1,721,098 research outputs found
Sviluppi metodologici per la cristallizzazione e l’analisi strutturale di proteine tramite Risonanza Magnetica Nucleare allo stato solido
Full text linkHigh-resolution solid-state NMR (ssNMR) has recently emerged as a powerful characterization technique for systems that cannot be investigated by solution NMR or X-ray crystallographic methods, and represents a subtle complementary technique for any atomic-scaled study.
This is particularly true in structural biology. There exist nowadays well established protocols for sample preparation, resonance assignment and collection of structural restraints, that have paved the way to the first three-dimensional structure determinations at atomic resolution of biomolecules in the solid state, from microcrystalline samples to fibrils and membrane-associated systems.
Despite rapid uptake in the field of structural biology, however, these methods for structure determination are far from being routine, and several important problems remain however to
be solved before ssNMR is applied to the study of challenging solid protein assemblies. Many methodological developments are still expected in this fast evolving field.
Most of the model systems used up-to-date for method development in biological solid-state NMR, are relatively small globular proteins, in the range of 50 to 80 residues (approximately 5.5
to 9.5 kDa). In order to extend the capabilities of ssNMR to larger substrates, the objectives of this thesis are twofold: a) to establish a new, large and more complex model system, and
b) to develop new, sophisticated NMR experiments in order to improve the sensitivity and the resolution of the currently existing schemes for resonance assignment, which is one of the main barrier to progress to structural investigation in solid proteins.
The N-terminal domain of the subunit of E. coli DNA polymerase III (186 : 186 residues, 18 kDa) was selected as a target. This domain represents the catalytic core of the E. coli replisome,
the large molecular machine that replicated DNA in bacteria.
In a first part, preparation conditions for solid-state NMR are obtained, notably in combination with automated screening processes for high-throughput protein crystallography, and almost
complete resonance assignment is performed by the application of established experiments based on high-power rf irradiations and slow magic-angle spinning (MAS) at high magnetic fields.
In a second part, we explore the use of MAS at so-called ultra-fast spinning rates (60 kHz).
We show that this makes possible the use of “totally low power” experiments. This yields an extraordinary increase in resolution and sensitivity, enabling the acquisition of selective cross-
polarization (CP) transfers, through-bond correlations and 1 H-detected correlations. In particular, we demonstrate that narrow 1 H NMR line widths can be obtained for fully protonated
protein samples in the solid state under ultra-fast magic-angle spinning for medium-size microcrystalline and non-crystalline proteins, without any need for dilution against a deuterated
background. This provides extensive, robust and expeditious assignments of the backbone 1 H, 15 N, 13 Cα and
13 CO resonances of proteins in different aggregation states, without the need of deuteration.
The final part of this thesis concerns the study of thermotropic liquid crystals (LC or LX) phases of a de Vries smectogen, the (S)-hexyl-lactate derivative abbreviated as 9HL, selectively deuterated in a phenyl moiety of the aromatic core. de Vries mesophases show a substantially constant layer spacing in the transition between smectic C and smectic A mesophases and are for
this reason of great interest for the development of new ferroelectric (FLC) and antiferroelectric (AFLC) electrooptic devices. Our work is the first attempt to apply NMR to characterize the nature of the de Vries transition, discriminating among possible models. It is also one of the
first examples in the scientific literature of application of high magnetic field (above 16 T) for the analysis of LX phases
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Documenting Italian Libraries on Wikidata: From Local Projects to a Multilayered National Knowledge Graph
No full textThe representation of Italian libraries in Wikidata has grown through two major data imports. In 2020, under commission from Tuscany region, the Sistema Cultura Toscana dataset was uploaded, raising the number of Italian libraries from fewer than 500 to 1,322 and documenting the methodology of this first large-scale project. A second step followed in 2022 with the addition of 11,239 entries from the ICCU Italian Libraries Database. This process involved merging CC0 datasets, entity alignment, and addressing gaps between the web versions of databases and their dumps. Together, these efforts illustrate both achievements and challenges in enriching Wikidata’s coverage of Italian libraries, specifically highlighting the role of iterative, human-curated workflows in large-scale data imports
Event Factuality in Italian: Annotation of News Stories from the Ita-TimeBank
Full text linkIn this paper we present ongoing work devoted to the extension of the Ita-TimeBank (Caselli et al., 2011) with event factuality annotation on top of TimeML annotation, where event factuality is represented on three main axes: time, polarity and certainty. We describe the annotation schema proposed for Italian and report on the results of our corpus analysis
Divide and Conquer: Crowdsourcing the Creation of Cross-Lingual Textual Entailment Corpora.
Full text linkWe address the creation of cross-lingual tex- tual entailment corpora by means of crowdsourcing. Our goal is to define a cheap and replicable data collection methodology that minimizes the manual work done by expert annotators, without resorting to preprocessing tools or already annotated monolingual datasets. In line with recent works empha- sizing the need of large-scale annotation efforts for textual entailment, our work aims to: i) tackle the scarcity of data available to train and evaluate systems, and ii) promote the re- course to crowdsourcing as an effective way to reduce the costs of data collection without sacrificing quality. We show that a complex data creation task, for which even experts usually feature low agreement scores, can be effectively decomposed into simple subtasks as- signed to non-expert annotators. The resulting dataset, obtained from a pipeline of different jobs routed to Amazon Mechanical Turk, contains more than 1,600 aligned pairs for each combination of texts-hypotheses in English, Italian and German
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Towards sentiment analysis for historical texts
No full textThis article presents the integration of sentiment analysis in ALCIDE, an online platform for historical content analysis. A prior polarity approach has been applied to a corpus of Italian historical texts, and a new lexical resource has been developed with a semi-automatic mapping starting from two English lexica. This article also reports on a first experiment on contextual polarity using both expert annotators and crowdsourced contributors. The long-term goal of our research is to create a system to support historical studies, which is able to analyse the sentiment in historical texts and to discover the opinion about a topic and its change over time
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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