
Turn-initial naja in German
Authors: Golato Andrea 
Published: July 2018

Abstract
This paper investigates the German token naja in
turn initial position in everyday conversation. The paper makes the
argument that naja is produced in situations when
speakers are negotiating some form of break with prior utterances in
the interaction:1 Prior
research has indicated that in second-pair parts,
naja prefaces disagreements. The current paper
shows that naja is also used in initiating actions
that serve to return to a previous sequence that was not brought to
completion due to actions by the coparticipant(s) or outsiders of
the interaction. In addition, naja is used in third
position turns in which speakers are backing down from a previously
held position. In initiating actions and third positions,
naja serves to indicate the break and
simultaneously initiates actions to overcome it. The findings hold
both for cases in which subsequent talk is prosodically integrated
to naja and the cases in which
naja is not prosodically integrated to the
subsequent talk.
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing
Authors: Han Renmin , Li Yu , Gao Xin , Wang Sheng 
Published: July 2018

Abstract

Motivation
Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the end-to-end mapping between the raw electrical current signal sequence and the reference expected signal sequence serves as the key building block to signal labeling, and the following signal visualization, variant identification and methylation detection. One of the classic algorithms to solve the signal mapping problem is the dynamic time warping (DTW). However, the ultra-long nanopore sequencing and an order of magnitude difference in the sampling speed complexify the scenario and make the classical DTW infeasible to solve the problem.

Results
Here, we propose a novel multi-level DTW algorithm, continuous wavelet DTW (cwDTW), based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can gain remarkable acceleration with tiny loss of the alignment accuracy. On the real nanopore datasets, cwDTW can finish an alignment task in few seconds, which is about 3000 times faster than the original DTW. By successfully applying cwDTW on the tasks of signal labeling and ultra-long sequence comparison, we further demonstrate the power and applicability of cwDTW.

Availability and implementation
Our program is available at https://github.com/realbigws/cwDTW.

Supplementary information
Supplementary data are available at Bioinformatics online.
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
Authors: Alshahrani Mona , Hoehndorf Robert 
Published: July 2018

Abstract

Motivation
In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease’s (or patient’s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse.

Results
We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprised of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

Availability and implementation
https://github.com/bio-ontology-research-group/SmuDGE
Predicting protein–protein interactions through sequence-based deep learning
Authors: Hashemifar Somaye , Neyshabur Behnam , Khan Aly A , Xu Jinbo 
Published: July 2018

Abstract

Motivation
High-throughput experimental techniques have produced a large amount of protein–protein interaction (PPI) data, but their coverage is still low and the PPI data is also very noisy. Computational prediction of PPIs can be used to discover new PPIs and identify errors in the experimental PPI data.

Results
We present a novel deep learning framework, DPPI, to model and predict PPIs from sequence information alone. Our model efficiently applies a deep, Siamese-like convolutional neural network combined with random projection and data augmentation to predict PPIs, leveraging existing high-quality experimental PPI data and evolutionary information of a protein pair under prediction. Our experimental results show that DPPI outperforms the state-of-the-art methods on several benchmarks in terms of area under precision-recall curve (auPR), and computationally is more efficient. We also show that DPPI is able to predict homodimeric interactions where other methods fail to work accurately, and the effectiveness of DPPI in specific applications such as predicting cytokine-receptor binding affinities.

Availability and implementation
Predicting protein-protein interactions through sequence-based deep learning): https://github.com/hashemifar/DPPI/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Topology independent structural matching discovers novel templates for protein interfaces
Authors: Mirabello Claudio , Wallner Björn 
Published: July 2018

AbstractMotivationProtein–protein interactions (PPI) are essential for the function of the cellular machinery. The rapid growth of protein–protein complexes with known 3D structures offers a unique opportunity to study PPI to gain crucial insights into protein function and the causes of many diseases. In particular, it would be extremely useful to compare interaction surfaces of monomers, as this would enable the pinpointing of potential interaction surfaces based solely on the monomer structure, without the need to predict the complete complex structure. While there are many structural alignment algorithms for individual proteins, very few have been developed for protein interfaces, and none that can align only the interface residues to other interfaces or surfaces of interacting monomer subunits in a topology independent (non-sequential) manner.ResultsWe present InterComp, a method for topology and sequence-order independent structural comparisons. The method is general and can be applied to various structural comparison applications. By representing residues as independent points in space rather than as a sequence of residues, InterComp can be applied to a wide range of problems including interface–surface comparisons and interface–interface comparisons. We demonstrate a use-case by applying InterComp to find similar protein interfaces on the surface of proteins. We show that InterComp pinpoints the correct interface for almost half of the targets (283 of 586) when considering the top 10 hits, and for 24% of the top 1, even when no templates can be found with regular sequence-order dependent structural alignment methods.Availability and implementationThe source code and the datasets are available at: http://wallnerlab.org/InterComp.Supplementary informationSupplementary data are available at Bioinformatics online.
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
Authors: Penfold Christopher A , Sybirna Anastasiya , Reid John E , Huang Yun , Wernisch Lorenz , Ghahramani Zoubin , Grant Murray , Surani M Azim 
Published: July 2018

Abstract

Motivation
A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may undergo further branching; the contrary is true during recombination, where two or more statistical processes converge. A key objective is to identify the time of this bifurcation (branch or recombination time) from time series measurements, e.g. by comparing a control time series with perturbed time series. Gaussian processes (GPs) represent an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here, we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs).

Results
We first benchmark the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns of Arabidopsis thaliana gene expression following inoculation with the hemibotrophic bacteria, Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and show that genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors.

Availability and implementation
https://github.com/cap76/BranchingGPs

Supplementary information
Supplementary data are available at Bioinformatics online.
Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics
Authors: Ranjan Ravi , Rani Asha , Finn Patricia W. , Perkins David L. 
Published: July 2018

ABSTRACTIt is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of the study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced and determine if the data are comparable on different platforms. In this study, we perform ultra-deep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We validated the sequencing and analysis methods using different Illumina platform, and with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are more highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome, and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.