Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of an Ammonia-Permeable Aquaporin

Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants.
A possible initial folding intermediate: the C-terminal proteolytic domain of tryptophan synthase beta chains folds in less than 4 milliseconds into a condensed state with non-native-like secondary structure.

The isolated F2-V8 peptide corresponding to the 101 C-terminal residues of Escherichia coli tryptophan synthase beta chains folds into a heat-stable, yet fluctuating, condensed state that contains a lot of secondary structure. However, this state has non-native-like secondary and supersecondary structures [Chaffotte, A. , Guillou, Y. , Delepierre, M. , Hinz, H. -J., & Goldberg, M. E. (1991) Biochemistry 30, 8067-8074]. To characterize the rate of appearance of this state, stopped-flow studies on the far-ultraviolet circular dichroism (CD) and on the binding of 1-anilino-8-naphthalenesulfonate (ANS) have been conducted during the folding of guanidine-unfolded F2-V8. It was shown that both the CD signal at 222 nm and the ANS binding properties of folded isolated F2-V8 were regained, at 20 degrees C, within the dead time of the stopped-flow apparatus, which was 4 ms. At 12 degrees C, the binding of ANS was also completed within this dead time, but the ellipticity showed some minor later changes. After a rapid overshoot of the CD signal that occurred during the 4-ms dead time, a small readjustment of the ellipticity to the final value occurred more slowly and was completed after about 25 ms. Thus, even at 12 degrees C, the hydrophobic core and most of the secondary structure of folded F2-V8 were formed in less than 4 ms. These observations strongly suggest that the previously described condensed non-native-like state of F2-V8 results from a very rapid, nonspecific, hydrophobic collapse. It is proposed that such a state may be a general early intermediate in protein folding.
Memory alloy actuator

The phase change in shape memory alloys (SMA) is highly nonlinear, and the development of advanced position ing applications for SMA actuators benefits from the availability of good models of this behaviour. One phenomenological model for SMA transformation kinetics is Madill’s model, which has recently been extended to include the effect of time varying stress. This extension allows for the modelling of stress disturbances and the simulation and prediction of stress-strain behaviour. In this work, we couple the phase kinetics of the extended model with a series-based mechanical model which includes both shape memory and superelastic behaviour. This coupled model is inverted and used to investigate different control architectures for sine tracking and stress disturbance rejection for an SMA actuator with constant load. Open-loop model-inverse feedforward control is compared with simple PI feedback and the combination of feedforward plus feedback. The results show in particular that using complicated inverse models does not always bring the expected increase in perfor mance, and that other limitations of SMA actuators can negate the benefit of model-inverse feedforward.
Interactive Memoirs: Coping with the Imminent Death and Leaving Legacies

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. CHI’12, May 5–10, 2012, Austin, Texas, USA. Copyright 2012 ACM 978-1-4503-1016-1/12/05. $10.00. Abstract Terminally ill patients and their caregivers suffer from high levels of stress. Coping is crucial to maintain and increase quality of life at its end. Building on previous research on virtual humans, personality, and legacy, we designed Memoirs, a tool for terminal patients to share experiences through the creation of virtual personas – conversational representations of themselves. We describe the design of Memoirs, as a tool to help patients nearing the end of life to cope with their illness and to offer an interactive legacy for their loved ones after their time has passed.
Gravity Influences Top-Down Signals in Visual Processing

Visual perception is not only based on incoming visual signals but also on information about a multimodal reference frame that incorporates vestibulo-proprioceptive input and motor signals. In addition, top-down modulation of visual processing has previously been demonstrated during cognitive operations including selective attention and working memory tasks. In the absence of a stable gravitational reference, the updating of salient stimuli becomes crucial for successful visuo-spatial behavior by humans in weightlessness. Here we found that visually-evoked potentials triggered by the image of a tunnel just prior to an impending 3D movement in a virtual navigation task were altered in weightlessness aboard the International Space Station, while those evoked by a classical 2D-checkerboard were not. Specifically, the analysis of event-related spectral perturbations and inter-trial phase coherency of these EEG signals recorded in the frontal and occipital areas showed that phase-locking of theta-alpha oscillations was suppressed in weightlessness, but only for the 3D tunnel image. Moreover, analysis of the phase of the coherency demonstrated the existence on Earth of a directional flux in the EEG signals from the frontal to the occipital areas mediating a top-down modulation during the presentation of the image of the 3D tunnel. In weightlessness, this fronto-occipital, top-down control was transformed into a diverging flux from the central areas toward the frontal and occipital areas. These results demonstrate that gravity-related sensory inputs modulate primary visual areas depending on the affordances of the visual scene.
Data Verification and Privacy-respecting User Remuneration in Mobile Crowd Sensing

The broad capabilities of current mobile devices have paved the way for Mobile Crowd Sensing (MCS) applications. The success of this emerging paradigm strongly depends on the quality of received data which, in turn, is contingent to mass user participation; the broader the participation, the more useful these systems become. This can be achieved if users are gratified for their contributions while being provided with strong guarantees for the security and the privacy of their sensitive information. But this very openness is a double-edge sword: any of the participants can be adversarial and pollute the collected data in an attempt to degrade the MCS system output and, overall, its usefulness. Filtering out faulty reports is challenging, with practically no prior knowledge on the participants trustworthiness, dynamically changing phenomena, and possibly large numbers of compromised devices. This work presents a holistic framework that can assess user-submitted data and sift malicious contributions while offering adequate incentives to motivate users to submit better quality data. With a rigorous assessment of our system’s security and privacy protection complemented by a detailed experimental evaluation, we demonstrate its accuracy, practicality and scalability. Overall, our framework is a comprehensive solution that significantly extends the state-of-the-art and can catalyze the deployment of MCS applications.
Optimization of Human Immunodeficiency Virus Gag Expression by Newcastle Disease Virus Vectors for the Induction of Potent Immune Responses

ABSTRACT One attractive strategy for the development of a human immunodeficiency virus (HIV) vaccine is the use of viral vectors with a proven safety profile and an absence of preexisting immunity in humans, such as Newcastle disease virus (NDV). Several NDV vaccine vectors have been generated, and their immunogenicities have been investigated with different animal models. However, a systematic study to evaluate the optimal insertion site of the foreign antigens into NDV that results in enhanced immune responses specific to the antigen has not yet been conducted. In this article, we describe the ability of NDV expressing HIV Gag to generate a Gag-specific immune response in mice. We also have determined the optimal insertion site into the NDV genome by generating recombinant NDV-HIVGag viruses in which HIV gag was located at different transcriptional positions throughout the NDV viral genome. All recombinant viruses were viable, grew to similar titers in embryonated chicken eggs, and expressed Gag in a stable manner. Our in vivo experiments revealed that higher HIV Gag protein expression positively correlates with an enhanced CD8+ T-cell-mediated immune response and protective immunity against challenge with vaccinia virus expressing HIV Gag. We also inserted a codon-optimized version of HIV gag in the described best location, between the P and M genes. Virus expressing the codon-optimized version of HIV gag induced a higher expression of the protein and an enhanced immune response against HIV Gag in mice. These results indicate that strategies directed toward increasing antigen expression by NDV result in enhanced immunogenicity and vaccine efficacy.
Bisque: a platform for bioimage analysis and management

MOTIVATION Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process and analyze. These tasks are further complicated by conflicting and proprietary image and metadata formats, that impede analyzing and sharing of images and any associated data. These obstacles have resulted in research resources being locked away in digital media and file cabinets. Current image management systems do not address the pressing needs of researchers who must quantify image data on a regular basis. RESULTS We present Bisque, a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend Bisque with both data model and analysis extensions in order to adapt the system to local needs. Bisque's extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel bioimage analyses. Several case studies using Bisque with specific applications are presented as an indication of how users can expect to extend Bisque for their own purposes.
Cherednik algebras and differential operators on quasi-invariants

We develop representation theory of the rational Cherednik algebra H associated to a finite Coxeter group W in a vector space h. It is applied to show that, for integral values of parameter `c', the algebra H is simple and Morita equivalent to D(h)#W, the cross product of W with the algebra of polynomial differential operators on h. We further study an algebra Q of quasi-invariant polynomials on h introduced by Chalykh, Feigin, and Veselov [CV], [FV], such that C[h]^W \subset Q \subset C[h]. We prove that the algebra D(Q) of differential operators on quasi-invariants is a simple algebra, Morita equivalent to D(h). The subalgebra D(Q)^W of W-invariant operators turns out to be isomorphic to the spherical subalgebra eHe \subset H. We also show that D(Q) is generated, as an algebra, by Q and its `Fourier dual Q*, and that D(Q) is a rank one projective (Q-Q*)-module (via multiplication-action on D(Q) on opposite sides).
Cooperation of an RNA Packaging Signal and a Viral Envelope Protein in Coronavirus RNA Packaging

ABSTRACT Murine coronavirus mouse hepatitis virus (MHV) produces a genome-length mRNA, mRNA 1, and six or seven species of subgenomic mRNAs in infected cells. Among these mRNAs, only mRNA 1 is efficiently packaged into MHV particles. MHV N protein binds to all MHV mRNAs, whereas envelope M protein interacts only with mRNA 1. This M protein-mRNA 1 interaction most probably determines the selective packaging of mRNA 1 into MHV particles. A short cis-acting MHV RNA packaging signal is necessary and sufficient for packaging RNA into MHV particles. The present study tested the possibility that the selective M protein-mRNA 1 interaction is due to the packaging signal in mRNA 1. Regardless of the presence or absence of the packaging signal, N protein bound to MHV defective interfering RNAs and intracellularly expressed non-MHV RNA transcripts to form ribonucleoprotein complexes; M protein, however, interacted selectively with RNAs containing the packaging signal. Moreover, only the RNA that interacted selectively with M protein was efficiently packaged into MHV particles. Thus, it was the packaging signal that mediated the selective interaction between M protein and viral RNA to drive the specific packaging of RNA into virus particles. This is the first example for any RNA virus in which a viral envelope protein and a known viral RNA packaging signal have been shown to determine the specificity and selectivity of RNA packaging into virions.
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting

MOTIVATION It is a question of whether the supramolecular organization of the protein complex has an impact on its function, or not. In the case of the photosystem II (PSII), water splitting might be influenced by cooperation of the PSIIs. Since PSII is the source of the atmospheric oxygen and because better understanding of the water splitting may contribute to the effective use of water as an alternative energy source, possible cooperation should be analyzed and discussed. RESULTS We suggest that the dimeric organization of the PSII induces cooperation in the water splitting. We show that the model of monomeric PSII is unable to produce the oxygen after the second short flash (associated with the double turnover of the PSII), in contrast to the experimental data and model of dimeric PSII with considered cooperation. On the basis of this fact and partially from the support from other studies, we concluded that the double turnover of the PSII induced by short flashes might be caused by the cooperation in the water splitting. We further discuss a possibility that the known pathway of the electron transport through the PSII might be incomplete and besides D1-Y161, other cofactor which is able to oxidize the special chlorophyll pair (P680) must be considered in the monomeric PSII to explain the oxygen production after the second short flash. AVAILABILITY Commented SBML codes (.XML files) of the monomeric and dimeric PSII models will be available (at the time of publication) in the BioModels database (www.ebi.ac.uk/biomodels).
An Efficient Image Retrieval Based on Fusion of Fast Features and Query Image Classification

Content Based Image Retrieval (CBIR) is an emerging research area in computer vision, in which, we yield similar images as per the query content. For the implementation of CBIR system, feature extraction plays a vital role, where colour feature is quite remarkable. But, due to unevenly colored or achromatic surfaces, the role of texture is also important. In this paper, an efficient and fast CBIR system is proposed, which is based on a fusion of computationally light weighted colour and texture features; chromaticity moment, colour percentile, and local binary pattern (LBP). Using these features with multiclass classifier, the authors propose a supervised query image classification and retrieval model, which filters all irrelevant class images. Basically, this model categorizes and recovers the class of a query image based on its visual content, and this successful classification of image significantly enhances the performance and searching time of retrieval system. Descriptive experimental analysis on benchmark databases confirms the effectiveness of proposed retrieval framework. KEywoRDS Chromaticity Moment, Classification, Content Based Image Retrieval, Feature Extraction, Similarity Measure
Changes in intake of key nutrients over 17 years during adult life of a British birth cohort

An investigation was carried out to determine whether there were significant changes in nutrient intake over 17 years of adult life. The Medical Research Council National Survey of Health and Development is a longitudinal study of a nationally representative cohort of singleton births in the UK in 1946. Of this cohort, 1253 survey members provided information on diet recorded in a 5 d diary at age 36 years in 1982, 43 years in 1989 and 53 years in 1999. The outcome measures were mean intakes of energy, macronutrients, minerals and vitamins. There were significant changes in the intake of most nutrients in 1999 compared with previous years. Intakes of fat, Na, Fe and Cu have fallen, but there was a rising trend in the intakes of Ca, P, carotene, thiamin, pyridoxine, folic acid and vitamins C, D and E in both men and women. Additionally, intakes of K, Mg and vitamin K1 have risen in women. There were significant gender differences, women showing a higher percentage rise in the intakes of carotene, riboflavin, folic acid, vitamin C and vitamin E. These changes were related to changes in the consumption of certain key foods, such as the increased consumption of fruit and vegetables and a shift away from whole milk, butter and red meat. Most of these trends are in line with accepted nutritional guidelines. How far these changes are due to consumer choice and real changes in food composition or are due to artefacts inherent in the methodology is discussed.
Explicit stochastic MPC approach to building temperature control

In this paper we show how to synthesize explicit representations of Model Predictive Control (MPC) feedback laws that maintain temperatures in a building within of a comfortable range while taking into account random evolution of external disturbances. The upside of such an explicit MPC solution stems from the fact that optimal control input can be obtained on-line by a mere function evaluation. This task can be accomplished quickly even on cheap hardware. To account for random disturbances, our formulation assumes probabilistic version of thermal comfort constraints. We illustrate how a finite-sampling approach can be used to convert probabilistic bounds into deterministic constraints. To reduce complexity, and to allow for synthesis of explicit feedbacks in reasonable time, we furthermore propose to prune the set of samples depending on activity of constraints. Performance of the stochastic explicit MPC controller is then compared against best-case and worst-case scenarios.
Flexible integration : a viable technique for the process of deeper integration in the Southern African Development Community (SADC)

Integration in the Southern African Development Community (SADC) is deepening to the extent that the organisation is being tasked with greater responsibilities. However, deeper integration is unlikely to occur within a framework of uniformity; hence, the process of deepening integration may demand flexibility. Flexibility is necessary because SADC member states are likely to differ in their views about the way forward, and how much of their national sovereignty they are willing to trade for the benefits of SADC membership. One example of a critical difference, as SADC prepares for the customs union, is the use of import tariffs. South Africa and Mauritius are increasingly using this as an instrument of industrial policy. On the other hand, poor countries such as Lesotho and Swaziland, are using it as a source of revenue. It is about time that SADC member states realise and accept that these differences will persist rather than wither away. Flexibility does not have to be read as a brake on integration. On the contrary, flexibility offers the most useful means of balancing different national interests, thereby allowing progress to be made in SADC as a whole. This paper seeks to draw lessons for flexible integration from the European Union (EU). Such an undertaking is considered relevant as SADC has made a laudable effort to follow the EU model of regional integration. Part 1 of this paper attempts to define flexible integration within the context of SADC regional integration and the experiences of the EU, while part 2 deals with the rationale for employing flexible integration in SADC. Part 3 discusses the challenges of flexibility and, finally, part 4 outlines ways in which SADC can make flexibility work.
Parieto-frontal Network Studied by Ccep Title Parieto-frontal Network in Humans Studied by Cortico-cortical Evoked Potential Parieto-frontal Network Studied by Ccep

Parieto−frontal network is essential for sensorimotor integration in various complex behaviors, and its disruption is associated with pathophysiology of apraxia and visuo-spatial disorders. Despite advances in knowledge regarding specialized cortical areas for various sensorimotor transformations, little is known about the underlying cortico-cortical connectivity in humans. We investigated inter-areal connections of the lateral parieto−frontal network in vivo by means of cortico-cortical evoked potentials (CCEPs). Six patients with epilepsy and one with brain tumor were studied. With the use of subdural electrodes implanted for presurgical evaluation, network configuration was investigated by tracking the connections from the parietal stimulus site to the frontal site where the maximum CCEP was recorded. It was characterized by i) a near-to-near and distant-to-distant, mirror symmetric configuration across the central sulcus, ii) preserved dorso-ventral organization (the inferior parietal lobule to the ventral premotor area and the superior parietal lobule to the dorsal premotor area) and iii) projections to more than one frontal cortical sites in 56% of explored connections. These findings were also confirmed by the standardized parieto-frontal CCEP connectivity map constructed in reference to the Jülich cytoarchitectonic atlas in the MNI standard space. The present CCEP study provided an anatomical blueprint underlying the lateral parieto-frontal network and demonstrated a connectivity pattern similar to non-human primates in the newly developed inferior parietal lobule in humans.