Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.

Voltage programmable dual-band bandpass/bandstop filter response in a single micro-electro-mechanical device

This paper reports on a switchable multi-band filter response achieved within a single micro-electro-mechanical device. A prototype device fabricated in a SOI process demonstrates a voltage programmable and tunable, dual-band, band-pass/band-stop response. Both analytical and finite element models are introduced in this paper to elucidate the operating principle of the filter and to guide filter design. Voltage programmability of the filter characteristic is demonstrated with the ability to independently tune the centre frequency and bandwidth for each band. A representative measurement shows that the minimum 3 dB-bandwidth (BW) is 155 Hz, 140Hz, and 20 dB-BW is 216 Hz, 203Hz for the upper-band and lower-band center frequencies located at 131.5 kHz and 130.7 kHz, respectively. © 2011 IEEE.

A self-regulating valve for single-phase liquid cooling of microelectronics

This paper reports on the design, optimization and testing of a self-regulating valve for single-phase liquid cooling of microelectronics. Its purpose is to maintain the integrated circuit (IC) at constant temperature and to reduce power consumption by diminishing flow generated by the pump as a function of the cooling requirements. It uses a thermopneumatic actuation principle that combines the advantages of zero power consumption and small size in combination with a high flow rate and low manufacturing costs. The valve actuation is provided by the thermal expansion of a liquid (actuation fluid) which, at the same time, actuates the valve and provides feed-back sensing. A maximum flow rate of 38 kg h-1 passes through the valve for a heat load up to 500 W. The valve is able to reduce the pumping power by up to 60% and it has the capability to maintain the IC at a more uniform temperature. © 2011 IOP Publishing Ltd.

Strong resonant intersubband magnetopolaron effect in heavily modulation-doped GaAs/AlGaAs single quantum wells at high magnetic fields

Electron cyclotron resonance (CR) has been studied in magnetic fields up to 32 T in two heavily modulation-delta-doped GaAs/Al0.3Ga0.7As single quantum well samples. Little effect on electron CR is observed in either sample in the region of resonance with the GaAs LO phonons. However, above the LO-phonon frequency energy E-LO at B > 27 T, electron CR exhibits a strong avoided-level-crossing splitting for both samples at energies close to E-LO + (E-2 - E-1), where E-2, and E-1 are the energies of the bottoms of the second and the first subbands, respectively. The energy separation between the two branches is large, reaching a minimum of about 40 cm(-1) around 30.5 T for both samples. This splitting is due to a three-level resonance between the second LI, of the first electron subband and the lowest LL of the second subband plus an LO phonon. The large splitting in the presence: of high electron densities is due to the absence of occupation (Pauli-principle) effects in the final states and weak screening for this three-level process. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

Principle of the moving-mirror-pair interferometer and the tilt tolerance of the double moving mirror

A novel type of interferometer, the moving-mirror-pair interferometer, is presented, and its principle and properties are studied. The new interferometer is built with three flat mirrors, which include two flat moving mirrors fixed as a single moving part by a rigid structure and one flat fixed mirror. The optical path difference (OPD) is obtained by the straight reciprocating motion of the double moving mirror, and the OPD value is four times the physical shift value of the double moving mirror. The tilt tolerance of the double moving mirror of the novel interferometer is systematically analyzed by means of modulation depth and phase error. Where the square aperture is concerned, the formulas of the tilt tolerance were derived. Due to the novel interferometer's large OPD value and low cost, it is very applicable to the high-spectral-resolution Fourier-transform spectrometers for any wavenumber region from the far infrared to the ultraviolet. (C) 2008 Optical Society of America.

2-DELTA-FUNCTION GENERALIZED PLASMA POLE MODEL FOR 1ST PRINCIPLE CALCULATIONS OF QUASI-PARTICLE ENERGIES IN MANY-ELECTRON SYSTEMS

To evaluate the dynamical effects of the screened interaction in the calculations of quasiparticle energies in many-electron systems a two-delta-function generalized plasma pole model (GPP) is introduced to simulate the dynamical dielectric function. The usual single delta-function GPP model has the drawback of over simplifications and for the crystals without the center of symmetry is inappropriate to describe the finite frequency behavior for dielectric function matrices. The discrete frequency summation method requires too much computation to achieve converged results since ab initio calculations of dielectric function matrices are to be carried out for many different frequencies. The two-delta GPP model is an optimization of the two approaches. We analyze the two-delta GPP model and propose a method to determine from the first principle calculations the amplitudes and effective frequencies of these delta-functions. Analytical solutions are found for the second order equations for the parameter matrices entering the model. This enables realistic applications of the method to the first principle quasiparticle calculations and makes the calculations truly adjustable parameter free.

Dying for 'Enduring Freedom': Accepting Responsibility for Civilian Casualties in the War against Terrorism

Wheeler, Nicholas, 'Dying for `Enduring Freedom': Accepting Responsibility for Civilian Casualties in the War against Terrorism', International Relations (2002) 16(2) pp.205-225 RAE2008

Single Canadian mothers of Jamaican heritage share experiences about their children's education

This thesis examines the experiences of four single Canadian mothers of Jamaican heritage with respect to their children’s education. Four themes suggested in the literature—beliefs, practices, barriers, and supports—guided the research. The interviews with the mothers largely confirmed previous research in the field. As such, all the mothers believed that it was a shared responsibility between parents and teachers in supporting children’s education. The mothers’ practices included primarily at-home support and to a lesser extent at-school support but did not include strict discipline. The barriers most salient for these mothers were lack of time and resources. To help overcome these barriers, the mothers relied on domestic kin networks. From these findings, the thesis provides implications for both research and practice.

A variational approach to the relaxation of single domain magnetic particles based on Brown's model

Brown's model for the relaxation of the magnetization of a single domain ferromagnetic particle is considered. This model results in the Fokker-Planck equation of the process. The solution of this equation in the cases of most interest is non- trivial. The probability density of orientations of the magnetization in the Fokker-Planck equation can be expanded in terms of an infinite set of eigenfunctions and their corresponding eigenvalues where these obey a Sturm-Liouville type equation. A variational principle is applied to the solution of this equation in the case of an axially symmetric potential. The first (non-zero) eigenvalue, corresponding to the largest time constant, is considered. From this we obtain two new results. Firstly, an approximate minimising trial function is obtained which allows calculation of a rigorous upper bound. Secondly, a new upper bound formula is derived based on the Euler-Lagrange condition. This leads to very accurate calculation of the eigenvalue but also, interestingly, from this, use of the simplest trial function yields an equivalent result to the correlation time of Coffey et at. and the integral relaxation time of Garanin. (C) 2004 Elsevier B.V. All rights reserved.

Atom cooling using the dipole force of a single retroreflected laser beam

We present a mechanism for cooling atoms by a laser beam reflected from a single mirror. The cooling relies on the dipole force and thus in principle applies to arbitrary refractive particles including atoms, molecules, or dielectric spheres. Friction and equilibrium temperatures are derived by an analytic perturbative approach. Finally, semiclassical Monte-Carlo simulations are performed to validate the analytic results.

Class Responsibility Assignment (CRA) for Use Case Specification to Sequence Diagrams (UC2SD)

Identifying responsibility for classes in object oriented software design phase is a crucial task. This paper proposes an approach for producing high quality and robust behavioural diagrams (e.g. Sequence Diagrams) through Class Responsibility Assignment (CRA). GRASP or General Responsibility Assignment Software Pattern (or Principle) was used to direct the CRA process when deriving behavioural diagrams. A set of tools to support CRA was developed to provide designers and developers with a cognitive toolkit that can be used when analysing and designing object-oriented software. The tool developed is called Use Case Specification to Sequence Diagrams (UC2SD). UC2SD uses a new approach for developing Unified Modelling Language (UML) software designs from Natural Language, making use of a meta-domain oriented ontology, well established software design principles and established Natural Language Processing (NLP) tools. UC2SD generates a well-formed UML sequence diagrams as output.

NAV Portugal's performance within the single European Sky Initiative

NAV Portugal is the Air Navigation Service Provider in Portugal, providing air traffic control services in the airspace under the country’s responsibility. Recently, the company has been included in an initiative launched by the European Commission, called the Single European Sky. This aims for a unification of the European airspace, improving it in four main pillars: safety, capacity, environment, and cost-efficiency. To each of them, Key Performance Indicators need to be computed and monitored, all having pre-defined targets. The presented work project will be analyzing how NAV Portugal is doing in the pillar of capacity, proving suggestions if needed.

Climate Change, Neutrality and the Harm Principle

This paper aims at evaluating the compatibility of coercive climate policies with liberal neutrality. More precisely, it focuses on the doctrine of state neutrality as associated with the "harm principle". It argues that given the difficulty of attributing causal responsibilities for climate harms to individuals, the harm principle doesn't work in this case, at least if one endorses a liberal atomistic ontology. Furthermore, the definition of what constitutes climate harms implies making moral assumptions, which makes it impossible to justify climate policies in a neutral way. Finally, the paper shows another consequence of applying neutrality to the case of climate change, that is the risk of a shift from political forms of decision-making to technocracy. Focusing too much on liberty of choice may (paradoxically) be to the detriment of political freedom. The paper concludes that climate change is an intrinsically moral issue and that it should be the occasion of a political debate about our current values and lifestyles. It should not be reduced to a mere question of carbon metric.

Corporate Social Responsibility in the Oil and Gas Industry: Environmental Management Systems as a Source of Sustainable Development

The environmental aspect of corporate social responsibility (CSR) expressed through the process of the EMS implementation in the oil and gas companies is identified as the main subject of this research. In the theoretical part, the basic attention is paid to justification of a link between CSR and environmental management. The achievement of sustainable competitive advantage as a result of environmental capital growth and inclusion of the socially responsible activities in the corporate strategy is another issue that is of special significance here. Besides, two basic forms of environmental management systems (environmental decision support systems and environmental information management systems) are explored and their role in effective stakeholder interaction is tackled. The most crucial benefits of EMS are also analyzed to underline its importance as a source of sustainable development. Further research is based on the survey of 51 sampled oil and gas companies (both publicly owned and state owned ones) originated from different countries all over the world and providing reports on sustainability issues in the open access. To analyze their approach to sustainable development, a specifically designed evaluation matrix with 37 indicators developed in accordance with the General Reporting Initiative (GRI) guidelines for non-financial reporting was prepared. Additionally, the quality of environmental information disclosure was measured on the basis of a quality – quantity matrix. According to results of research, oil and gas companies prefer implementing reactive measures to the costly and knowledge-intensive proactive techniques for elimination of the negative environmental impacts. Besides, it was identified that the environmental performance disclosure is mostly rather limited, so that the quality of non-financial reporting can be judged as quite insufficient. In spite of the fact that most of the oil and gas companies in the sample claim the EMS to be embedded currently in their structure, they often do not provide any details for the process of their implementation. As a potential for the further development of EMS, author mentions possible integration of their different forms in a single entity, extension of existing structure on the basis of consolidation of the structural and strategic precautions as well as development of a unified certification standard instead of several ones that exist today in order to enhance control on the EMS implementation.

"Welcome to my life" : the experiences of single mothers who are the recipients of multiple state provided benefits

Abstract This research takes the lens of social reproduction as a starting point for an examination of the effects of recent social welfare reforms on the lives o.fsingle mothers. As the cumulative effects o.f diminishing state provided benefits take hold, tensions are heightened as single mothers internalize the insecurity of earning an income in 11 capitalist labour market, while trying to carry out all that is involved in social reproduction with inadequate means of survival. Through interviewing single mothers who are the recipients of mUltiple state provided benefits (social assistance, student loans, subsidized housing and subsidized childcare), this thesis illuminates the cOl1linued regulation of women in an effort to assure that social reproduction is occurring at the lowest cost possible. State provided benefits are set lip in such a way that it is near impossible for single mothers to make ends meet without entering the labour force or entering into co-residential relationships. This push towards the labour force and/or marriage via punitive welfare policies illuminates the devaluation of the labour that is done at home. Through interviewing 5 single mothers, I will demonstrate the extensive labour that goes into maintaining their households. In addition .J case managers are interviewed. The employees of social assistance, subsidized hOllsing, subsidized childcare and student loans, have much agency in deeming who is worthy of receiving benefits. The employees of these agencies have the ability to make these women's lives easier or more complicated by how the workers interpret the policy regulations. Social policies are of paramount importance in the quest for women's equality and thus have consequences for how women's daily lives are organized. The rules and regulations that govern the individual policies are complex and bureaucratic and have implications for the ways in which women must organize their lives in order to survive. The shifts in social policy have been guided by neo-liberal assumptions with a focus on individual responsibility and a market-modeled welfare state. The caring work that is involved in raising children to be productive in a capitalist society is ignored or devalued in current policies. The emphasis in each polic.:v is on getting women who receive benefits into the paid work force, with little facilitation or investment into the caring work these women do on a daily basis that in turn supports capitalism. Policies, such as social assistance, subsidized housing, subsidized childcare and student loans, are set up in such a way that ignores the reality of women's day-to-day lives and devalues the necessary work done at home. It takes an abundance of labour and strategizing for women to seek out necessary means of survival, labour that is amplified when a woman is dealing with mUltiple slate provided benefits.