Epidemiology and outcome of fungemia in a cancer Cohort of the Infectious Diseases Group (IDG) of the European Organization for Research and Treatment of Cancer (EORTC 65031).

BACKGROUND: Anti-cancer treatment and the cancer population have evolved since the last European Organisation for Research and Treatment of Cancer (EORTC) fungemia survey, and there are few recent large epidemiological studies. METHODS: This was a prospective cohort study including 145 030 admissions of patients with cancer from 13 EORTC centers. Incidence, clinical characteristics, and outcome of fungemia were analyzed. RESULTS: Fungemia occurred in 333 (0.23%; 95% confidence interval [CI], .21-.26) patients, ranging from 0.15% in patients with solid tumors to 1.55% in hematopoietic stem cell transplantation recipients. In 297 evaluable patients age ranged from 17 to 88 years (median 56 years), 144 (48%) patients were female, 165 (56%) had solid tumors, and 140 (47%) had hematological malignancies. Fungemia including polymicrobial infection was due to: Candida spp. in 267 (90%), C. albicans in 128 (48%), and other Candida spp. in 145 (54%) patients. Favorable overall response was achieved in 113 (46.5%) patients by week 2. After 4 weeks, the survival rate was 64% (95% CI, 59%-70%) and was not significantly different between Candida spp. Multivariable logistic regression identified baseline septic shock (odds ratio [OR] 3.04, 95% CI, 1.22-7.58) and tachypnoea as poor prognostic factors (OR 2.95, 95% CI, 1.66-5.24), while antifungal prophylaxis prior to fungemia (OR 0.20, 95% CI, .06-.62) and remission of underlying cancer (OR, 0.18; 95% CI, .06-.50) were protective. CONCLUSIONS: Fungemia, mostly due to Candida spp., was rare in cancer patients from EORTC centers but was associated with substantial mortality. Antifungal prophylaxis and remission of cancer predicted better survival.

Quantum chaos in SU(3) models with trapped ions

A scheme to generate long-range spin-spin interactions between three-level ions in a chain is presented, providing a feasible experimental route to the rich physics of well-known SU(3) models. In particular, we demonstrate different signatures of quantum chaos which can be controlled and observed in experiments with trapped ions.

Quantum Hall Phases of two-component bosons

The recent production of synthetic magnetic fields acting on electroneutral particles, such as atoms or photons, has boosted interest in the quantum Hall physics of bosons. Adding pseudospin 1/2 to the bosons greatly enriches the scenario, as it allows them to form an interacting integer quantum Hall (IQH) phase with no fermionic counterpart. Here we show that, for a small two-component Bose gas on a disk, the complete strongly correlated regime, extending from the integer phase at filling factor ν = 2 to the Halperin phase at filling factor ν = 2 / 3, is well described by composite fermionization of the bosons. Moreover we study the edge excitations of the IQH state, which, in agreement with expectations from topological field theory, are found to consist of forward-moving charge excitations and backward-moving spin excitations. Finally, we demonstrate how pair-correlation functions allow one to experimentally distinguish the IQH state from competing states, such as non-Abelian spin singlet (NASS) states.

Topological phases in small quantum Hall samples

Topological order has proven a useful concept to describe quantum phase transitions which are not captured by the Ginzburg-Landau type of symmetry-breaking order. However, lacking a local order parameter, topological order is hard to detect. One way to detect it is via direct observation of anyonic properties of excitations which are usually discussed in the thermodynamic limit, but so far has not been realized in macroscopic quantum Hall samples. Here we consider a system of few interacting bosons subjected to the lowest Landau level by a gauge potential, and theoretically investigate vortex excitations in order to identify topological properties of different ground states. Our investigation demonstrates that even in surprisingly small systems anyonic properties are able to characterize the topological order. In addition, focusing on a system in the Laughlin state, we study the robustness of its anyonic behavior in the presence of tunable finite-range interactions acting as a perturbation. A clear signal of a transition to a different state is reflected by the system's anyonic properties.

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Unidirectional quantum walks: Evolution and exit times

In this paper we focus our attention on a particle that follows a unidirectional quantum walk, an alternative version of the currently widespread discrete-time quantum walk on a line. Here the walker at each time step can either remain in place or move in a fixed direction, e.g., rightward or upward. While both formulations are essentially equivalent, the present approach leads us to consider discrete Fourier transforms, which eventually results in obtaining explicit expressions for the wave functions in terms of finite sums and allows the use of efficient algorithms based on the fast Fourier transform. The wave functions here obtained govern the probability of finding the particle at any given location but determine as well the exit-time probability of the walker from a fixed interval, which is also analyzed.

The hpx genetic system for hypoxanthine assimilation as a nitrogen source in Klebsiella pneumoniae: gene organization and transcriptional regulation.

Growth experiments showed that adenine and hypoxanthine can be used as nitrogen sources by several strains of K. pneumoniae under aerobic conditions. The assimilation of all nitrogens from these purines indicates that the catabolic pathway is complete and proceeds past allantoin. Here we identify the genetic system responsible for the oxidation of hypoxanthine to allantoin in K. pneumoniae. The hpx cluster consists of seven genes, for which an organization in four transcriptional units, hpxDE, hpxR, hpxO and hpxPQT, is proposed. The proteins involved in the oxidation of hypoxanthine (HpxDE) or uric acid (HpxO) did not display any similarity to other reported enzymes known to catalyze these reactions, but instead are similar to oxygenases acting on aromatic compounds. Expression of the hpx system is activated by nitrogen limitation and by the presence of specific substrates, with hpxDE and hpxPQT controlled by both signals. Nitrogen control of hpxPQT transcription, which depends on 54, is mediated by the Ntr system. In contrast, neither NtrC nor NAC is involved in the nitrogen control of hpxDE, which is dependent on 70 for transcription. Activation of these operons by the specific substrates is also mediated by different effectors and regulatory proteins. Induction of hpxPQT requires uric acid formation, whereas expression of hpxDE is induced by the presence of hypoxanthine through the regulatory protein HpxR. This LysR-type regulator binds to a TCTGC-N4-GCAAA site in the intergenic hpxD-hpxR region. When bound to this site for hpxDE activation, HpxR negatively controls its own transcription.

Modeling and manufacturability assessment of bistable quantum-dot cells

We have investigated the behavior of bistable cells made up of four quantum dots and occupied by two electrons, in the presence of realistic confinement potentials produced by depletion gates on top of a GaAs/AlGaAs heterostructure. Such a cell represents the basic building block for logic architectures based on the concept of quantum cellular automata (QCA) and of ground state computation, which have been proposed as an alternative to traditional transistor-based logic circuits. We have focused on the robustness of the operation of such cells with respect to asymmetries derived from fabrication tolerances. We have developed a two-dimensional model for the calculation of the electron density in a driven cell in response to the polarization state of a driver cell. Our method is based on the one-shot configuration-interaction technique, adapted from molecular chemistry. From the results of our simulations, we conclude that an implementation of QCA logic based on simple ¿hole arrays¿ is not feasible, because of the extreme sensitivity to fabrication tolerances. As an alternative, we propose cells defined by multiple gates, where geometrical asymmetries can be compensated for by adjusting the bias voltages. Even though not immediately applicable to the implementation of logic gates and not suitable for large scale integration, the proposed cell layout should allow an experimental demonstration of a chain of QCA cells.

Electronic properties of a quantum wire with arbitrary bending angle

The electron transmission and bound state properties of a quantum wire with a sharp bend at arbitrary angle are studied, extending results on the right angle sharp bend (the L¿shaped wire). These new results are compared to those of a similar structure, the circular bend wire. The possibility of using a bent wire to perform transistor action is also discussed.

Structural and optical properties of InAs/GaAs quantum structures

The goal of the thesis was to study fundamental structural and optical properties of InAs islands and In(Ga)As quantum rings. The research was carried out at the Department of Micro and Nanosciences of Helsinki University of Technology. A good surface quality can be essential for the potential applications in optoelectronic devices. For such device applications it is usually necessary to control size, density and arrangement of the islands. In order to study the dependence of the structural properties of the islands and the quantum rings on growth conditions, atomic force microscope was used. Obtained results reveal that the size and the density of the In(Ga)As quantum rings strongly depend on the growth temperature, the annealing time and the thickness of the partial capping layer. From obtained results it is possible to conclude that to get round shape islands and high density one has to use growth temperature of 500 ̊C. In the case of formation of In(Ga)As quantum rings the effect of mobility anisotropy is observed that so the shape of the rings is not symmetric. To exclude this effect it is preferable to use a higher annealing temperature of 570 ̊C. Optical properties were characterized by PL spectroscopy. PL emission was observed from buried InAs quantum dots and In(Ga)As quantum rings grown with different annealing time and temperature and covered with a various thickness of the partial capping layer.

Photoluminescence of GaAs/AlGaAs quantum wells

In this thesis is studied the influence of uniaxial deformation of GaAs/AlGaAs quantum well structures to photoluminescence. Uniaxial deformation was applied along [110] and polarization ratio of photoluminescence at T = 77 K and 300 K was measured. Also the physical origin of photoluminescence lines in spectrum was determined and the energy band splitting value between states of heavy and light holes was estimated. It was found that the dependencies of polarization ratio on uniaxial deformation for bulk GaAs and GaAs/AlGaAs are different. Two observed lines in photoluminescence spectrum are induced by free electron recombination to energy sublevels of valence band corresponding to heavy and light holes. Those sublevels are splited due to the combination of size quantization and external pressure. The quantum splitting energy value was estimated. Also was shown a method, which allows to determine the energy splitting value of sublevels at room temperature and at comparatively low uniaxial deformation, when the other method for determining of the splitting becomes impossible.

Implementing Agile Software Development Methods in a Small Organization

Currently there is a vogue for Agile Software Development methods and many software development organizations have already implemented or they are planning to implement agile methods. Objective of this thesis is to define how agile software development methods are implemented in a small organization. Agile methods covered in this thesis are Scrum and XP. From both methods the key practices are analysed and compared to waterfall method. This thesis also defines implementation strategy and actions how agile methods are implemented in a small organization. In practice organization must prepare well and all needed meters are defined before the implementation starts. In this work three different sample projects are introduced where agile methods were implemented. Experiences from these projects were encouraging although sample set of projects were too small to get trustworthy results.

Innovation – from individual intuition to collaborative innovation. The role of individual key actor in facilitation of innovation in large organization context

The objective of this research was to study the role of key individuals in facilitation of technology enabled bottom-up innovation in large organization context. The development of innovation was followed from the point of view of individual actor (key individual) in two cases, through three levels: individual, team and organization, by using knowledge creation and innovation models. This study provides theoretical synthesis and framework through which the study is driven. The results of the study indicate, that in bottom-up initiated innovations the role of key individuals is still crucial, but innovation today is collective effort and there acts several entrepreneurial key individuals: innovator, user champion and organizational sponsor, whose collaboration and developing interaction drives innovation further. The team work is functional and fluent, but it meets great problems in interaction with organization. The large organizations should develop its practices and ability to react on emerging bottom-up initiations, in order to embed innovation to organization and gain sustainable innovation. In addition, bottom-up initiated innovations are demonstrations of peoples knowing, tacit knowledge and therefore renewing of an organization.

Customer-Related Internal Communication in a Global Matrix Organization

The objective of the thesis was to explore the nature and characteristics of customer-related internal communication in a global industrial matrix organization during a specific customer relationship, and how it could be improved. The theoretical part of the study views the field of the concepts of intra-organizational information and knowledge sharing. The theoretical part also views the internal communications influences to customer relationships, its problematic, and the suggestions to improve internal communication in literature. The empirical part of the study was conducted with the Content Analysis and the Social Network Analysis as research methods. The data was collected by interviews and a questionnaire. Internal communication was observed first generally within the organization from the point of view of a certain business, and secondly, during a specific customer relationship at personal level and at departmental level. The results of the study describe the nature and characteristics of internal communication in the organization. The results give 13 suggestions for improving internal communication in the organization. Although the study has been done in one specific organization, it also offers insights for other organizations as well as managers to improve their internal communication.