Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules

Background
It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein networks are one particular network type of special importance, because proteins form the functional base units of every biological cell. On a mesoscopic level of protein networks, modules are of significant importance because these building blocks may be the next elementary functional level above individual proteins allowing to gain insight into fundamental organizational principles of biological cells.
Results
In this paper, we provide a comparative analysis of five popular and four novel module detection algorithms. We study these module prediction methods for simulated benchmark networks as well as 10 biological protein interaction networks (PINs). A particular focus of our analysis is placed on the biological meaning of the predicted modules by utilizing the Gene Ontology (GO) database as gold standard for the definition of biological processes. Furthermore, we investigate the robustness of the results by perturbing the PINs simulating in this way our incomplete knowledge of protein networks.
Conclusions
Overall, our study reveals that there is a large heterogeneity among the different module prediction algorithms if one zooms-in the biological level of biological processes in the form of GO terms and all methods are severely affected by a slight perturbation of the networks. However, we also find pathways that are enriched in multiple modules, which could provide important information about the hierarchical organization of the system

Quantitative evaluation of visual function 12 months after bilateral implantation of a diffractive trifocal IOL

PURPOSE: To quantitatively evaluate visual function 12 months after bilateral implantation of the Physiol FineVision® trifocal intraocular lens (IOL) and to compare these results with those obtained in the first postoperative month. METHODS: In this prospective case series, 20 eyes of 10 consecutive patients were included. Monocular and binocular, uncorrected and corrected visual acuities (distance, near, and intermediate) were measured. Metrovision® was used to test contrast sensitivity under static and dynamic conditions, both in photopic and low-mesopic settings. The same software was used for pupillometry and glare evaluation. Motion, achromatic, and chromatic contrast discrimination were tested using 2 innovative psychophysical tests. A complete ophthalmologic examination was performed preoperatively and at 1, 3, 6, and 12 months postoperatively. Psychophysical tests were performed 1 month after surgery and repeated 12 months postoperatively. RESULTS: Final distance uncorrected visual acuity (VA) was 0.00 ± 0.08 and distance corrected VA was 0.00 ± 0.05 logMAR. Distance corrected near VA was 0.00 ± 0.09 and distance corrected intermediate VA was 0.00 ± 0.06 logMAR. Glare testing, pupillometry, contrast sensitivity, motion, and chromatic and achromatic contrast discrimination did not differ significantly between the first and last visit (p>0.05) or when compared to an age-matched control group (p>0.05). CONCLUSIONS: The Physiol FineVision® trifocal IOL provided satisfactory full range of vision and quality of vision parameters 12 months after surgery. Visual acuity and psychophysical tests did not vary significantly between the first and last visit.

Anti-VEGF treatment of patients with diabetic macular edema : Studies of visual acuity, macular edema and patient-reported outcomes

The aim of this thesis was to describe and evaluate visual acuity, macular edema and patientreported outcomes (PRO) following anti-VEGF treatment of diabetic macular edema (DME) patients in a real-world setting. Using a longitudinal study design, a cohort of DME patients was followed from baseline to 1 year after treatment start. Data were collected from two eye clinics at two county hospitals. Social background characteristics, medical data and PRO were measured before treatment initiation, at four month and after 1 year. A total of 57 patients completed the study. Mean age was 69 years and the sample was equally distributed regarding sex. At baseline, the patients described their general health as low. One year after treatment initiation, 30 patients had improved visual acuity and 27 patients had no improvement in visual acuity. The patients whose visual acuity improved reported an improvement in several subscales in patient-reported outcome measures (PROM), which was in contrast to the group that experienced a decline in visual acuity, where there was no improvement in PROM. Outcomes from the study can be useful for developing and providing relevant information and support to patients undergoing this treatment.

Inlärningseffekten på Limits of Stability på Transtibialt Amputerade Protesbrukare

Syftet med studien är att undersöka om det finns någon inlärningseffekt på testet Limits of Stability (LoS) för transtibialt amputerade protesbrukare och en kontrollgrupp. Sju transtibialt amputerade protesbrukare och en kontrollgrupp bestående av sju friska vuxna män upprepade testet LoS  fem gånger under fyra testtillfällen. Två kraftplattor och 69 reflexmarkörer användes för att samla in data. Testpersonerna placerades med en fot på varje kraftplatta och blev instruerade att förflytta sin center of pressure genom att luta kroppen från anklarna mot åtta mål som visades på en skärm tillsammans med deras center of pressure. Ordningen på målen var slumpvist utvalda. Datan analyserades med Friedmans test, eftersom den inte var normalfördelad, för att se om det fanns någon skillnad i resultatet mellan upprepningarna av testet och resultatet mellan testtillfällena. Det fanns några signifikanta skillnader mellan upprepningarna och mellan testtillfällena som tyder på att det finns en inlärningseffekt efter första upprepningen och första testtillfället, men resultatet var inte tillräckligt entydigt för att kunna dra några konkreta slutsatser. Vidare studier rekommenderas.

Assessment of visual function in children with multiple disabilities: two case studies of children with cerebral palsy

Purpose: a) multiply handicapped children have a high incidence of disorders affecting the visual system; b) assessment and management of visual disorders in this group of children presents a complex challenge; c) this study describes the results of visual function assessment in two children with neurological disability over a one-year period.

A survey of intrusion detection system technologies

This paper provides an overview of IDS types and how they work as well as configuration considerations and issues that affect them. Advanced methods of increasing the performance of an IDS are explored such as specification based IDS for protecting Supervisory Control And Data Acquisition (SCADA) and Cloud networks. Also by providing a review of varied studies ranging from issues in configuration and specific problems to custom techniques and cutting edge studies a reference can be provided to others interested in learning about and developing IDS solutions. Intrusion Detection is an area of much required study to provide solutions to satisfy evolving services and networks and systems that support them. This paper aims to be a reference for IDS technologies other researchers and developers interested in the field of intrusion detection.

Indications for and limits of conservative surgery in breast cancer

Improvements in diagnostic techniques and, above all, breast cancer screening campaigns - essential for early diagnosis - have enabled the objectives of conservative surgery to be pursued: disease control, no or low incidence of recurrences and an excellent esthetic result. However, to reach these objectives, it is essential to ensure a careful evaluation of the medical history of every patient, a detailed clinical examination and the correct interpretation of imaging. Particular attention should be paid to all factors influencing the choice of treatment and/or possible local recurrence: age, site, tumor volume, genetic predisposition, pregnancy, previous radiotherapy, pathological features, and surgical margins. The decision to undertake conservative treatment thus requires a multidisciplinary approach involving pathologists, surgeons and oncological radiologists, as well, of course, as the patient herself.

Approximation limits of linear programs (beyond hierarchies)

We develop a framework for proving approximation limits of polynomial size linear programs (LPs) from lower bounds on the nonnegative ranks of suitably defined matrices. This framework yields unconditional impossibility results that are applicable to any LP as opposed to only programs generated by hierarchies. Using our framework, we prove that O(n^1/2-ε)-approximations for CLIQUE require LPs of size 2^nΩ(ε). This lower bound applies to LPs using a certain encoding of CLIQUE as a linear optimization problem. Moreover, we establish a similar result for approximations of semidefinite programs by LPs. Our main technical ingredient is a quantitative improvement of Razborov's [38] rectangle corruption lemma for the high error regime, which gives strong lower bounds on the nonnegative rank of shifts of the unique disjointness matrix.

Humankindness: Illness, Animality, and the Limits of the Human in the Victorian Novel

This project posits a link between representations of animals or animality and representations of illness in the Victorian novel, and examines the narrative uses and ideological consequences of such representations. Figurations of animality and illness in Victorian fiction have been examined extensively as distinct phenomena, but examining their connection allows for a more complex view of the role of sympathy in the Victorian novel. The commonplace in novel criticism is that Victorian authors, whether effectively or not, constructed their novels with a view to the expansion of sympathy. This dissertation intervenes in the discussion of the Victorian novel as a vehicle for sympathy by positing that texts and scenes in which representations of illness and animality are conjoined reveal where the novel draws the boundaries of the human, and the often surprising limits it sets on sympathetic feeling. In such moments, textual cues train or direct readerly sympathies in ways that suggest a particular definition of the human, but that direction of sympathy is not always towards an enlarged sympathy, or an enlarged definition of the human. There is an equally (and increasingly) powerful antipathetic impulse in many of these texts, which estranges readerly sympathy from putatively deviant, degenerate, or dangerous groups. These two opposing impulses—the sympathetic and the antipathetic—often coexist in the same novel or even the same scene, creating an ideological and affective friction, and both draw on the same tropes of illness and animality. Examining the intersection of these different discourses—sympathy, illness, and animality-- in these novels reveals the way that major Victorian debates about human nature, evolution and degeneration, and moral responsibility shaped the novels of the era as vehicles for both antipathy and sympathy. Focusing on the novels of the Brontës and Thomas Hardy, this dissertation examines in depth the interconnected ways that representations of animals and animality and representations of illness function in the Victorian novel, as they allow authors to explore or redefine the boundary between the human and the non-human, the boundary between sympathy and antipathy, and the limits of sympathy itself.

Quantitative evaluation of visual function 12 months after bilateral implantation of a diffractive trifocal IOL

PURPOSE: To quantitatively evaluate visual function 12 months after bilateral implantation of the Physiol FineVision® trifocal intraocular lens (IOL) and to compare these results with those obtained in the first postoperative month. METHODS: In this prospective case series, 20 eyes of 10 consecutive patients were included. Monocular and binocular, uncorrected and corrected visual acuities (distance, near, and intermediate) were measured. Metrovision® was used to test contrast sensitivity under static and dynamic conditions, both in photopic and low-mesopic settings. The same software was used for pupillometry and glare evaluation. Motion, achromatic, and chromatic contrast discrimination were tested using 2 innovative psychophysical tests. A complete ophthalmologic examination was performed preoperatively and at 1, 3, 6, and 12 months postoperatively. Psychophysical tests were performed 1 month after surgery and repeated 12 months postoperatively. RESULTS: Final distance uncorrected visual acuity (VA) was 0.00 ± 0.08 and distance corrected VA was 0.00 ± 0.05 logMAR. Distance corrected near VA was 0.00 ± 0.09 and distance corrected intermediate VA was 0.00 ± 0.06 logMAR. Glare testing, pupillometry, contrast sensitivity, motion, and chromatic and achromatic contrast discrimination did not differ significantly between the first and last visit (p>0.05) or when compared to an age-matched control group (p>0.05). CONCLUSIONS: The Physiol FineVision® trifocal IOL provided satisfactory full range of vision and quality of vision parameters 12 months after surgery. Visual acuity and psychophysical tests did not vary significantly between the first and last visit.

Towards a gravitational wave observatory designer: sensitivity limits of spaceborne detectors

The most promising concept for low frequency (millihertz to hertz) gravitational wave observatories are laser interferometric detectors in space. It is usually assumed that the noise floor for such a detector is dominated by optical shot noise in the signal readout. For this to be true, a careful balance of mission parameters is crucial to keep all other parasitic disturbances below shot noise. We developed a web application that uses over 30 input parameters and considers many important technical noise sources and noise suppression techniques to derive a realistic position noise budget. It optimizes free parameters automatically and generates a detailed report on all individual noise contributions. Thus one can easily explore the entire parameter space and design a realistic gravitational wave observatory. In this document we describe the different parameters, present all underlying calculations, and compare the final observatory's sensitivity with astrophysical sources of gravitational waves. We use as an example parameters currently assumed to be likely applied to a space mission proposed to be launched in 2034 by the European Space Agency. The web application itself is publicly available on the Internet at http://spacegravity.org/designer. Future versions of the web application will incorporate the frequency dependence of different noise sources and include a more detailed model of the observatory's residual acceleration noise.

The 1996 BFA Graduating Class Department of Visual arts

The work presented in this catalogue represent ten years of study, thought, practice and application. While each member of the fourth-year visual arts class has selected just one image and chosen only a few words for inclusion in this record of our graduates and the program, it is important that we understand the dimensions of experience and learning symbolized on these pages. The women and men represented here have all passed through a rigorous course of academic study,personal and professional development, and technical training. They have engaged issues and concepts from both theoretical and practical perspectives, and have been challenged to stretch their thinking about community, society and the world in terms past, present and future. These Students have translated ideas and insights into works of art in a variety of media.

The 1997 BFA Graduating Class: Department of Visual Arts.

This catalogue of works by senior students of the visual arts program continues our tradition of recognizing and recording the accomplishments of each graduating class. It Provides a historical record of those who are about to receive their bachelor of fine arts degrees from Sir Wilfred Grenfell College, as well as a contemporary reflection of the diverse array of creative talents and technical skills these students have refined and honed during four years of study - attributes and abilities that will be brought fully into play in their many future endevours.

The 1998 BFA Graduating Class: Department of Visual Arts

The exhibition of works by Sir Wilfred Grenfell College's graduating Class in visual arts constitutes the culmination of four years of intensive study and practice. our students are trained in the fundamentals of their craft and exposed tio a variety of media and styles ranging from the traditional to the avant garde. But their education has more to do with the exploration and development of their creativity, the enlargement of their capacity to see, and their mastery of the vocabulary of sight, enabling them to discover, uncover and represent. Each of the students ha sustained and nurtured an individual and unique quest over the four years of this rigorous programme.