A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as “histogram binning” inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. ^ Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. ^ The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. ^ These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. ^ In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation. ^

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as "histogram binning" inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation.

‘The past was never simply there to begin with and the future is not simply what will unfold’ : a posthumanist performative approach to qualitative longitudinal research

Peer reviewed

‘The past was never simply there to begin with and the future is not simply what will unfold’ : a posthumanist performative approach to qualitative longitudinal research

Peer reviewed

‘The past was never simply there to begin with and the future is not simply what will unfold’ : a posthumanist performative approach to qualitative longitudinal research

Peer reviewed

The Life of an Author: Samuel Egerton Brydges and the Copyright Act 1814

The history of literary copyright in nineteenth century Britain is dominated - understandably perhaps - by a preoccupation with the passing and impact of the Copyright Amendment Act 1842, so ably lobbied for by Sir Thomas Noon Talfourd. This article, however, draws attention away from the 1842 Act towards the Copyright Act 1814, the first legislative provision within British copyright law to introduce a lifetime term of protection for the author. Why and on what basis did the legislature do so?
In bringing a renewed attention to this often overlooked legislative measure, we consider the context and logic that underpinned to grant of a copyright term that was tethered to the life of the author. In doing so, we might also find a useful prism through which to look afresh at current copyright debates concerning the appropriate nature and scope of copyright protection in the 21st century.

Professional exposure to fungal pathogens: an update to exposure conditions and exposure measurement

In many occupational settings an exposure to fungi occurs. Fungal exposure may occur for instance in the form of dermatocytes, yeasts or mold. Associated to the fungi themselves an exposure to cell wall components like ß(1 ? 3)-D-glucans, to mycotoxins or to microbial volatile compounds can occur. Health hazards may differ across species because fungi may produce different allergens and mycotoxins, and some species can infect humans. Occupational settings are often characterized by special exposure conditions with respect to duration, frequency and especially to the level of exposure resulting at least sometimes to high or very high fungal exposure. Because of these special conditions occupational settings are suitable for epidemiologic studies. However, the knowledge about occupational exposure to fungi and associated compounds like mycotoxins is still fragmentary and not well disseminated. An indication for a high fungal exposure is for instance the handling of dry natural products like grain, hay or herbal plants with a high specific surface and the tendency to release dust during handling. The fungal components often form the determinative part of such dusts and might be a vehicle to respiratory airways. The authors will present results of exposure measurements of occupational settings and exposure conditions which are only rarely investigated.

An Approach to Manage Reconfigurations and Reduce Area Cost in Hard Real-Time Reconfigurable Systems

This article presents a methodology to build real-time reconfigurable systems that ensure that all the temporal constraints of a set of applications are met, while optimizing the utilization of the available reconfigurable resources. Starting from a static platform that meets all the real-time deadlines, our approach takes advantage of run-time reconfiguration in order to reduce the area needed while guaranteeing that all the deadlines are still met. This goal is achieved by identifying which tasks must be always ready for execution in order to meet the deadlines, and by means of a methodology that also allows reducing the area requirements.

Vaspin association with insulin resistance is related to physical activity and body fat in Brazilian adolescents: a cross-sectional study

Background: Vaspin is a newly-identified adipocytokine associated with insulin resistance (IR). Objective: The aim of this study was to investigate the correlation between plasma vaspin concentrations and IR and determine whether this association is affected by body composition, physical activity and pubertal stage in adolescents. Methods: Were studied 484 Brazilian adolescents aged 10-14 years whose anthropometric, clinical, biochemical, and lifestyle measurements were analized. We evaluated the correlation between vaspin and risk factors for IR in adolescents with normal and high body fat percentage (%BF) and did a logistic regression to calculate the odds ratio for IR according to vaspin quartiles sex specific for the sample. Results: Vaspin was positively correlated with IR in adolescents with high %BF (r = 0.23, p = 0.003). The logistic regression analysis adjusted for sex, age, BMI, and pubertal stage showed that adolescents in the 2nd (OR = 0.43, 95% CI = 0.23-0.80, p = 0.008) and 3rd (OR = 0.46, 95% CI = 0.25-0.85, p = 0.014) quartile of vaspin concentration had a lower risk for IR. When the model was adjusted for %BF and physical activity, the association remained statically significant only for adolescents in the 2nd quartile. Conclusion: Vaspin was correlated positively with risk factors associated with insulin metabolism in adolescents with high %BF. Vaspin was associated with a reduced risk of IR independently of BMI and pubertal stage and the association was influenced by body fat and physical activity in these adolescents.

Conversation Circles as a Teaching Strategy: An Experience to Reflect on and Implement in Higher Education

The experience approached in this paper aims at reflecting, reasoning, planning and implementing the “Conversation Circles” as a teaching strategy in the PF-4237 course “Theory of Education: Multiculturalism and Education” of the Latin American Doctoral Program in Education, University of Costa Rica. This training experience, based on the communicative action theory, intended to integrate the assistance of the teacher, the confrontation to otherness and the building of knowledge, skills and social attitudes in higher education.

Spatial based approach to fisheries management. An application to bottom trawling in the strait of Sicily

At the beginning of my thesis project, considering that some stocks are in overfishing status due to both high fishing effort and high level of juveniles in the catch, my main purpose was to understand how to contribute to improving the state of the fishery resources of the Mediterranean Sea. To mitigate the overfishing, the General Fisheries Commission for the Mediterranean (GFCM) adopted several Fishery Restricted Areas, which are geographically defined areas where some specific fishing activities are temporarily or permanently banned or restricted in order to reduce the exploitation patterns and conservation of specific stocks as well as of habitats and deep-sea ecosystems, including the Essential Fish Habitats (EFH) and the Vulnerable Marine Ecosystems (VME). Considering that GFCM established 3 Fisheries Restricted Areas (FRAs) in the Strait of Sicily (SoS) in 2016 aimed at protecting the nursery areas of the deep-water rose shrimp (DPS, Parapenaeus longirostris – Lucas, 1846) and the European hake (HKE, Merluccius merluccius – Linnaeus, 1758) to reduce the exploitation pattern of undersized species, in my thesis project I devoted myself to evaluate the effect of the FRAs on the status stock and the fishery performance using a spatial bio-economic model.

The ocular morphology of the southern hemisphere lamprey Geotria australis gray with special reference to optical specialisations and the characterisation and phylogeny of photoreceptor types

This paper describes the ocular morphology of young adults of the southern hemisphere lamprey Geotria australis, the sole representative of the Geotriidae, and makes comparisons with those of holarctic lampreys (Petromyzontidae). As previously reported for the holarctic lamprey Ichthyomyzon unicuspis [Collin and Fritzsch, 1993], the lens of G. australis is non-spherical and possesses a cone-shaped posterior that may be capable of mediating variable focus. The avascular retina of G. australis is well differentiated, containing three retinal ganglion cell populations, three layers of horizontal cells and three photoreceptor types, in contrast to petromyzontids that contain only two photoreceptor types (short and long), G. australis possesses one rod-like (R1) and two cone-like (C1 and C2) photoreceptors. Although the rodlike receptor in G. australis may be homologous with the short receptors of holarctic lampreys, the two cone-like receptors have morphological characteristics that differ markedly from those of the long receptors of their holarctic counterparts. The features which distinguish the two cone-like receptors from those of the long receptor type in holarctic lampreys are the characteristics of the mitochondria and the presence of large amounts of two different types of stored secretory material in the endoplasmic reticulum of the myoid (refractile bodies). The endoplasmic reticulum of each receptor type has a different shape and staining profile and is polymorphic, each showing a continuum of distension. It is proposed that the presence of two cone-like photoreceptors with different characteristics would increase the spectral range of G. australis and thus be of value during the parasitic phase, when this lamprey lives in the surface marine waters. The irideal flap, present in G. australis but not petromyzontids, would assist in reducing intraocular flare during life in surface waters. The results of this study, which are discussed in the context of the proposed evolution of lampreys, emphasise that it is important to take into account the characteristics of the eyes of southern hemisphere lampreys when making generalizations about the eyes of lampreys as a whole.