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Knowledge of protein hot spots and the ability to successfully predict them while using only primary protein structure has been a worldwide scientific goal for several decades. This thesis describes the importance of hot spots and sums up advances achieved in this field of study so far. Besides that we introduce hot spot prediction algorithm using only a primary protein structure, based primarily on signal processing techniques. To convert protein sequence to numerical signal we use the EIIP attribute, while further processing is carried out via means of S-transform. The algorithm achieves sensitivity of more than 60 %, positive predictive value exceeds 50 % and the main advantage over competitive algorithms is its simplicity and low computational requirements.

Jana Jíchová: Crime and its Perception in Urban Environment ABSTRACT Crime is an important social phenomenon that affects many aspects of the functioning of society and the life of every person. It also represents an important interdisciplinary topic that deals with a number of disciplines, including geography. Logically, there is a thematic and methodological overlap; each of the sciences emphasize on different aspects of crime, using various methods and research approaches, interpretations, and therefore contributes to the knowledge of crime differently. The importance of geography is particularly in the enrichment of the crime research on spatial dimension and contributes to its cognition through analysis of the distribution of crime and studies of perception of crime. Although this type of studies is well established in Western crime research, in the Czech geography is paid to them only little attention. This doctoral thesis introduces geography of crime in the Czech context, discusses its theoretical and methodological developments and its applicability and application in our cities.. More emphasis is put on the concept of fear of crime, which constitutes an essential component of feeling of safety affecting daily life, the use of urban space and spatial mobility of individuals. Better understanding of...

<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.</p><p>A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.</p><p>A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.</p><p>The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.</p>

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

The focus of this report is to discuss graphical password systems and how they can contribute to handle security problems that threaten authentication processes. One such threat is shoulder-surfing attacks, which are also reviewed in this report. Three already existing systems that are claimed to be shoulder-surfing resilient are described and a new proposed system is presented and evaluated through a user study. Moreover, the system is compared to the mentioned existing systems to further evaluate the usability, memorability and the time it takes to authenticate. The user study shows that test subjects are able to remember their chosen password one week after having registered and signed in once. It is also shown that the average time to sign in to the system after five minutes of practice is within a range of 3.30 to 5.70 seconds. The participants in the experiments gave the system an average score above 68 on the System Usability Scale, which is the score of an average system.

Background: The whole of society is facing major challenges regarding the ongoing climate change and the possibility of creating sustainable development. This also largely applies to today's trafficsystem, which needs to change to more sustainable trffic system. Increased active travel is a nescessery for reaching the set goals that exist when it comes to sustainable travel. Increased active travel will lead to more unprotected road users in the trafficsystem, one group of unprotected road users are pedestrians. An increased number of pedestrians in the trafficsystem requires additional efforts to ensure traffic safety for that group. Method: An scoping review is carried out in which police and legislative measures aimed at increasing road safety for pedestrians are evaluated. The purpose of the study is to gain knowledge about what measures the current research proposes to increase traffic safety and to come up with proposals for additional areas where more research is needed. The study builds on two previous literature studies that superficially touched on the subject. Seven scientific articles are taken from these literature studies, a further 13 scientific articles are selected after a literature search. A total of 20 scientific articles that meet the inclusion criteria are included and analyzed. In order to assess whether Swedish authorities implement effective police and legislative measures with the aim of increasing traffic safety for pedestrians, a comparison is made between the measures proposed by the research and the measures that two Swedish authorities, the Swedish Transport Agency and the Swedish Police Agency, present in their documents Aktionsplan för säker vägtrafik 2022–2025 - 250 åtgärder som 33 myndigheter och aktörer avser att vidta för ökad trafiksäkerhet samt Polismyndighetens strategi inom trafiksäkerhetsarbetet. Results: The study shows that targeted police measures aimed at fining individuals who break traffic rules in a certain place during a certain time have a positive effect on pedestrian traffic safety. The focus should be on increasing rule compliance and reducing the number of speed limit violations by motorists, as well as encouraging pedestrians not to walk against red lights. The legislative measures that the scoping review shows have the best effect are lowering the speed limit and car-free zones on stretches of road where many pedestrians are moving. Conclusions: The conclusions that thos scoping review draws are that further research is required in the connection between reduced average speed and the number of traffic accidents which leads to personal injuries to pedestrians, as well as the part of police and legislative measures in different action programs that include several different measures that are implemented together. The police authority is working towards a reduced average speed of motorists through targeted police measures, which is in line with the measures proposed by the existing research in the area. However, there is nothing in the document about targeted police measures against pedestrians in order to increase rule compliance by that group, which is something that the Police Authority is recommended to develop. In the Swedish Transport Agency's action plan for the years 2022-2025, no measures are mentioned to increase pedestrian traffic safety linked to traffic accidents. Only measures to reduce the number of fall injuries are presented. The Swedish Transport Agency is therefore recommended to further develop its action plan and also have it include legislative measures such as reduced speed limits or car-free zones on road sections where many pedestrians move.

Digitalization has been reshaping the media landscape in recent years, often conveying an implicit promise of becoming less dependent on physical resources. At the same time, the current understanding of digital reading goes beyond dedicated e-readers or definable digital media products such as magazines or newspapers. In fact, it must be perceived as a function or service obtained from existing and ever-expanding “digital ecosystems”. There is furthermore a clear and unambiguous trend that relatively small and mobile devices are on the rise for consuming all kinds of media. Next to potentially enabling environmental gains compared to traditional paper-based media consumption, there are agreeing indications of a shift from overall electricity consumption dominated by end-user devices towards an increasing importance of less tangible data transmission networks and data centers. Therefore, a bottom-up analysis is deemed to compliment more general top-down observations and assessments. To this end, an elaborated reference scenario is proposed as to bridge the mere analytical method of Life Cycle Assessment (LCA) with behavioral aspects based on German market observations and surveys. The prevailing aim of this study is to detect environmental hot-spots and absolute impacts linked to the service of accessing text-based content via connected electronic devices. In doing so, this study takes the position that both types of media consumption – digital and paper-based - are incommensurable due to the very evident differences in provided functions, markets, and industries. Therefore, an attributional and stand-alone LCA is considered appropriate. The perceived current situation (reference scenario) evolves around substantiated estimates and assumptions concerning production of devices, use of devices as well as operation of essential data transmission network components. Looking at potential hot-spots, electricity consumption linked to data transmission could be a decisive factor for the environmental performance of digital reading. However, the actual importance of data transmission infrastructures depends on both methodological choices and a range of parameters or trends. For instance, the relative importance is shifted when more recent estimates of electricity intensities are incorporated. Depending on actual and localized electricity intensity of data transmission, the amount of data required to provide an expected function may inhibit environmental potentials of digital media consumption. Postulating average annual consumption of digital contents and assuming actual substitution of equivalent printed media products, about 50 kg CO2-equivalents. could potentially be avoided. This theoretical potential is based on the calculated global warming potential (GWP) associated with digital reading according to the reference scenario which amounts to about 29 kg CO2-equivalents. Therefore, this study supports findings from previous studies that indicated environmental benefits of digital reading. Compared to other functions or services (e.g. video/music streaming, podcasts, audio books) embedded in the same “digital ecosystems”, reading requires little amount of data. If allocation of upstream effects is based on time, the relative importance of data transmission networks could be gauged and compared by adopting a “data-to-service time” ratio. Taking the reference scenario as a starting point, a perceivable ratio for digital reading is 0.015 GB/h, including systemic inefficiencies. In contrast, streaming of high-definition video contents can easily consume 3 GB/h, a 200-fold increase. The audience of this study comprises providers of digital reading services and/or other media services as well as end-users as integral element in “digital ecosystems”. Besides, the report proposes a conceptual assessment framework which can be applied to other contemporary digital services or functions. / De senaste åren har digitalisering omformat medielandskapet, med ett implicit löfte om att minska beroendet av fysiska resurser. Dessutom finns det tydliga trender som pekar mot en ökad användning av små, mobila enheter för att konsumera alla sorters media. En uppdaterad bottom-up analys bedöms komplettera mer generella observationer och bedömningar. Om man antar årliga genomsnittliga konsumtionsmönster i Tyskland, så är tillverkningen av elektroniska slutanvändarenheter – oavsett om de är till för enskilda ändamål (e-läsare) eller om de är multifunktionella (smartphone, surfplatta) – onekligen en miljömässigt kritisk punkt för digitalt läsande. Elförbrukningen, som sker i samband med dataöverföringen, kan också vara en avgörande faktor för den övergripande miljöpåverkan av digital läsning. Dock beror den faktiska påverkan av dataöverförningsinfrastrukturer dels på metodologiska val men även på ett antal andra parametrar och trender. Genom att undersöka indikatorn för global uppvärmning kan denna studie konstatera att resultaten stödjer tidigare forskning, som redan pekar på de miljömässiga vinsterna av digitalt läsande. Målgruppen för denna studie innefattar både distributörer av digitala läs-tjänster och/eller andra media tjänster såväl som slutanvändare som ett integrerat element i ”digitala ekosystem”.