Relating thermodynamics to information theory : the equality of free energy and mutual information

In this thesis we uncover a new relation which links thermodynamics and information theory. We consider time as a channel and the detailed state of a physical system as a message. As the system evolves with time, ever present noise insures that the "message" is corrupted. Thermodynamic free energy measures the approach of the system toward equilibrium. Information theoretical mutual information measures the loss of memory of initial state. We regard the free energy and the mutual information as operators which map probability distributions over state space to real numbers. In the limit of long times, we show how the free energy operator and the mutual information operator asymptotically attain a very simple relationship to one another. This relationship is founded on the common appearance of entropy in the two operators and on an identity between internal energy and conditional entropy. The use of conditional entropy is what distinguishes our approach from previous efforts to relate thermodynamics and information theory.

Wide Field-of-view Microscopes and Endoscopes for Time-lapse Imaging and High-throughput Screening

Wide field-of-view (FOV) microscopy is of high importance to biological research and clinical diagnosis where a high-throughput screening of samples is needed. This thesis presents the development of several novel wide FOV imaging technologies and demonstrates their capabilities in longitudinal imaging of living organisms, on the scale of viral plaques to live cells and tissues.

The ePetri Dish is a wide FOV on-chip bright-field microscope. Here we applied an ePetri platform for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm at 30 min intervals. A density-based clustering algorithm is used to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. We also demonstrate the capabilities of the ePetri in viral titer count and dynamically monitoring plaque formation, growth, and the influence of antiviral drugs.

We developed another wide FOV imaging technique, the Talbot microscope, for the fluorescence imaging of live cells. The Talbot microscope takes advantage of the Talbot effect and can generate a focal spot array to scan the fluorescence samples directly on-chip. It has a resolution of 1.2 μm and a FOV of ~13 mm². We further upgraded the Talbot microscope for the long-term time-lapse fluorescence imaging of live cell cultures, and analyzed the cells’ dynamic response to an anticancer drug.

We present two wide FOV endoscopes for tissue imaging, named the AnCam and the PanCam. The AnCam is based on the contact image sensor (CIS) technology, and can scan the whole anal canal within 10 seconds with a resolution of 89 μm, a maximum FOV of 100 mm × 120 mm, and a depth-of-field (DOF) of 0.65 mm. We also demonstrate the performance of the AnCam in whole anal canal imaging in both animal models and real patients. In addition to this, the PanCam is based on a smartphone platform integrated with a panoramic annular lens (PAL), and can capture a FOV of 18 mm × 120 mm in a single shot with a resolution of 100─140 μm. In this work we demonstrate the PanCam’s performance in imaging a stained tissue sample.

Gender equality in life insurance

[EN]This project is going to study the implications of the gender of an individual in the rate-setting process of life insurance. In order to do so there is a review of the continuous changes that have taken place in the national and European legislation following the enactment of the Directive 2004/113/EC, as well as its consequences from the prohibition to differentiate the premiums and benefits on the grounds of gender. In this area, the evolution of the Spanish insurance sector and the influence of the new legislation are examined. Furthermore, there is an analysis of the differences between men and women, which to some extent have a direct impact in the management and development of the life insurance companies. Finally, methods to calculate the premium and the benefits are proposed with the purpose of preventing the restrictions imposed by the Directive 2004/113/EC. In order to check the repercussions of the use of unisex tables a comparison is made between the premiums obtained for a whole life insurance by allocating the same weighing to the actuarial male and female mortality tables and those that would result if the distinction by gender were allowed.

Transforming aquatic agricultural systems towards gender equality: a five country review

Aquatic agricultural systems (AAS) are systems in which the annual production dynamics of freshwater and/or coastal ecosystems contribute significantly to total household income. Improving the livelihood security and wellbeing of the estimated 250 million poor people dependent on AAS in Bangladesh, Cambodia, the Philippines, the Solomon Islands and Zambia is the goal of the Worldfish Center-led Consortium Research Program (CRP), “Harnessing the development potential of aquatic agricultural systems for development.” One component expected to contribute to sustainably achieving this goal is enhancing the gender and wider social equity of the social, economic and political systems within which the AAS function. The CRP’s focus on social equity, and particularly gender equity, responds to the limited progress to date in enhancing the inclusiveness of development outcomes through interventions that offer improved availability of resources and technologies without addressing the wider social constraints that marginalized populations face in making use of them. The CRP aims to both offer improved availability and address the wider social constraints in order to determine whether a multi-level approach that engages with individuals, households and communities, as well as the wider social, economic and political contexts in which they function, is more successful in extending development’s benefits to women and other excluded groups. Designing the research in development initiatives to test this hypothesis requires a solid understanding of each CRP country’s social, cultural and economic contexts and of the variations across them. This paper provides an initial input into developing this knowledge, based on a review of literature on agriculture, aquaculture and gender relations within the five focal countries. Before delving into the findings of the literature review, the paper first justifies the expectation that successfully achieving lasting wellbeing improvements for poor women and men dependent on AAS rests in part on advances in gender equity, and in light of this justification, presents the AAS CRP’s conceptual framew

PCR-SSCP and Isoelectric Focusing as Screening Methods for Identification of (Sub-) Tropical Fish Species

To ensure the authentication of fishery products lacking biological characters, rapid species identification methods are required. Two DNA- and protein-based methods, PCR-SSCP (polymerase chain reaction - single strand conformation polymorphism) of a 464 bp segment of the cytochrome b – gene and isoelectric focusing (IEF) of water-soluble proteins from fish fillets, were applied to identify fillets of (sub-) tropical fish species available on the European market. Among the samples analysed were two taxonomically identified species from the family Sciaenidae and one from Sphyraenidae. By comparison of DNA- and protein patterns of different samples, information about intra-species variability of patterns, and homogeneity of batches (e.g. fillet blocks or bags) can be obtained. PCR-SSCP and IEF may be useful for pre-checking of a large number of samples by food control laboratories. Zusammenfassung Zur Sicherstellung der Authentizität von Fischerei-Erzeugnissen ohne biologische Merkmale sind schnelle Verfahren zur Speziesidentifizierung hilfreich. Zwei Methoden der DNA- bzw. Protein-Analyse wurden eingesetzt, um Filets (sub-) tropischer Fischarten, die auf dem europäischen Markt angeboten werden, zu identifizieren. Bei diesen Methoden handelt es sich um die PCR-SSCP (Polymerase-Kettenreaktion – Einzelstrang-Konformationspolymorphismus) – Analyse der PCR-Produkte und die IEF (isoelektrische Fokussierung) der wasserlöslichen Fischmuskelproteine. Unter den untersuchten Proben waren zwei taxonomisch bestimmte Arten aus der Familie Sciaenidae und eine Spezies aus der Familie Sphyraenidae. Durch Vergleich der DNA- bzw. Proteinmuster lassen sich Informationen über die intra-spezifische Variabilität solcher Muster und die Einheitlichkeit von Partien (beispielsweise Filetblöcke oder Filetbeutel) gewinnen. PCR-SSCP und IEF können in Laboratorien der Lebensmittelüberwachung als Vortest gerade bei hohen Probenzahlen sinnvoll eingesetzt werden.

Phosphate treatment of frozen prawns. Pt. 1. Screening of various phosphates for prevention of drip loss

Various phosphates and their mixtures were screened for their efficiency of preventing drip loss in frozen prawns. The effectiveness of the phosphates decreased in the following order: Sodium tripolyphosphate — Sodium pyrophosphate — Sodium hexametaphosphate Sodium metaphosphate — Sodium dihydrogen phosphate; the last two being ineffective. Even though thaw drip loss was reduced by the above treatments the organoleptic quality of the thawed as well as cooked products was unsatisfactory, discoloration being the major defect. A solution of a mixture of 12% sodium tripolyphosphate and 8.6% sodium dihydrogen phosphate or 2% citric acid in water when used as dip prevented thaw drip loss, improved cooked yield and organoleptic quality without adversely affecting the biochemical characteristics. Commercial scale trials showed that the results are highly reproducible.

The long road to freedom: the end of apartheid has signalled a new beginning for women in South Africa’s fisheries but real equality is still a far-off dream

Women in fishing communities are increasingly moving from traditional, community based occupations to seeking employment in the labour market. While this is an opportunity for women, their employment is also largely in the male dominated fishing industry, where job segregation into ‘less skilled and low paid’ jobs for women define employment opportunities. However, engagement as members in local non-government networks help women to challenge these stereotypes. In South Africa, for instance, the recent legislation promoting opportunity for women in male dominated sectors of employment is an opportunity for women to earn wages equal to those of men.

Screening of healthcare workers for tuberculosis: development and validation of a new health economic model to inform practice

Methods for determining cost-effectiveness of different treatments are well established, unlike appraisal of non-drug interventions, including novel diagnostics and biomarkers.

Nonequilibrium dynamics of photoexcited electrons in graphene: Collinear scattering, Auger processes, and the impact of screening

We present a combined analytical and numerical study of the early stages (sub-100-fs) of the nonequilibrium dynamics of photoexcited electrons in graphene. We employ the semiclassical Boltzmann equation with a collision integral that includes contributions from electron-electron (e-e) and electron-optical phonon interactions. Taking advantage of circular symmetry and employing the massless Dirac fermion (MDF) Hamiltonian, we are able to perform an essentially analytical study of the e-e contribution to the collision integral. This allows us to take particular care of subtle collinear scattering processes - processes in which incoming and outgoing momenta of the scattering particles lie on the same line - including carrier multiplication (CM) and Auger recombination (AR). These processes have a vanishing phase space for two-dimensional MDF bare bands. However, we argue that electron-lifetime effects, seen in experiments based on angle-resolved photoemission spectroscopy, provide a natural pathway to regularize this pathology, yielding a finite contribution due to CM and AR to the Coulomb collision integral. Finally, we discuss in detail the role of physics beyond the Fermi golden rule by including screening in the matrix element of the Coulomb interaction at the level of the random phase approximation (RPA), focusing in particular on the consequences of various approximations including static RPA screening, which maximizes the impact of CM and AR processes, and dynamical RPA screening, which completely suppresses them. © 2013 American Physical Society.

Identification of a WSSV neutralizing scFv antibody by phage display technology and in vitro screening

White spot syndrome virus (WSSV) is one of the most significant viral pathogens causing high mortality and economic damage in shrimp aquaculture. Although intensive efforts were undertaken to detect and characterize WSSV infection in shrimp during the last decade, we still lack methods either to prevent or cure white spot disease. Most of the studies on neutralizing antibodies from sera have been performed using in vivo assays. For the first time, we report use of an in vitro screening method to obtain a neutralizing scFv antibody against WSSV from a previously constructed anti-WSSV single chain fragment variable region (scFv) antibody phage display library. From clones that were positive for WSSV by ELISA, 1 neutralizing scFv antibody was identified using an in vitro screening method based on shrimp primary lymphoid cell cultures. The availability of a neutralizing antibody against the virus should accelerate identification of infection-related genes and the host cell receptor, and may also enable new approaches to the prevention and cure of white spot disease.

A screening study on persistent bioaccumulation toxins (PBT) in fuel combustion soot

Persistent bioaccumulative toxins (PBTs) are organic substances that are persistent, bioaccumulative and can cause severe toxic effects (e.g. potential oncogens, mutagenic, endocrine disrupters) to human health or environment which are the ones that need special attention. PBT chemicals could be released to the environment from several types of sources and are ubiquitous in environment. However, fast and efficiency monitoring and assessment methods to investigate PBTs in environment are still lacking. In this study, a cleaning-up procedure of analyzing PBTs in fuels combustion soot was developed and its performance was assessed through comparing the chromatograms of crude extracts with their cleaned extracts after the cleaning-up procedure. The results showed that polycyclic aromatic compounds (PACs) were the main components in fuel combustion soot and the clean-up procedure developed in this paper can be well used as the method of analyzing PBTs in fuels combustion soot.