Multilevel mixed-type data analysis for validating partitions of scrapie isolates

The dissertation arises from a joint study with the Department of Food Safety and Veterinary Public Health of the Istituto Superiore di Sanità. The aim is to investigate and validate the existence of distinct strains of the scrapie disease taking into account the availability of a priori benchmark partition formulated by researchers. Scrapie of small ruminants is caused by prions, which are unconventional infectious agents of proteinaceous nature a ecting humans and animals. Due to the absence of nucleic acids, which precludes direct analysis of strain variation by molecular methods, the presence of di erent sheep scrapie strains is usually investigated by bioassay in laboratory rodents. Data are collected by an experimental study on scrapie conducted at the Istituto Superiore di Sanità by experimental transmission of scrapie isolates to bank voles. We aim to discuss the validation of a given partition in a statistical classification framework using a multi-step procedure. Firstly, we use unsupervised classification to see how alternative clustering results match researchers’ understanding of the heterogeneity of the isolates. We discuss whether and how clustering results can be eventually exploited to extend the preliminary partition elicited by researchers. Then we motivate the subsequent partition validation based on the predictive performance of several supervised classifiers. Our data-driven approach contains two main methodological original contributions. We advocate the use of partition validation measures to investigate a given benchmark partition: firstly we discuss the issue of how the data can be used to evaluate a preliminary benchmark partition and eventually modify it with statistical results to find a conclusive partition that could be used as a “gold standard” in future studies. Moreover, collected data have a multilevel structure and for each lower-level unit, mixed-type data are available. Each step in the procedure is then adapted to deal with multilevel mixed-type data. We extend distance-based clustering algorithms to deal with multilevel mixed-type data. Whereas in supervised classification we propose a two-step approach to classify the higher-level units starting from the lower-level observations. In this framework, we also need to define an ad-hoc cross validation algorithm

Representation of Jews and Anti-Jewish Bias in 19th-Century French Public Discourse: Distant and Close Reading

We explore through the lens of distant reading the evolution of discourse on Jews in France during the XIX century. We analyze a large textual corpus including heterogeneous sources-literary works, periodicals, songs, essays, historical narratives-to trace how Jews are associated to different semantic domains, and how such associations shift over time. Our analysis deals with three key aspects of such changes: the overall transformation of embedding spaces, the trajectories of word associations, and the comparative projection of different religious groups over different, historically relevant semantic dimensions or streams of discourse. This allows to show changes in the association between words and semantic domains (referring e.g. to economic and moral behaviors), the evolution of stereotypes, and the dynamics of bias over a long time span characterized by major historical transformations. We suggest that the analysis of large textual corpora can be fruitfully used in a dialogue with more traditional close reading approaches-by pointing to opportunities of in-depth analyses that mobilize more qualitative approaches and a detailed inspection of the sources that distant reading inevitably tends to aggregate. We offer a short example of such a dialogue between different approaches in our discussion of the Second Empire transformations, where we mobilize the historian's tools to start disentangling the complex interactions between changes in French society, the nature of sources, and representations of Jews. While our example is limited in scope, we foresee large potential payoffs in the cooperative interaction between distant and close reading

Application of ATR-far-infrared spectroscopy to the analysis of natural resins

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Organogel Coupled with Microstructured Electrospun Polymeric Nonwovens for the Effective Cleaning of Sensitive Surfaces

Hydrogels and organogels are widely used as cleaning materials, especially when a controlled solvent release is necessary to prevent substrate damage. This situation is often encountered in the personal care and electronic components fields and represents a challenge in restoration, where the removal of a thin layer of aged varnish from a painting may compromise the integrity of the painting itself. There is an urgent need for new and effective cleaning materials capable of controlling and limiting the use of solvents, achieving at the same time high cleaning efficacy. In this paper, new sandwich-like composites that fully address these requirements are developed by using an organogel (poly(3-hydroxybutyrate) + \u3b3-valerolactone) in the core and two external layers of electrospun nonwovens made of continuous submicrometric fibers produced by electrospinning (either poly(vinyl alcohol) or polyamide 6,6). The new composite materials exhibit an extremely efficient cleaning action that results in the complete elimination of the varnish layer with a minimal amount of solvent adsorbed by the painting layer after the treatment. This demonstrates that the combined materials exert a superficial action that is of utmost importance to safeguard the painting. Moreover, we found that the electrospun nonwoven layers act as mechanically reinforcement components, greatly improving the bending resistance of organogels and their handling. The characterization of these innovative cleaning materials allowed us to propose a mechanism to explain their action: electrospun fibers play the leading role by slowing down the diffusion of the solvent and by conferring to the entire composite a microstructured rough superficial morphology, enabling to achieve outstanding cleaning performance

Do I Need to Operate on That in the Middle of the Night? Development of a Nomogram for the Diagnosis of Severe Acute Cholecystitis

Background Some authors have proposed different predictive factors of severe acute cholecystitis, but generally, the results of risk analyses are expressed as odds ratios, which makes it difficult to apply in the clinical practice of the acute care surgeon. The severe form of acute cholecystitis should include both gangrenous and phlegmonous cholecystitis, due to their severe clinical course, and cholecystectomy should not be delayed. The aim of this study was to create a nomogram to obtain a graphical tool to compute the probability of having a severe acute cholecystitis. Methods This is a retrospective study on 393 patients who underwent emergency cholecystectomy between January 2010 and December 2015 at the Acute Care Surgery Service of the S. Anna University Hospital of Ferrara, Italy. Patients were classified as having a non-severe acute cholecystitis or a severe acute cholecystitis (i.e., gangrenous and phlegmonous) based on the final pathology report. The baseline characteristics, pre-operative signs, and abdominal ultrasound (US) findings were assessed with a stepwise multivariate logistic regression analysis to predict the risk of severe acute cholecystitis, and a nomogram was created. Results Age as a continuous variable, WBC count ≥ 12.4 × 103/μl, CRP ≥9.9 mg/dl, and presence of US thickening of the gallbladder wall were significantly associated with severe acute cholecystitis at final pathology report. A significant interaction between the effect of age and CRP was found. Four risk classes were identified based on the nomogram total points. Conclusions Patients with a nomogram total point ≥ 74 should be considered at high risk of severe acute cholecystitis (at 74 total point, sensitivity = 78.5%; specificity = 78.2%; accuracy = 78.3%) and this finding could be useful for surgical planning once confirmed in a prospective study comparing the risk score stratification and clinical outcomes

Do I Need to Operate on That in the Middle of the Night? Development of a Nomogram for the Diagnosis of Severe Acute Cholecystitis

Background Some authors have proposed different predictive factors of severe acute cholecystitis, but generally, the results of risk analyses are expressed as odds ratios, which makes it difficult to apply in the clinical practice of the acute care surgeon. The severe form of acute cholecystitis should include both gangrenous and phlegmonous cholecystitis, due to their severe clinical course, and cholecystectomy should not be delayed. The aim of this study was to create a nomogram to obtain a graphical tool to compute the probability of having a severe acute cholecystitis. Methods This is a retrospective study on 393 patients who underwent emergency cholecystectomy between January 2010 and December 2015 at the Acute Care Surgery Service of the S. Anna University Hospital of Ferrara, Italy. Patients were classified as having a non-severe acute cholecystitis or a severe acute cholecystitis (i.e., gangrenous and phlegmonous) based on the final pathology report. The baseline characteristics, pre-operative signs, and abdominal ultrasound (US) findings were assessed with a stepwise multivariate logistic regression analysis to predict the risk of severe acute cholecystitis, and a nomogram was created. Results Age as a continuous variable, WBC count ≥ 12.4 × 103/μl, CRP ≥9.9 mg/dl, and presence of US thickening of the gallbladder wall were significantly associated with severe acute cholecystitis at final pathology report. A significant interaction between the effect of age and CRP was found. Four risk classes were identified based on the nomogram total points. Conclusions Patients with a nomogram total point ≥ 74 should be considered at high risk of severe acute cholecystitis (at 74 total point, sensitivity = 78.5%; specificity = 78.2%; accuracy = 78.3%) and this finding could be useful for surgical planning once confirmed in a prospective study comparing the risk score stratification and clinical outcomes

Morphology of planktonic zoeal stages of Palicus caronii (Decapoda, Brachyura), identified by DNA barcoding, provides novelties to Palicoidea larval systematics

The zoeal development of the brachyuran crab, Palicus caronii, comprises two zoeal stages and the morphology is described and illustrated in detail. The zoeae were collected in plankton samples from the Southern Ligurian Sea (Western Mediterranean). Although the morphology of the larval stages of this species was unknown, a combination of characters allowed the zoeae to initially be assigned to the Palicidae, based on the previous unique known first zoeal description of one species of this family. Later, the identification of the larvae as Palicus caronii was confirmed through molecular analysis. The morphological features of the zoeae that characterize the Palicidae and separate them from the Crossotonotidae are confirmed. Also, the larval development comprising only two zoeal stages observed in Palicus caronii, the peculiar and uncommon carapace surface setation, and the presence of anterodorsal and posterodorsal sensory dorsal organs suggest that these characters could be common to the Palicoidea.The collection of the larval stages used in the present work was performed in the context of a project carried out with the financial support of the Italian Ministero della Salute (Research Project IZSPLV 14/14 RC). COI sequence of adult crab of Palicus caronii was obtained within the framework of the MEGALOPADN project (CGL2009-11225) funded by the “Ministerio de Economía y Competividad (MINECO)” Spanish Plan R + D + I and FEDER. Authors would like to thank Prof. Simona Bonelli, Department of Life Sciences and Systems Biology (UNITO), for her support, and the entomology laboratory of Department of Agriculture, Forestry and Food Sciences (UNITO) for loaning the camera lucida, with a special thanks to Enrico Busato for his availability. The study was funded by the Italian Ministero della Salute (Research Project IZSPLV 14/14 RC)

Cr(III) Complexes Bearing a β-Ketoimine Ligand for Olefin Polymerization: Are There Differences between Coordinative and Covalent Bonding?

β-ketoimines are extensively applied for the synthesis of organometallic complexes intended as (pre)catalysts for a variety of chemical transformations. We were interested in the synthesis of two Cr complexes bearing a simple bidentate β-ketoimine (L), with different ligand binding modes, as well as their application as a precatalyst in the polymerization of olefins. Complex 1 (L2CrCl3) was obtained by direct reaction of L with CrCl3(THF)3, while, for the synthesis of complex 2 (LCrCl2), the ligand was first deprotonated with nBuLi, giving the β-ketoiminato ligand L─Li+, and then reacted with CrCl3(THF)3. Characterization of the complexes proved that the Cr(III) ion is coordinatively bonded to L in 1, while it is covalently bonded to L in 2. The complexes were then used as precatalysts for the polymerization of ethylene and various cyclic olefins. Upon activation with methylaluminoxane, both the complexes exhibited poor activity in the polymerization of ethylene, whilst they exhibit good productivity in the polymerization of cyclic olefins, affording semicrystalline oligomers, without a significant difference between 1 and 2. To gain more insight, we investigated the reaction of the complexes with the Al-cocatalyst by IR and UV-Vis spectroscopies. The results proved that, in case of 1, the Al-activator deprotonates the ligand, bringing to the formation of an active species analogous to that of 2

Near-infrared hyperspectral imaging to map collagen content in prehistoric bones for radiocarbon dating

Many of the rarest prehistoric bones found by archaeologists are enormously precious and are considered to be part of our cultural and historical patrimony. Radiocarbon dating is a well-established technique that estimates the ages of bones by analysing the collagen still present. However, this method is destructive, and its use must be limited. In this study, we used imaging technology to quantify the presence of collagen in bone samples in a non-destructive way to select the most suitable samples (or sample regions) to be submitted to radiocarbon dating analysis. Near-infrared spectroscopy (NIR) that was connected to a camera with hyperspectral imaging (HSI) was used along with a chemometric model to create chemical images of the distribution of collagen in ancient bones. This model quantifies the collagen at every pixel and thus provides a chemical mapping of collagen content. Our results will offer significant advances for the study of human evolution as we will be able to minimise the destruction of valuable bone material, which is under the protection and enhancement of European cultural heritage and thus allow us to contextualise the valuable object by providing an accurate calendar age.The collagen present in rare prehistoric bones allows for their age to be estimated by radiocarbon dating, but this method is destructive towards these precious archaeological remains. Here, the authors report a non-destructive method based on near-infrared hyperspectral imaging to precisely localize the collagen preserved in parts of ancient specimens suitable for radiocarbon dating