Developing Quantitative Methodologies for the Digital Humanities: A Case Study of 20th Century American Commentary on Russian Literature

Using scientific methods in the humanities is at the forefront of objective literary analysis. However, processing big data is particularly complex when the subject matter is qualitative rather than numerical. Large volumes of text require specialized tools to produce quantifiable data from ideas and sentiments. Our team researched the extent to which tools such as Weka and MALLET can test hypotheses about qualitative information. We examined the claim that literary commentary exists within political environments and used US periodical articles concerning Russian literature in the early twentieth century as a case study. These tools generated useful quantitative data that allowed us to run stepwise binary logistic regressions. These statistical tests allowed for time series experiments using sea change and emergency models of history, as well as classification experiments with regard to author characteristics, social issues, and sentiment expressed. Both types of experiments supported our claim with varying degrees, but more importantly served as a definitive demonstration that digitally enhanced quantitative forms of analysis can apply to qualitative data. Our findings set the foundation for further experiments in the emerging field of digital humanities.

New data inversion formulae in confocal scanning microscopy

Whereas the resolving power of an ordinary optical microscope is determined by the classical Rayleigh distance, significant super-resolution, i.e. resolution improvement beyond that Rayleigh limit, has been achieved by confocal scanning light microscopy. Furthermore is has been shown that the resolution of a confocal scanning microscope can still be significantly enhanced by measuring, for each scanning position, the full diffraction image by means of an array of detectors and by inverting these data to recover the value of the object at the focus. We discuss the associated inverse problem and show how to generalize the data inversion procedure by allowing, for reconstructing the object at a given point, to make use also of the diffraction images recorded at other scanning positions. This leads us to a whole family of generalized inversion formulae, which contains as special cases some previously known formulae. We also show how these exact inversion formulae can be implemented in practice.

Super-resolution in confocal scanning microscopy: generalized inversion formulae

It was shown in previous papers that the resolution of a confocal scanning microscope can be significantly improved by measuring, for each scanning position, the full diffraction image and by inverting these data to recover the value of the object at the confocal point. In the present work, the authors generalize the data inversion procedure by allowing, for reconstructing the object at a given point, to make use of the data samples recorded at other scanning positions. This leads them to a family of generalized inversion formulae, either exact or approximate. Some previously known formulae are re-derived here as special cases in a particularly simple way.

Super-resolution in confocal scanning microscopy: II :The incoherent case

For pt.I see ibid. vol.3, p.195 (1987). The authors have shown that the resolution of a confocal scanning microscope can be improved by recording the full image at each scanning point and then inverting the data. These analyses were restricted to the case of coherent illumination. They investigate, along similar lines, the incoherent case, which applies to fluorescence microscopy. They investigate the one-dimensional and two-dimensional square-pupil problems and they prove, by means of numerical computations of the singular value spectrum and of the impulse response function, that for a signal-to-noise ratio of, say 10%, it is possible to obtain an improvement of approximately 60% in resolution with respect to the conventional incoherent light confocal microscope. This represents a working bandwidth of 3.5 times the Rayleigh limit.

A new inversion procedure for confocal scanning microscopy and other bandlimited signal processing problems

We find a simple analytic expression for the inverse of an infinite matrix related to the problem of data reduction in confocal scanning microscopy and other band-limited signal processing problems. Potential applications of this result to practical problems are outlined. The matrix arises from a sampling expansion approach to the integral equation.

Quantitative laboratory spectroscopy of atmospheric trace gases

info:eu-repo/semantics/published

Observation of C60 film formation on a highly oriented pyrolitic graphite substrate via scanning tunnelling microscopy

We have investigated the early stages in the adsorption process of C60 molecules on a highly oriented pyrolitic graphite (HOPG) substrate. C60 powder was thermally evaporated in UHV of 10−8 Pa conditions onto a freshly cleaved HOPG surface. We did not observe individual fullerenes on the substrate for the case of short deposition times and low evaporation rates. However, small islands of C60 molecules with an fcc structure could be observed when the deposition rate was about 0.2 nm/min and the total thickness was above 1 nm. The islands did not grow in the vicinity of the HOPG steps. The typical lateral dimensions of these islands were of the order of a few hundred square nanometers, having thickness of up to five monolayers. We modified the shapes and positions of these islands by the STM tip, using a small (less than 1 V) bias voltage.

Surface physics at the nano-scale via scanning probe microscopy and molecular dynamics simulations

Probe-based scanning microscopes, such as the STM and the AFM, are used to obtain the topographical and electronic structure maps of material surfaces, and to modify their morphologies on nanoscopic scales. They have generated new areas of research in condensed matter physics and materials science. We will review some examples from the fields of experimental nano-mechanics, nano-electronics and nano-magnetism. These now form the basis of the emerging field of Nano-technology. A parallel development has been brought about in the field of Computational Nano-science, using quantum-mechanical techniques and computer-based numerical modelling, such as the Molecular Dynamics (MD) simulation method. We will report on the simulation of nucleation and growth of nano-phase films on supporting substrates. Furthermore, a theoretical modelling of the formation of STM images of metallic clusters on metallic substrates will also be discussed within the non-equilibrium Keldysh Green function method to study the effects of coherent tunnelling through different atomic orbitals in a tip-sample geometry.

The use of fluorescence microscopy to define polymer localisation to the late endocytic compartments in cells that are targets for drug delivery

Macromolecular therapeutics and nano-sized drug delivery systems often require localisation to specific intracellular compartments. In particular, efficient endosomal escape, retrograde trafficking, or late endocytic/lysosomal activation are often prerequisites for pharmacological activity. The aim of this study was to define a fluorescence microscopy technique able to confirm the localisation of water-soluble polymeric carriers to late endocytic intracellular compartments. Three polymeric carriers of different molecular weight and character were studied: dextrin (Mw~50,000 g/mol), a N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer (Mw approximately 35,000 g/mol) and polyethylene glycol (PEG) (Mw 5000 g/mol). They were labelled with Oregon Green (OG) (0.3-3 wt.%; <3% free OG in respect of total). A panel of relevant target cells were used: THP-1, ARPE-19, and MCF-7 cells, and primary bovine chondrocytes (currently being used to evaluate novel polymer therapeutics) as well as NRK and Vero cells as reference controls. Specific intracellular compartments were marked using either endocytosed physiological standards, Marine Blue (MB) or Texas-red (TxR)-Wheat germ agglutinin (WGA), TxR-Bovine Serum Albumin (BSA), TxR-dextran, ricin holotoxin, C6-7-nitro-2,1,3-benzoxadiazol-4-yl (NBD)-labelled ceramide and TxR-shiga toxin B chain, or post-fixation immuno-staining for early endosomal antigen 1 (EEA1), lysosomal-associated membrane proteins (LAMP-1, Lgp-120 or CD63) or the Golgi marker GM130. Co-localisation with polymer-OG conjugates confirmed transfer to discreet, late endocytic (including lysosomal) compartments in all cells types. The technique described here is a particularly powerful tool as it circumvents fixation artefacts ensuring the retention of water-soluble polymers within the vesicles they occupy.