Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational studies on membrane proteins and membrane-drug interactions

The cell membrane is a gateway to the cell and immersion point for membrane proteins and thus is of interest for pharmacology and structural biology. This thesis aims to study its interaction with water, small molecules, polymers and proteins through molecular dynamics simulation and statistical analysis. In the first part of the thesis, I have performed a statistical analysis of membrane proteins present in the PDB databank and enumerated in a structure database of known membrane proteins. Based on a statistical analysis of 127 proteins it was shown that extracellular cysteines are not solvent accessible. This rule has not previously been stated and was poorly followed by the participants of the GPCR DOCK competitions in 2008 and 2010. Thus it can provide qualitative guidelines to improve structural modeling. In a second study, based on a statistical analysis of 39 membrane proteins of three or more transmembrane helices, all of different fold, we have shown and clustered different spatial arrangements that sets of three interacting or consecutive helices can take, in addition to visualizing their abundance. In the second part of the thesis, I performed 200 ns simulations of both membranes in the gel (DSPC) and liquid-crystalline (DLPC) states with solvent and ions; These simulations were repeated with functionalized PEG polymers included (PEGylation). We also performed 200ns lipid membrane simulations in the liquid-crystalline (POPC) state with hematoporphyrin. Our studies provide a new, more accurate description of interactions between lipid membrane ions and featuring PEG polymers rather as dynamic molecules looping around Na+ ions and penetrating to liquid crystalline membrane rather than just a steric barrier outside of membrane. This sheds new light on the mechanism of liposome protection by PEG as well as triggering the release of liposome content through a heat induced lipid phase transition. Hematoporphyrin was shown to reside in the lipid headgroup carbonyl region. Ionized hematoporphyrin has lower affinity to the membrane as iv well as forming stable dimers in the aqueous phase. The research was in agreement with experimental data and has provided a molecular level view of the interactions between photosensitizers and the membrane. ACKNOWLEDGEMENTS I would like to thank the ISB for funding and accepting me as a member and giving me the opportunity to mingle with great people and researchers during our great meetings in Lapland and, additionally, the Magnus Ehrnrooth foundation for funding. I would like to thank the head of the department …
Ideological Shift: Explaining the Liberal Media Myth ⁄

A recent article by Groseclose and Milyo (2005) has provided a novel measure of a media outlet’s ideology. Nonetheless, this measure has garnered a large amount of criticism. We show that the measure is not sensitive to alternative speciflcations of the ideology of members of Congress. We then investigate whether the estimated ideological positions of the media outlets are stable over time, and flnd that they are not. The estimated positions are sensitive to the time period of observation. Moreover, we flnd that there has been a conservative shift in ideology across all major media outlets studied.
The Effects of Enzyme Complex on Performance, Intestinal Health and Nutrient Digestibility of Weaned Pigs

Two experiments were conducted to evaluate the effect of supplementing a corn-soybean meal-based diet with an enzyme complex containing amylase, protease and xylanase on the performance, intestinal health, apparent ileal digestibility of amino acids and nutrient digestibility of weaned pigs. In Exp. 1, 108 piglets weaned at 28 d of age were fed one of three diets containing 0 (control), 100, or 150 ppm enzyme complex for 4 wks, based on a two-phase feeding program namely 1 to 7 d (phase 1) and 8 to 28 d (phase 2). At the end of the experiment, six pigs from the control group and the group supplemented with 150 ppm enzyme complex were chosen to collect digesta samples from intestine to measure viscosity and pH in the stomach, ileum, and cecum, as well as volatile fatty acid concentrations and composition of the microflora in the cecum and colon. There were linear increases (p<0.01) in weight gain, gain: feed ratio and digestibility of gross energy with the increasing dose rate of enzyme supplementation during the whole experiment. Supplementation with enzyme complex increased the digesta viscosity in the stomach (p<0.05) and significantly increased (p<0.01) the concentrations of acetic, propionic and butyric acid in the cecum and colon. Enzyme supplementation also significantly increased the population of Lactobacilli (p<0.01) in the cecum and decreased the population of E. coli (p<0.05) in the colon. In Exp. 2, six crossbred barrows (initial body weight: 18.26±1.21 kg), fitted with a simple T-cannula at the distal ileum, were assigned to three dietary treatments according to a replicated 3×3 Latin Square design. The experimental diets were the same as the diets used in phase 2 in Exp. 1. Apparent ileal digestibility of isoleucine (p<0.01), valine (p<0.05) and aspartic acid (p<0.05) linearly increased with the increasing dose rate of enzyme supplementation. In conclusion, supplementation of the diet with an enzyme complex containing amylase, protease and xylanase improved piglet performance. This is likely a result of improvement in nutrient digestibility, volatile fatty acid concentrations and bacteria ratio in the large intestine.
The thermodynamic state of the Arctic atmosphere observed by AIRS: comparisons during the record minimum sea ice extents of 2007 and 2012

Abstract. The record sea ice minimum (SIM) extents observed during the summers of 2007 and 2012 in the Arctic are stark evidence of accelerated sea ice loss during the last decade. Improving our understanding of the Arctic atmosphere and accurate quantification of its characteristics becomes ever more crucial, not least to improve predictions of such extreme events in the future. In this context, the Atmospheric Infrared Sounder (AIRS) instrument onboard NASA's Aqua satellite provides crucial insights due to its ability to provide 3-D information on atmospheric thermodynamics. Here, we facilitate comparisons in the evolution of the thermodynamic state of the Arctic atmosphere during these two SIM events using a decade-long AIRS observational record (2003–2012). It is shown that the meteorological conditions during 2012 were not extreme, but three factors of preconditioning from winter through early summer played an important role in accelerating sea ice melt. First, the marginal sea ice zones along the central Eurasian and North Atlantic sectors remained warm throughout winter and early spring in 2012 preventing thicker ice build-up. Second, the circulation pattern favoured efficient sea ice transport out of the Arctic in the Atlantic sector during late spring and early summer in 2012 compared to 2007. Third, additional warming over the Canadian archipelago and southeast Beaufort Sea from May onward further contributed to accelerated sea ice melt. All these factors may have lead the already thin and declining sea ice cover to pass below the previous sea ice extent minimum of 2007. In sharp contrast to 2007, negative surface temperature anomalies and increased cloudiness were observed over the East Siberian and Chukchi seas in the summer of 2012. The results suggest that satellite-based monitoring of atmospheric preconditioning could be a critical source of information in predicting extreme sea ice melting events in the Arctic.
Is the International Convergence of Capital Adequacy Regulation Desirable?

The merit of having international convergence of bank capital requirements in the presence of divergent closure policies of different central banks is examined. While the privately optimal level of bank capital decreases with regulatory forbearance (they are strategic substitutes), the socially optimal level of bank capital increases with regulatory forbearance (they are strategic complements). Hence, in optimal regulatory design, the level of minimum bank capital requirement increases with the forbearance in central bank closure policy. The lack of such linkage leads to a spillover from more forbearing to less forbearing economies and reduces the competitive advantage of banks in less forbearing economies. Linking the central bank’s forbearance to its alignment with domestic bankowners, it is shown that in equilibrium a regression towards the worst closure policy may result: the central banks of initially less forbearing economies have to adopt greater forbearance as well.
NADP-Dependent Isocitrate Dehydrogenase from Arabidopsis Roots Contributes in the Mechanism of Defence against the Nitro-Oxidative Stress Induced by Salinity

NADPH regeneration appears to be essential in the mechanism of plant defence against oxidative stress. Plants contain several NADPH-generating dehydrogenases including isocitrate dehydrogenase (NADP-ICDH), glucose-6-phosphate dehydrogenase (G6PDH), 6-phosphogluconate dehydrogenase (6PGDH), and malic enzyme (ME). In Arabidopsis seedlings grown under salinity conditions (100 mM NaCl) the analysis of physiological parameters, antioxidant enzymes (catalase and superoxide dismutase) and content of superoxide radical (O2 ∙−), nitric oxide (NO), and peroxynitrite (ONOO−) indicates a process of nitro-oxidative stress induced by NaCl. Among the analysed NADPH-generating dehydrogenases under salinity conditions, the NADP-ICDH showed the maximum activity mainly attributable to the root NADP-ICDH. Thus, these data provide new insights on the relevance of the NADP-ICDH which could be considered as a second barrier in the mechanism of response against the nitro-oxidative stress generated by salinity.
Virtual structures for high-precision cooperative mobile robotic control

A key problem in cooperative robotics is the maintenance of a geometric configuration during movement. To address this problem, the concept of a virtual structure is introduced. Control methods are developed to force an ensemble of robots to behave as if they were particles embedded in a rigid structure. The method was tested both using simulation and experimentation with a set of three robots. Results are presented which demonstrate that this approach is capable of achieving high precision movement which is fault tolerant and exhibits graceful degradation of performance. In addition, this algorithm does not require leader selection as in other cooperative robotic strategies. Finally, the method is highly flexible in the kinds of geometric formations that can be maintained.
Mobility management for personal communications systems

Using a combination of empirical data and theoretical models, this paper develops a model of user behavior for a personal communications system environment. This model is used to analyze a mobility management strategy that combines automatic updates by the users-either when they make significant moves or when they go extended periods without network interaction; multiple hysteresis in the form of dynamic registration areas and delayed updates; and a focused paging strategy that minimizes the number of pages given a constraint on the time allowed to a page. Over a range of system and user parameters, the total paging and update traffic can be kept below 1 per 2000 user seconds. The impact on the user's handset is less than ten brief updates per day. The total traffic is only a factor of three more than the minimum, immobile users case.
Discriminative Classifiers for Deterministic Dependency Parsing

Deterministic parsing guided by treebank-induced classifiers has emerged as a simple and efficient alternative to more complex models for data-driven parsing. We present a systematic comparison of memory-based learning (MBL) and support vector machines (SVM) for inducing classifiers for deterministic dependency parsing, using data from Chinese, English and Swedish, together with a variety of different feature models. The comparison shows that SVM gives higher accuracy for richly articulated feature models across all languages, albeit with considerably longer training times. The results also confirm that classifier-based deterministic parsing can achieve parsing accuracy very close to the best results reported for more complex parsing models.
A Chance Lost in the Prevention of School Dropout? Teacher-Student Relationships Mediate the Effect of Mental Health Problems on Noncompletion of Upper-Secondary School

ABSTRACT There is increasing awareness of the challenges that young people who do not complete upper-secondary school may encounter. The aim of the current study was to investigate teacher-student relationship as a possible mechanism to reduce the associations between mental health problems, grades, and subsequent noncompletion. Mental health problems and teacher-student relationships were assessed through students’ self-reports in 10th grade, and linked with Norwegian registries of education and sociodemography (n = 10,931). A dual-factor serial mediator model was specified, allowing the effect of mental health problems on school dropout to be mediated by the teacher-student relationship via school grades. Results indicated that teacher-student relationship is a potential mechanism to reduce the negative associations between mental health problems and later noncompletion. However, students with mental health problems seemed to experience less supportive teachers; therefore, interventions targeting teacher-student relationships may be required. The patterns were similar between genders.
The Whole is Greater Than the Sum of its Parts: Experiences of Co-Working as Music Therapists

This paper describes the experiences of two music therapists who have been working together for ten years and the benefits of this partnership. It shows how working practices and therapeutic processes have evolved over a decade. It demonstrates that working as a team over this length of time resulted in significant improvements to the therapy given to children with special needs aged between 2 and 18 and also to the support offered to their parents. The various topics covered include the development of a co-therapy assessment procedure, group psychodynamic music therapy for children with special needs, sessions for children and their parents, the significance of counter-transference and the importance of supervision.
MirrorCameraRoom: the gendered multi-(in)stabilities of the selfie

ABSTRACT This paper proposes benefits of the entanglement of feminist new materialist theory with post-phenomenology. The paper focuses on an empirical study of interviews using photo-elicitation with four young women to document their lived experiences producing self-images to share via social media. Drawing on post-phenomenology, the cellphone is discussed as a multi-stable technology wherein the selfie is experienced at once as a mirror, a camera, and a window to social media platforms. But this paper also draws on glitch feminism, which, via metaphors of technological failure, challenges ossified conceptual boundaries between the body, desire, and technology. Through this coupling the paper suggests that what are identified as corporeal, photographic, and performative glitches by the participants are worked out, thereby erasing any experiential delineation between mirror, camera, and cellphone. Whereas post-phenomenology often refrains from examining the complex power dynamics that shape technological–human relations, this paper argues that such dynamics are crucial when examining gendered technological phenomena like selfies. Contributing empirical data to recent post-phenomenological work on cellphones, this paper details the gendered material-discursive dimensions of the selfie via the work of contemporary feminist new materialist thinkers.
Distinctive Structural and Effective Connectivity Changes of Semantic Cognition Network across Left and Right Mesial Temporal Lobe Epilepsy Patients

Occurrence of language impairment in mesial temporal lobe epilepsy (mTLE) patients is common and left mTLE patients always exhibit a primary problem with access to names. To explore different neuropsychological profiles between left and right mTLE patients, the study investigated both structural and effective functional connectivity changes within the semantic cognition network between these two groups and those from normal controls. We found that gray matter atrophy of left mTLE patients was more severe than that of right mTLE patients in the whole brain and especially within the semantic cognition network in their contralateral hemisphere. It suggested that seizure attacks were rather targeted than random for patients with hippocampal sclerosis (HS) in the dominant hemisphere. Functional connectivity analysis during resting state fMRI revealed that subregions of the anterior temporal lobe (ATL) in the left HS patients were no longer effectively connected. Further, we found that, unlike in right HS patients, increased causal linking between ipsilateral regions in the left HS epilepsy patients cannot make up for their decreased contralateral interaction. It suggested that weakened contralateral connection and disrupted effective interaction between subregions of the unitary, transmodal hub of the ATL may be the primary cause of anomia in the left HS patients.
Separating lexical-semantic access from other mnemonic processes in picture-name verification

We present a novel paradigm to identify shared and unique brain regions underlying non-semantic, non-phonological, abstract, audio-visual (AV) memory vs. naming using a longitudinal functional magnetic resonance imaging experiment. Participants were trained to associate novel AV stimulus pairs containing hidden linguistic content. Half of the stimulus pairs were distorted images of animals and sine-wave speech versions of the animal's name. Images and sounds were distorted in such a way as to make their linguistic content easily recognizable only after being made aware of its existence. Memory for the pairings was tested by presenting an AV pair and asking participants to verify if the two stimuli formed a learned pairing. After memory testing, the hidden linguistic content was revealed and participants were tested again on their recollection of the pairings in this linguistically informed state. Once informed, the AV verification task could be performed by naming the picture. There was substantial overlap between the regions involved in recognition of non-linguistic sensory memory and naming, suggesting a strong relation between them. Contrasts between sessions identified left angular gyrus and middle temporal gyrus as key additional players in the naming network. Left inferior frontal regions participated in both naming and non-linguistic AV memory suggesting the region is responsible for AV memory independent of phonological content contrary to previous proposals. Functional connectivity between angular gyrus and left inferior frontal gyrus and left middle temporal gyrus increased when performing the AV task as naming. The results are consistent with the hypothesis that, at the spatial resolution of fMRI, the regions that facilitate non-linguistic AV associations are a subset of those that facilitate naming though reorganized into distinct networks.
A Photovoltaic Power System Using a High Step-up Converter for DC Load Applications

This paper presents a power system using a high step-up converter for dc load applications. The high step-up converter adopts a boost converter with interleaved mode and a coupled inductor to raise its powering ability and increase its step-up voltage ratio, respectively. In order to increase conversion efficiency, an active clamp circuit is introduced into the proposed one to provide soft-switching features to reduce switching losses. Moreover, switches in the converter and active clamp circuit are integrated with a synchronous switching technique to reduce circuit complexity and component counts, resulting in a lower cost and smaller volume. A perturb and observe method is adopted to extract the maximum power from photovoltaic (PV) arrays. Furthermore, a microchip associated with PWM IC is used to implement maximum power point tracking operation, voltage regulation and power management. Finally, a prototype PV power system with 400 V/6 A has been implemented for verifying the feasibility of the proposed PV power system. It is shown to be suitable for PV energy conversion applications when the duty ratios of switches in the dc/dc converter are less than 0.5.
From marginal to mainstream: The role of perceived social norms in the rise of a far‐right movement

The present research intends to shed light on the processes enabling political minorities to transition into normatively acceptable groups, by investigating how a previously marginalised far-right movement (the French National Front) is progressively becoming mainstream. Drawing on the social representations approach, we argue that perceived social norms play a pivotal role in this process. Using a longitudinal and experimental design, the study (N = 233) was implemented in the ecological context of the 2012 French presidential election at a Parisian university campus, a traditional anti-far-right bastion. We tested whether the electoral campaign altered the perceptions of social norms, whether the perceived social norms were easily malleable in this specific context and, most important, whether they influenced people's willingness to speak out in public against the far-right movement. The findings support affirmative answers to all three questions. We conclude that, in periods of collective uncertainty, changing perceptions of social norms might play an important role in the weakening of public opposition to far-right movements. This, in turn, helps to explain the recent transition to mainstream recognition of a number of previously marginalised political movements in Europe and around the globe.
APOE Polymorphism Is Associated with C-reactive Protein Levels but Not with White Blood Cell Count: Dong-gu Study and Namwon Study

We evaluated the association of the APOE polymorphism with serum C-reactive protein levels and white blood cell count in two large population-based studies in Korean. The datasets included the Dong-gu study (n = 8,893) and the Namwon Study (n = 10,032). APOE genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism. Multivariable linear regression analysis was performed to evaluate the relationship of APOE genotypes with C-reactive protein levels and white blood cell count with adjustments for age, sex, body mass index, smoking, diabetes, hypertension, and serum lipids. In the multivariate model, carriers of E3E4 or E4E4 genotype had significantly lower C-reactive protein levels compared with carriers of E3E3 genotype group (0.50 mg/L vs. 0.67 mg/L; 0.37 mg/L vs. 0.67 mg/L, respectively, for the Dong-gu Study and 0.47 mg/L vs. 0.66 mg/L; 0.45 mg/L vs. 0.66 mg/L, respectively, for the Namwon Study). However, there was no difference in white blood cell count among APOE genotypes. We found that the APOE E4 allele is associated with lower C-reactive protein levels, but not white blood cell count. Our results suggest that APOE genotype may influence C-reactive protein levels through non-inflammatory pathway. Graphical Abstract