Microbial interactions represent an understudied facet of human health and disease. In this study, the interactions that occur between Chlamydia trachomatis and the opportunistic fungal pathogen, Candida albicans were investigated. Candida albicans is a common component of the oral and vaginal microbiota responsible for thrush and vaginal yeast infections. Normally, Candida exist in the body as yeast. However, disruptions to the microbiota create conditions that allow expanded growth of Candida, conversion to the hyphal form, and tissue invasion. Previous studies have shown that a myriad of outcomes can occur when Candida albicans interacts with pathogenic bacteria. To determine if C. trachomatis physically interacts with C. albicans, we incubated chlamydial elementary bodies (EB) in medium alone or with C. albicans yeast or hyphal forms for 1 h. Following incubation, the samples were formaldehyde-fixed and processed for immunofluorescence assays using anti-chlamydial MOMP or anti- chlamydial LPS antibodies. Replicate samples were replenished with culture medium and incubated at 35°C for 0-120 h prior to fixation for immunofluorescence analysis or collection for EB infectivity assays. Data from this study indicates that both C. trachomatis serovar E and C. muridarum EB bind to C. albicans yeast and hyphal forms. This interaction was not blocked by pre-incubation of EB with the Candida cell wall components, mannan or β-glucans, suggesting that EB interact with a Candida cell wall protein or other structure. Bound EB remained attached to C. albicans for a minimum of 5 days (120 h). Infectivity assays demonstrated that EB bound to C. albicans are infectious immediately following binding (0h). However, once bound to C. albicans, EB infectivity decreased at a faster rate than EB in medium alone. At 6h post binding, 40% of EB incubated in medium alone remained infectious compared to only 16% of EB bound to C. albicans. Likewise, pre-incubation of EB with laminarin, a soluble preparation of β-glucan, alone or in combination with other fungal cell wall components significantly decreases chlamydial infectivity in HeLa cells. These data indicate that interactions between EB and C. albicans inhibit chlamydial infectivity, possibly by physically blocking EB interactions with host cell receptors.

The expected technical lifetime for a wind turbine is 20-25 years (Wizelius, 2007). In the process of planning a wind farm on a site an estimation of the average wind speed and the energy yield is required from the site. Due to large fluctuations in wind velocity from one year to another it is, from a climatologically point of view, not sufficient to measure the wind for a short period of time, e.g. one year. The year measured may have uncommonly high or uncommonly low winds and thereby generate an average not representative of the wind climate on the site. In the same time it is neither practical nor economically desirable to measure for a longer time period. Instead the measured data collected for a short period of time is scaled into a normal year before it is used to calculate the energy content. This normal year correction can be preformed using different methods. Principally, the methods relate the short time series, measured on the site, to one or more variables of a long time reference series. As a long time reference series the geostrophic wind on the site or a series of measured wind nearby can be used. If the correlation between the two series is sufficiently high a normal year correction may be done using the relation. Normal year correction has foremost been done using the relation between the velocities of the measured wind and a reference wind. The purpose in this study is to evaluate and implement a part of an algorithm for normal year correction considering additional variables besides wind velocity. The relationships studied are between measured wind speed and geostrophic wind speed, geostrophic wind direction and time of the year. For the purpose of evaluating the algorithm two wind data series from Näsudden, on the Swedish island of Gotland, for a period of 15 years has been used. Measured wind on 75 meters and geostrophic wind on 850hPa. Where the geostrophic wind has been used as a long time reference and the measured wind for one year at the time has been related to this reference. The relation has then been used together with the geostrophic wind data to create an estimation of the wind climate on Näsudden in three steps. Step one establishes the estimation due to the relation of geostrophic wind speed. Step two corrects the estimation due to the relation of geostrophic wind direction and step three corrects the estimation due to the relation of time of year. The conclusions from this study showed that with the method used for implementing the algorithm the normal year correction using only the relation between the velocities of the measured wind and the geostrophic wind gives the best estimation of the climatically mean wind speed. The standard deviation gives a 5 % risk for more than 0.436 m/s error for estimation of the mean wind on the site, which is comparable to earlier studies. The introduction of the wind direction dependence overestimates the mean wind on the site and amplifies the error. The introduction of the season dependence amplifies the error further and overestimates the mean wind additionally. / En vindturbin har en planerad livslängd på 20-25 år (Wizelius, 2007). Vid planering av en vindkraftspark behöver en estimering av medelvinden och energiutvinningen utföras för platsen man är intresserad av. På grund av stora fluktuationer av vindhastighet från år till år är det ur klimatologisk synpunkt inte tillräckligt att mäta under en kort period, exempelvis ett år. Det år man mäter kan ha ovanligt starka eller ovanligt svaga vindar och ge en icke representativ bild av vindklimatet på platsen. Samtidigt är det inte praktiskt eller ekonomiskt önskvärt att mäta under en längre tidsperiod. Istället kan den korta mätserie som insamlats korrigeras till ett normalår med hjälp av en långtidsreferens innan den används för att beräkna energiinnehållet. I princip går normalårskorrigering ut på att relatera den korta mätserien till en eller flera variabler i långtidsreferensen. Som långtidsreferensdata kan den geostrofiska vinden på platsen eller en lång mätserie från en närliggande plats användas. Om korrelationen mellan de två serierna är tillräckligt hög kan en normalårskorrigering göras med hjälp av relationen. Tidigare har man vid normalårskorrigering främst sett till relationen mellan vindhastigheterna för den uppmätta vinden och en referensvind. Syftet i detta arbete är att utvärdera en del av en algoritm för normalårskorrigering där hänsyn tas till fler variabler än endast vindhastighet. Samband som studeras är mellan uppmätt vindhastighet och geostrofisk vindhastighet, geostrofisk vindriktning och tid på året. För utvärderingen av algoritmen har två vinddataserier från Näsudden på Gotland använts för en period av 15 år med uppmätt vind på 75m och geostrofisk vind på 850hPa. Där den geostrofiska vinden fått representera långtidsreferensen och den uppmätta vinden för ett år i taget har relaterats till denna. Efter normalårskorrigeringen har den uppmätta vinden för 15 år fått representera vindklimatet på platsen som jämförelse. Enligt algoritmen har uppskattning av vindklimatet på Näsudden skapats i tre steg. Steg 1 är en uppskattning av vinden från sambandet för geostrofisk vindhastighet. Steg 2 är en korrektion av uppskattningen genom sambandet till geostrofisk vindriktning och steg 3 en korrektion av uppskattningen genom sambandet till tid på året. Efter vart steg skickas det aktuella estimatet vidare till nästa steg där det korrigeras med avseende på nästa samband. Slutsatserna från undersökningen visade att med den metod som använts ger normalårskorrigeringen med enbart sambandet till hastighet bäst uppskattning av den klimatologiska medelvinden. Standardavvikelsen för estimatet ger 5 % risk för mer än 0,436 m/s fel vid uppskattning av klimatologisk medelvind vilket är jämförbart med tidigare studier. Vidare överskattar införandet av vindriktningsberoendet den uppskattade medelvindhastigheten samt ökar osäkerheten. Även införandet av säsongsberoendet överskattar medelvindhastigheten ytterligare samt även osäkerheten.

Background. CoGNIT is a computerized test battery for cognitive assessment, used in diagnosing and treating patients with idiopathic normal pressure hydrocephalus (INPH). The disorder causes symptoms of dementia, among other things. Apart from other diseases with similar symptoms, like Alzheimer’s, INPH can be countered. CoGNIT is performed by a patient before and after drainage of cerebrospinal fluid. If a significant improvement in cognition is detected after the extraction, the patient receives shunt surgery which reduces all symptoms. The test battery is long and tedious, which makes it difficult for people with cognitive impairments to complete. Objectives. The objectives of this study are to rework original CoGNIT with carefully selected game design elements and analyze the effects of the alteration on performance and user experience. If users perform better in a gamified environment, the validity of gathered data will have improved as the data should better reflect their cognitive capabilities. Another objective is to introduce gamification to the medical field. Methods. Game design elements were picked and designed based on suitability for elderly people and with the impairments of INPH patients in mind. A gamified prototype was developed and put to test with healthy individuals against the original version in an experiment. The effects of gamification on performance was examined by comparing resulting score values from both versions of the test. Participants also filled in a questionnaire as proxy for the test’s target group, meaning that questions were answered with how the participants expected a cognitively impaired person to answer. Answers were used to investigate the effect of gamification ofuser experience. Results. The gamified version of CoGNIT shows an improvement in test segments regarding attention, psychomotor speed, executive function, and manual dexterity, but a negative inclination in segments regarding memory. Results from the user experience questionnaire indicates that the gamified version feels less dramatic, more playful, less "test-like" and less tedious compared to the non-gamified version. This suggests that the added game elementsare affecting the user experience in the desired way. Conclusions. An overall positive impact on both performance and user experience from gamification is concluded. The negative effect on memory tests could not be determined to be a cause of the gamification per se. / Bakgrund. CoGNIT är ett datoriserat testbatteri för kognitiv bedömning som används vid diagnos och behandling av patienter med idiopatisk normaltryckshydrocefalus (INPH). Sjukdomen orsakar bland annat symptom som demens. Till skillnad från andra sjukdomar med liknande symptom, som Alzheimers, kan INPH motverkas. CoGNIT utförs av en patient före och efter dränering av cerebrospinalvätska. Om en förbättring av patientens kognitiva förmågor upptäcks efter dräneringen, shuntoperaras patienten och alla symptom minskas. Testbatteriet är långt och tråkigt, vilket gör det svårt för personer med kognitiva nedsättningar att slutföra. Syfte. Syftet med denna studie är att omarbeta CoGNIT med noggrant utvalda speldesignelement och analysera hur prestation och användarupplevelse påverkas av förändringen. Om användare presterar bättre i en spelifierad miljö kommer validiteten av insamlad data att förbättras eftersom datan borde bättre återspegla deras kognitiva förmågor. Ett annat mål är att introducera spelifiering till det medicinska området. Metod. Speldesignelement valdes ut och utformades baserat på dess lämplighet för äldre och med de funktionsnedsättnigar som INPH-patienter har i åtanke. En spelifierad prototyp utvecklades och testades med friska individer mot originalversionen i ett experiment. Effekterna av spelifiering på prestation undersöktes genom att jämföra poängvärden från båda versionerna av testet. Deltagarna fyllde också i ett frågeformulär som "proxy" för testets målgrupp, vilket innebär att frågorna besvarades med hur deltagarna förväntade sig att en kognitivt nedsatt person hade svarat. Svaren användes för att undersöka effekten av spelifiering på användarupplevelsen. Resultat. Den spelifierade versionen av CoGNIT visar en förbättring i testsegmenten som utvärderar uppmärksamhet, psykomotorisk hastighet, exekutiva funktioner och fingerfärdighet, men en försämring i segmenten som utvärderar minne. Resultat från frågeformuläret indikerar att den spelifierade versionen upplevs mindre dramatisk, mer lekfull, mindre "testliknande" och mindre tråkig jämfört medden icke-spelifierade versionen. Detta visar att de tillagda spelelementen påverkar användarupplevelsen som önskat. Slutsatser. En övergripande positiv inverkan på både prestanda och användarupplevelse från spelfiering fastställs. Den negativa effekten på minnestesterna kunde inte bedömas vara en orsak av spelifiering i sig.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18800号 / 理博第4058号 / 新制||理||1584(附属図書館) / 31751 / 京都大学大学院理学研究科地球惑星科学専攻 / (主査)教授 平原 和朗, 教授 澁谷 拓郎, 准教授 久家 慶子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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The enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are inhibited by nerve agents such as sarin and tabun. In general, the inhibited enzymes are reactivated by bisquaternary ammonium compounds (oximes). The binding free energies of the oximes; 2-PAM, MMB-4, HI-6, and obidoxime bound to human AChE (hAChE) and human BChE (hBChE) inhibited by sarin and tabun and also to the uninhibited enzymes were calculated using various computational methods. Using thermodynamic integration, the binding free energies of all the inhibited and uninhibited systems of MMB-4 and obidoxime were evaluated. The standard binding free energies (dA) were more negative than the experimental values due to limitations of the ff99 forcefield. The RMS error of dA for the inhibited systems of MMB-4 was 2.1 kcal/mol, and for obidoxime systems it was 4.8 kcal/mol with respect to the experimental free energies. The binding enthalpies calculated using MM-GBSA and MM-PBSA methods for 2-PAM, MMB-4, HI-6, and obidoxime systems were negative, except for hBChE-sarin-MMB-4 and hBChE-sarin-obidoxime. For all the systems the TdS values calculated using normal mode analysis were equal to or lower in magnitude than their corresponding binding enthalpies. As a result, the estimated free energies were positive for most of the systems. Clearly, the present algorithms cannot effectively estimate the binding entropies for a protein-ligand system. Met81 has commonly shown favorable interactions, and lysine or arginine exhibited unfavorable interactions with the reactivator in all the systems. Second, the interactions between chloropyrifos-oxon (Cpo) and experimentally tested neutral and monopyridinium oximes bound to the Q192 or R192 polymorphs of human paraoxonase1 (hPON1) were studied. The equilibrated Q192 and R192 hPON1 were structurally different than the crystal structure of recombinant PON1. The neutral oximes have shown more favorable interactions with Cpo in Q192 hPON1 + Cpo system compared to R192 hPON1 + Cpo. Whereas the monopyridinium oximes interacted more affectively with Cpo in R192 hPON1 than Q192 hPON1. The relative deprotonation energy of the monopyridinium oxime was lower than the neutral oxime. Hence, the monopyridinium oxime can hydrolyze an organophosphate at a higher rate than a neutral oxime.

In this thesis we have employed two computational approaches, temperature-dependent molecular dynamics (MD) and normal mode analysis (NMA), to gain insights into the structureunction relationships between three structurally-related proteins, each possessing a central alpha/beta core. The three proteins studied here are: pnbCE from Bacillus subtilis, cutinase from Fusarium solani - both belong to the serine hydrolase family - and TTHA1554, from the thermophile Thermus thermophilus. Mutations at the gate residue 362, located at the side-door of the pnbCE enzyme, are known to alter the catalytic activity of this enzyme. In this work the modifications induced by mutating LEU362 on the structural and dynamical properties of pnbCE are also explored. From MD simulations at several temperatures, we propose a mechanism by which mutations at position 362 of pnbCE affect the stability and functionality of this enzyme. We have identified two coil residues, SER218 and GLN276, whose interactions with residue 362 in wild-type and mutant pnbCE enzymes control the dynamics of the side-door domain of pnbCE. A hydrogen bond between the GLN276 and ARG362 residues in the arginine substituted (L362R) pnbCE mutant enzyme appears to be responsible for locking the sidedoor domain region of the L362R enzyme, thus lowering the catalytic rates of the L362R mutant pnbCE enzyme compared to the wild-type. Similarly, a hydrogen bond formed between SER218 and ARG362 in L362R provides thermal stability to the arginine substituted mutant enzyme. This hydrogen bond is not as prevalent in the wild-type or other mutated pnbCEs, making them prone to structural fluctuations upon increasing temperature. The predominant lowrequency mode, obtained from normal mode analysis, reveals a collective scissor-like motion of residues surrounding the openings to the active site that validates the results of MD simulations on pnbCE systems. The collective motion of large loops also appear in the lowrequency modes of cutinase and TTHA1554, which correspond to particularly mobile regions in these proteins. An attempt to locate a putative active site of the thermophilic protein TTHA1554 was inconclusive. In general, useful comparisons of the flexibility, stability, and dynamic changes were calculated for the three selected proteins.

In the era of a pandemic, public spaces have been reshaped for better, but also for worse. Humans are social beings. We need interaction with others to thrive, but doing this over a screen over a long period of time has proven we must adapt in new ways. “As society begins to build the “new normal” of emergence from the pandemic, efforts to rebuild and strengthen trust and solidarity are of as much importance as the ongoing distribution of vaccines and vigilance against coronavirus variants,” (The EditorsFebruary, 2022, Unpaginated). The transitional restart for issues relating to public spaces in the post pandemic period has highlighted the challenge of making public spaces not only safe to gather, but also vibrant. There is much room for society to start exploring new systems to create safe spaces for the public that veer away from the stale solutions we have implemented. What would happen if we shy away from digital as a social distancing method and instead explore craft or nature as a way of rethinking the new normal?  The EditorsFebruary, et al. “The Key to a Post-Pandemic 'New Normal'? Solidarity.”America Magazine, 17 Feb. 2022, https://www.americamagazine.org/politics-society/2022/02/17/covid- omicron-normal-masks-242404.

This study proposed a finite element procedure for protein normal mode analysis (NMA). The finite element model adopted the protein solvent-excluded surface to generate a homogeneous and isotropic volume. A simplified triangular approximation of coarse molecular surface was generated from the original surface model by using the Gaussian-based blurring technique. Similar to the widely adopted elastic network model, the finite element model holds a major advantage over standard all-atom normal mode analysis: the computationally expensive process of energy minimization that may distort the initial protein structure has been eliminated. This modification significantly increases the efficiency of normal mode analysis. In addition, the finite element model successfully brings out the capability of normal mode analysis in low-frequency/high collectivity molecular motion by capturing protein shape properties. Fair results from six protein models in this study have fortified the capability of the finite element model in protein normal mode analysis.

Visualization and image filtering are important parts of cryo-electron tomography analysis. ArtiaX, a plugin developed for UCSF ChimeraX, has been extended to improve the functionality of these two parts. For the visualization, a method of moving 3D surfaces to remove overlap between them has been developed and implemented. To accommodate this, a Monte Carlo approach using Poisson disc sampling for approximating volume of overlap between 3D surfaces is used, and a novel method for measuring overlap has been invented, called the Normal Projection Method, useful for measuring the depth of overlap between surfaces. For the image filtering, tomogram averaging and frequency filters have been added to the ArtiaX toolbox. / Visualisering och bildfiltrering är viktiga delar inom kryoelektrontomografianalys. ArtiaX, ett plugin utvecklat för UCSF ChimeraX, har utökats för att förbättra funktionaliteten inom dessa två områden. För visualiseringen har en metod för att flytta 3D ytor så att de inte överlappar utvecklats och implmenterats. För att skapa denna funktion används en Monte Carlo metod med Poisson disk sampling för att uppskatta volymen av 3D ytor, och normalprojektionsmetoden, en ny metod för att mäta överlappsdjup har skapts och implementerats. För att förbättra bildfiltreringen har tomogram-snittning och frekvensfilter lagts till bland verktygen i ArtiaX.