bluuebunny/crossref_metadata_2025_split huggingface dataset:
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information
Authors: Ghosh Pritha , Mathew Oommen K. , Sowdhamini Ramanathan 
Published: October 2016

Abstract
Background
RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information.

Results
The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search.

Conclusions
RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential information pertaining to an RBP, like overall function annotations, are provided. The web server can be accessed at the following link: http://caps.ncbs.res.in/rstrucfam.
Combining graph embedding and sparse regression with structure low-rank representation for semi-supervised learning
Authors: You Cong-Zhe , Palade Vasile , Wu Xiao-Jun 
Published: October 2016

AbstractIn this paper, we propose a novel method for semi-supervised learning by combining graph embedding and sparse regression, termed as graph embedding and sparse regression with structure low rank representation (GESR-LR), in which the embedding learning and the sparse regression are performed in a combined approach. Most of the graph based semi-supervised learning methods take into account the local neighborhood information while ignoring the global structure of the data. The proposed GESR-LR method learns a low-rank weight matrix by projecting the data onto a low-dimensional subspace. The GESR-LR makes full use of the supervised learning information in the construction of the affinity matrix, and the affinity construction is combined with graph embedding in a single step to guarantee the global optimal solution. In the dimensionality reduction procedure, the proposed GESR-LR can preserve the global structure of the data, and the learned low-rank weight matrix can effectively reduce the influence of the noise. An effective novel algorithm to solve the corresponding optimization problem was designed and is presented in this paper. Extensive experimental results demonstrate that the GESR-LR method can obtain a higher classification accuracy than other state-of-the-art methods.
Flow cytometry dataset for cells collected from touched surfaces
Authors: Kwon Ye Jin , Stanciu Cristina E. , Philpott M. Katherine , Ehrhardt Christopher J. 
Published: October 2016

‘Touch’ or trace cell mixtures submitted as evidence are a significant problem for forensic laboratories as they can render resulting genetic profiles difficult or even impossible to interpret. Optical signatures that distinguish epidermal cell populations from different contributors could facilitate the physical separation of mixture components prior to genetic analysis, and potentially the downstream production of single source profiles and/or simplified mixtures. This dataset comprises the results from antibody hybridization surveys using Human Leukocyte Antigen (HLA) and Cytokeratin (CK) probes, as well as surveys of optical properties of deposited cells, including forward scatter (FSC), side scatter (SSC), and fluorescence emissions in the Allophycocyanin (APC) channel. All analyses were performed on “touch” samples deposited by several different contributors on multiple days to assess inter- and intra-contributor variability.
Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests
Authors: McKernan Kevin , Spangler Jessica , Helbert Yvonne , Lynch Ryan C. , Devitt-Lee Adrian , Zhang Lei , Orphe Wendell , Warner Jason , Foss Theodore , Hudalla Christopher J. , Silva Matthew , Smith Douglas R. 
Published: October 2016

Background: The presence of bacteria and fungi in medicinal or recreationalCannabisposes a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation.Methods: A set of 15 medicinalCannabissamples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media.Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, includingAcinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinumandPenicillium steckii.Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure ofAspergillusspecies to grow well on either platform. Substantial growth ofClostridium botulinumand other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample.Conclusions: These findings have important implications for theCannabisand food safety testing industries.
Experiences of student midwives in the care of women with perinatal loss: A qualitative descriptive study
Authors: Alghamdi Reem , Jarrett Patricia 
Published: October 2016

Background: Student midwives often encounter perinatal loss, such as stillbirth and neonatal death, as part of their experience of clinical practice. Coping with these events can be challenging because loss and death are the antitheses of birth, which predominates midwifery practice. There has been limited research on how student midwives are supported when caring for women with bereavement; however, poor support may have repercussions for future practice. Aim: The aim of this study is to explore the experiences of final-year student midwives when caring for women with perinatal loss. Methods: Two focus groups were conducted with 10 final-year BSc (Hons) Midwifery students. The focus groups lasted approximately 1 hour and used a semi-structured interview schedule. Data were analysed using thematic analysis. Findings: Four key themes were identified from the data: preparation for perinatal loss; ‘just dealing with it’; contradiction and challenges with the role of the midwife; and emotional impact and coping strategies. Conclusions: Final-year student midwives believed they were ill-prepared in caring for women with perinatal loss, reported difficulties in communicating with women and believed they were excluded from their care. Students valued support from the bereavement midwife and identified effective strategies which helped them cope with bereavement and loss.
High-energy pilon fractures management
Authors: Tomás-Hernández Jordi 
Published: October 2016

High-energy pilon fractures are challenging injuries. Multiple options are described for the definitive surgical management of these fractures, but there is no level I evidence for optimal management. The current management and recommendations for treatment will be reviewed in this article. Anatomical reduction of the fracture, restoration of joint congruence and reconstruction of the posterior column with a correct limb axis minimising the soft-tissue insult are the key points to a good outcome when treating pilon fractures. Even when these goals are achieved, there is no guarantee that results will be acceptable in the mid-term due to the frequent progression to post-traumatic arthritis. In high-energy fractures with soft-tissue compromise, a staged treatment is generally accepted as the best way to take care of these devastating fractures and is considered a local ‘damage control’ strategy. The axial cuts from the CT scan images are essential in order to define the location of the main fracture line, the fracture pattern (sagittal or coronal) and the number of fragments. All of this information is crucial for pre-operative planning, incision placement and articular surface reduction. No single method of fixation is ideal for all pilon fractures, or suitable for all patients. Definitive decision making is mostly dependent on the fracture pattern, condition of the soft-tissues, the patient’s profile and surgical expertise. Cite this article: Tomás-Hernández J. High-energy pilon fractures management: state of the art. EFORT Open Rev 2016;1:354-361. DOI: 10.1302/2058-5241.1.000016.
Los derechos humanos fundamentados mediante la legitimación y la moral jurídica.
Authors: Galán Galindo Astrid Rocío 
Published: October 2016

El Estado colombiano está inmerso en el proceso de paz y posconflicto, si llegara a concretarse tal acuerdo, razón por la cual debe enfrentar una etapa de transición continua en la que se replanteen aspectos como el modelo de justicia que se ha venido aplicando y que terminará por modificar el sistema jurídico y las políticas públicas que hasta la fecha se han venido ejecutando. Es por ello que, a la hora de plantear políticas públicas cuyo objetivo sea la consecución de la paz, estas deben ser entendidas desde la esfera de la sana convivencia y la aceptación del otro. Todo aquello se lograría a partir de una evolución del sistema jurídico y cultural de la sociedad colombiana que permita incluir la moral jurídica, la cual, tiene como requisito fundamental el reconocimiento recíproco entre personas y se materializa con un sistema jurídico que abarque más allá de una simple protección a los derechos humanos. Lo anterior hace referencia a la pluricultural existente en todo el territorio nacional, por ejemplo, las minorías étnicas gitanas, afrodescendientes, etc. y a cómo deben ser incluidas de forma efectiva en un modelo social sostenible.
A Fresh Look at P.Beatty III (P47) Towards an Integrative Study of an Early Christian Codex
Authors: Malik Peter 
Published: October 2016

Abstract
Chester Beatty Biblical Papyrus III is the earliest extensive manuscript of the Apocalypse of John. It has, however, received very little scholarly attention. This gap in our knowledge will be filled by the author’s current research, where physical and nontextual features are analysed in connection with scribal habits and textual characteristics. This preliminary article draws attention to two aspects where such an integrative method has proven particularly fruitful.
Recheneffiziente Trajektorienoptimierung für Fahrzeuge mittels quadratischem Programm
Authors: Gutjahr Benjamin , Pek Christian , Gröll Lutz , Werling Moritz 
Published: October 2016

Zusammenfassung
Die aus der Literatur bekannten Verfahren zur Optimierung von Fahrtrajektorien überfordern kurz und mittelfristig die
Fahrzeugsteuergeräte hinsichtlich ihrer Rechenleistung. Um auch neu aufkommenden Qualitätsanforderungen zu entsprechen,
nutzt die vorliegende Arbeit die aus der Literatur bekannten Vorteile der beschränkten, linear-quadratischen Optimierung
zur recheneffizienten Lösungsfindung gewinnbringend aus. Hierbei führt die ausgewählte Problemformulierung basierend auf
dem anwendungsspezifischem Einsatz von Schlupfvariablen zu funktionalen Weiterentwicklungen, sodass neben der
priorisierten Kollisionsvermeidung auch Aspekte natürlichen Fahrverhaltens auf besondere Weise berücksichtigt werden
können. Die Erprobung der umgesetzten Fahrzeuglängs- und -querführung im Realversuch verdeutlicht das große Potential
dieses Ansatzes für automatisierte Fahrfunktionen.
Fostering engagement with the Common European Framework of Reference for Languages and the European Language Portfolio: Learning from good practice in university language centres
Authors: Carson Lorna 
Published: October 2016

AbstractThis article begins with a brief overview of the aims and activities of the CercleS CEFR/ELP Focus Group. It goes on to report on some of the outcomes of the 2015 CercleS CEFR/ELP seminar hosted by the Centre for Language and Communication Studies at Trinity College Dublin. The five examples presented during the seminar’s plenary sessions are summarised, illustrating how the CEFR and ELP have been used in university language centres both to foster student engagement and reflection and to meet the increasingly urgent need for benchmarking language learning outcomes in higher education.
From the learning diary to the ELP: An e-portfolio for autonomous language learning
Authors: Bertolotti Greta , Beseghi Micol 
Published: October 2016

AbstractIn 2011 the Language Centre of the University of Parma introduced a self-study programme aimed at creating an autonomy-inspired language learning environment. Students are actively engaged in the management of their own learning and co-directed by advisors and teachers in the phases of planning, monitoring and assessment. Reflective diary writing has played such a crucial role in the programme that it was decided to extend the learner diary and implement the ELP. The model used is an online version of the canonical ELP (Little and Perclová 2001), consisting of a language passport, a language biography and a dossier; it is based on the principles of reflective learning, self-assessment and learner autonomy (Little et al. 2011,
The classroom and beyond: Creating a learning environment to support learners of Japanese at CEFR levels A2.2 towards B1
Authors: Ijichi Nobuko 
Published: October 2016

AbstractJapanese is a popular choice amongst higher education students on IWLPs (Institution-Wide Language Programmes), but the language presents challenges for many learners. Students on university elective programmes begin their courses with enthusiasm but often become discouraged and drop out at the post-beginner stage. Thus Japanese elective programmes in universities can be over-represented at beginner level but then tail off. There are many examples of good practice in teaching beginners Japanese but fewer models at higher levels. This activity report focuses on the development of a student learning environment suitable for Japanese at A2.2 towards B1 levels, incorporating classroom activities but also opportunities for learning in a “beyond the classroom” context. It is now widely accepted that the CEFR can provide much support and open up new opportunities. A common approach is to begin by defining appropriate “can do” descriptors, which can then be set as classroom objectives for learners. But very often there is not enough time or opportunity to use the language in the classroom. This report shows how classroom learning can be supplemented in contexts outside the institutional setting. Such contexts can provide real-world tasks, stimuli for interaction, a range of authentic documents, and culture discovery opportunities. All these support learning in a dynamic manner and ideally should link back to the CEFR’s “can do” objectives, which are identified in the core curriculum.
Copula–Induced Measures of Concordance
Authors: Fuchs Sebastian 
Published: October 2016

Abstract
We study measures of concordance for multivariate copulas and copulas that induce measures of
concordance. To this end, for a copula A, we consider the maps C → R given by

where C denotes the collection of all d–dimensional copulas, M is the Fréchet–Hoeffding upper bound, Π is the product copula, [. , .] : C × C → R is the biconvex form given by
[C, D] := ∫ [0,1]d C(u) dQD(u) with
the probability measure QD associated with the copula D, and ψΛ C → C is a transformation of copulas.
We present conditions on ψΛ and on A under which these maps are measures of concordance. The resulting
class of measures of concordance is rich and includes the well–known examples Spearman’s rho and Gini’s
gamma.
Quality assurance and standardization in view of non-invasive prenatal testing (NIPT)
Authors: Schenk Peter W. 
Published: October 2016

Abstract:
The development and utilization of non-invasive prenatal tests have provided new and exciting challenges for quality assurance. Quality managers, scientists and technicians have been faced with the question of appropriate validation and quality controls for these innovative tests. Guidelines on quality assurance and quality control are still lacking and the need is growing inexorably. To integrate non-invasive prenatal tests into existing guidelines, attention must be paid to ISO standard 15189 which describes the requirements for medical laboratories and therefore diagnostic molecular genetics laboratories. Performing the test in an accredited molecular genetics laboratory according to ISO 15189 ensures the adherence to, and compliance with, all important principles. In this article, an overview of quality requirements applied to non-invasive prenatal testing is given from a quality manager’s point of view.
Language as Mechanisms for Interaction
Authors: Kempson Ruth , Cann Ronnie , Gregoromichelaki Eleni , Chatzikyriakidis Stergios 
Published: October 2016

Abstract
Language use is full of subsentential shifts of context, a phenomenon dramatically illustrated in conversation where non-sentential utterances displaying seamless shifts between speaker/hearer roles appear regularly. The hurdle this poses for standard assumptions is that every local linguistic dependency can be distributed across speakers, with the content of what they are saying and the significance of each conversational move emerging incrementally. Accordingly, we argue that the modelling of a psychologically-realistic grammar necessitates recasting the notion of natural language in terms of our ability for interaction with others and the environment, abandoning the competence-performance dichotomy as standardly envisaged. We sketch Dynamic Syntax, a model in which underspecification and incremental time-relative update is central, showing how interactive effects of conversation follow directly. Finally, we note the changing cognitive-science horizons to be explored once a language-as-action view is adopted.
What ellipsis can do for phases and what it can’t, but not how
Authors: Aelbrecht Lobke 
Published: October 2016

AbstractThe study of ellipsis, being a mismatch between form and meaning, has already proven to have consequences for our understanding of language in general, as it has helped us gain insights in other domains of the grammar. This paper focuses on one of these domains, namely the notion of Spell-Out and the theory of phases that has been developed within the Minimalist Program (Chomsky 1995,
Performance, Performativity, and the Medium of Poetry: W. B. Yeats’s “Among School Children”
Authors: Haekel Ralf 
Published: October 2016

AbstractPerformance theory has a long and complex history. Initiated by J. L. Austin’sHow To Do Things With Words, it has been critically discussed by Émile Benveniste, Jacques Derrida, and Paul de Man among others. Most recently, media studies and the concept of cultural techniques have added yet another facet to what originated in speech act theory. Although poetry with its musical dimension seems especially prone to be investigated in the field, this is rarely the case. After an overview of the relevant theoretical developments, I analyze William Butler Yeats’s “Among School Children” – with a special focus on its final verse “How can we know the dancer from the dance?” – as a powerful reflection on the performative nature of poetry in general.
Evolutionary Genomics of Peach and Almond Domestication
Authors: Velasco Dianne , Hough Josh , Aradhya Mallikarjuna , Ross-Ibarra Jeffrey 
Published: October 2016

AbstractThe domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.