Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles

Recent work has shown that the choice of the type and concentration of detergent used for the solubilization of membrane proteins can strongly influence the results of functional experiments. In particular, the amino acid transporter LeuT can bind two substrate molecules in low concentrations of n-dodecyl β-d-maltopyranoside (DDM), whereas high concentrations reduce the molar binding stoichiometry to 1:1. Subsequent molecular dynamics (MD) simulations of LeuT in DDM proteomicelles revealed that DDM can penetrate to the extracellular vestibule and make stable contacts in the functionally important secondary substrate binding site (S2), suggesting a potential competitive mechanism for the reduction in binding stoichiometry. Because annular lipids can be retained during solubilization, we performed MD simulations of LeuT proteomicelles at various stages of the solubilization process. We find that at low DDM concentrations, lipids are retained around the protein and penetration of detergent into the S2 site does not occur, whereas at high concentrations, lipids are displaced and the probability of DDM binding in the S2 site is increased. This behavior is dependent on the type of detergent, however, as we find in the simulations that the detergent lauryl maltose-neopentyl glycol, which is approximately twice the size of DDM and structurally more closely resembles lipids, does not penetrate the protein even at very high concentrations. We present functional studies that confirm the computational findings, emphasizing the need for careful consideration of experimental conditions, and for cautious interpretation of data in gathering mechanistic information about membrane proteins.
2 9 A pr 2 00 8 Linearisation of conservative toral homeomorphisms

We give an equivalent characterisation of the semi-conjugacy class of an irrational rotation within the space of conservative homeomorphisms of the two-torus. This leads to an analogue of Poincaré's classification of circle homeomorphisms for conservative toral home-omorphisms with unique rotation vector and a certain bounded mean motion property. For minimal toral homeomorphisms, the result extends to arbitrary dimensions. Further, we provide a basic classification for the dynamics of non-wandering toral homeomorphisms homotopic to the identitiy.
Explaining Restrictive TANF Policies: Group Threat Hypothesis and State Economy Conditions

ABSTRACT This study examined whether TANF policies' restrictiveness is related to states' racial composition and economic conditions. The data were extracted from various reports dated 2000–2014. Results from generalized least squares random-effects modeling showed the number of restrictive TANF policies to be associated positively with larger populations of Hispanic individuals and associated negatively with larger populations of African American individuals. No association was found between policies' restrictiveness and “other” minority population, nor between restrictiveness and either poverty or unemployment. One conclusion suggested by the analysis is that restrictive TANF policies result from dramatic increases in the Hispanic population that trigger the dominant group's resentment of ethnic minorities. Several policy implications are stated.
Measurement Matrix Optimization and Mismatch Problem Compensation for DLSLA 3-D SAR Cross-Track Reconstruction

With a short linear array configured in the cross-track direction, downward looking sparse linear array three-dimensional synthetic aperture radar (DLSLA 3-D SAR) can obtain the 3-D image of an imaging scene. To improve the cross-track resolution, sparse recovery methods have been investigated in recent years. In the compressive sensing (CS) framework, the reconstruction performance depends on the property of measurement matrix. This paper concerns the technique to optimize the measurement matrix and deal with the mismatch problem of measurement matrix caused by the off-grid scatterers. In the model of cross-track reconstruction, the measurement matrix is mainly affected by the configuration of antenna phase centers (APC), thus, two mutual coherence based criteria are proposed to optimize the configuration of APCs. On the other hand, to compensate the mismatch problem of the measurement matrix, the sparse Bayesian inference based method is introduced into the cross-track reconstruction by jointly estimate the scatterers and the off-grid error. Experiments demonstrate the performance of the proposed APCs’ configuration schemes and the proposed cross-track reconstruction method.
A dialectical reflection on the emergence of the ‘citizen as consumer’ as neoliberal citizenship: The 2013 Brazilian protests

In this article, we argue that citizenship conceived within a context of neoliberal rationality helps explain the emergence of what we term the ‘citizen as consumer’. We define the citizen as consumer as someone who relates to the state and the public realms from the private perspective of consumption. We ask how this emergent neoliberal citizen is configured in peripheral countries that are regarded as exemplifying ‘weak’ citizenship. To respond to this question, we consider the protests that occurred in Brazil in 2013 as an empirical illustration. Our main objective is to rethink the citizen/state relationship in consumer studies, employing a dialectical analysis to understand how the better-known consumer-citizen movement, in which the consumer acts as a citizen and gives birth, under a neoliberal rationality, to a movement that somehow disrupts these roles such that the citizen starts to act as a consumer. The Brazilian protests provide insights that advance debate on the scope and limits of the hybridisation between citizens and consumers and on the transformations in the relationship between citizenship and politics.
A mixed-game agent-based model of financial contagion

Over the past two decades, financial market crises with similar features have occurred in different regions of the world. Unstable cross-market linkages during financial crises are referred to as financial contagion. We simulate the transmission of financial crises in the context of a model of market participants adopting various strategies; this allows testing for financial contagion under alternative scenarios. Using a minority game approach, we develop an agent-based multinational model and investigate the reasons for contagion. Although contagion has been extensively investigated in the financial literature, it has not been studied yet through computational intelligence techniques. Our simulations shed light on parameter values and characteristics which can be exploited to detect contagion at an earlier stage, hence recognising financial crises with the potential to destabilise cross-market linkages. In the real world, such information would be extremely valuable to develop appropriate risk management strategies.
Comparison of different diagnostic techniques against Fasciolosis in Buffaloes

The present study was conducted to compare different diagnostic tests viz., Direct Smear (DS), Agar gel precipitation (AGP), Sedimentation (Sd), and Zinc Sulfate (ZnSO 4 ) flotation for fasciolosis in dairy buffaloes as well as the economic losses due to fasciolosis. A total of 200 faecal samples were examined and DS, AGP, Sd, and ZnSO 4 flotation techniques showed an overall prevalence of 2, 8, 5 and 4%, respectively. The highest agreement was observed between Sd and ZnSO 4 (0.88, 95%CI; 0.74-1.02) followed by AGP and Sd (0.75, 95%CI; 0.62-0.88), ZnSO 4 and DS (0.65, 95%CI; 0.52-0.78), AGP and ZnSO 4 (0.648, 95%CI; 0.51-0.77), DS and Sd (0.55, 95%CI; 0.430.68), and DSM and AGP (0.38, 95%CI; 0.27-0.48). By taking DS as a gold standard, all tests showed 100 percent sensitivity results and same trend was observed in case of negative predictive values (NPV). Highest specificity was shown by ZnSO4, followed by Sd and AGP. Similar trends were observed in the positive predictive values (PPV). Then, by taking AGP as gold standard, all tests showed 100 percent specificity and positive predictive values (PPV) while, Sd showed highest sensitivity followed by ZnSO4 and AGP and similar trend was observed regarding NPV of tests. To this end, most effective test is AGP followed by Sd, ZnSO 4 and DS method. Moreover, AGP is the most suitable method for diagnosing the fasciolosis in early stages. Total economic losses due to fasciolosis during three months (Oct. – Dec. 2004) were found very high i.e Rs. 1016400.
A New Approach on Interactive SOA Security Model Based on Automata

Service oriented architecture is a new important approach for all electronic devices and applications such as e-payment systems. Statelessness of basic service architecture model is based on four principles: loose coupling, abstraction, autonomy, and security. Statelessness eliminates a lot of benefits in service providing. This paper presents automata-based model for interactive services and focuses on security for interactive SOA in state-full environments. The purpose of this paper is to propose a new extended solution for e-applications to communicate simpler while session management is been done by server helps the client to have better development and interaction.
Differential regulation of synchronous versus asynchronous neurotransmitter release by the C2 domains of synaptotagmin 1

Synaptic vesicle fusion at many synapses has been kinetically separated into two distinct Ca2+-dependent temporal components consisting of a rapid synchronous phase followed by a slower asynchronous component. Mutations in the synaptic vesicle Ca2+ sensor Synaptotagmin 1 (Syt 1) reduce synchronous neurotransmission while enhancing the slower asynchronous phase of release. Syt 1 regulation of vesicle fusion requires interactions mediated by its tandem cytoplasmic C2 domains (C2A and C2B). Although Ca2+ binding by Syt 1 is predicted to drive synchronous release, it is unknown if Ca2+ interactions with either C2 domain is required for suppression of asynchronous release. To determine if Ca2+ binding by Syt 1 regulates these two phases of release independently, we performed electrophysiological analysis of transgenically expressed Syt 1 mutated at Ca2+ binding sites in C2A or C2B in the background of Drosophila Syt 1-null mutants. Transgenic animals expressing mutations that disrupt Ca2+ binding to C2A fully restored the synchronous phase of neurotransmitter release, whereas the asynchronous component was not suppressed. In contrast, rescue with Ca2+-binding mutants in C2B displayed little rescue of the synchronous release component, but reduced asynchronous release. These results suggest that the tandem C2 domains of Syt 1 play independent roles in neurotransmission, as Ca2+ binding to C2A suppresses asynchronous release, whereas Ca2+ binding to C2B mediates synchronous fusion.
Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis

Biofilm formation enhances the survival and persistence of the facultative human pathogen Vibrio cholerae in natural ecosystems and its transmission during seasonal cholera outbreaks. A major component of the V. cholerae biofilm matrix is the Vibrio polysaccharide (VPS), which is essential for development of three-dimensional biofilm structures. The vps genes are clustered in two regions, the vps-I cluster (vpsU, vpsA–K, VC0916–27) and the vps-II cluster (vpsL–Q, VC0934–39), separated by an intergenic region containing the rbm gene cluster that encodes biofilm matrix proteins. In-frame deletions of the vps clusters and genes encoding matrix proteins drastically altered biofilm formation phenotypes. To determine which genes within the vps gene clusters are required for biofilm formation and VPS synthesis, we generated in-frame deletion mutants for all the vps genes. Many of these mutants exhibited reduced capacity to produce VPS and biofilms. Infant mouse colonization assays revealed that mutants lacking either vps clusters or rbmA (encoding secreted matrix protein RbmA) exhibited a defect in intestinal colonization compared to the wild-type. Understanding the roles of the various vps gene products will aid in the biochemical characterization of the VPS biosynthetic pathway and elucidate how vps gene products contribute to VPS biosynthesis, biofilm formation and virulence in V. cholerae.
A Segmentation and Abstraction of Blood Vessels from Volume Data for Surgical Simulation

In this paper, we present a robust segmentation method of blood vessels from medical volume data. It extracts the blood vessels with their important geometric features such as bifurcations, a location of centroid, diameter, and tangent vectors. It also generates an abstract model which has a tree structure in which the nodes store important features of the vessels. We use the extracted vessels data to simulate a variety of vascular and interventional radiology procedures.
Inhibition of H9N2 Virus Invasion into Dendritic Cells by the S-Layer Protein from L. acidophilus ATCC 4356

Probiotics are essential for the prevention of virus invasion and the maintenance of the immune balance. However, the mechanism of competition between probiotics and virus are unknown. The objectives of this study were to isolate the surface layer (S-layer) protein from L. acidophilus ATCC 4356 as a new antiviral material, to evaluate the stimulatory effects of the S-layer protein on mouse dendritic cells (DCs) and to verify its ability to inhibit the invasion of H9N2 avian influenza virus (AIV) in DCs. We found that the S-layer protein induced DCs activation and up-regulated the IL-10 secretion. The invasion and replication of the H9N2 virus in mouse DCs was successfully demonstrated. However, the invasion of H9N2 virus into DCs could be inhibited by treatment with the S-layer protein prior to infection, which was verified by the reduced hemagglutinin (HA) and neuraminidase (NA) mRNA expression, and nucleoprotein (NP) protein expression in the DCs. Furthermore, treatment with the S-layer protein increases the Mx1, Isg15, and Ddx58 mRNA expressions, and remits the inflammatory process to inhibit H9N2 AIV infection. In conclusion, the S-layer protein stimulates the activation of mouse DCs, inhibits H9N2 virus invasion of DCs, and stimulates the IFN-I signaling pathway. Thus, the S-layer protein from Lactobacillus is a promising biological antiviral material for AIV prevention.
The Fundamental Characteristics and Unique Outcomes of Christian Summer Camp Experiences

Very little research is available on the unique characteristics and outcomes of Christian summer camps, in spite of their prevalence in the industry. The Effective Camp Research Project is a mixed-methods study seeking to close the research gap. This article presents the major findings of the study, detailing the emergence of a distinct Christian camp model with five fundamental characteristics: relational, safe space, participatory, unplugged from home, and faith-centered. A multi-test survey of campers provides compelling evidence for outcomes that are immediate, subsequent, and lasting. Some of these outcomes are common to all camp types, though many are unique to the contextual realities of Christian camps that effectively partner with the ministries of churches and homes. Camper outcomes identified in other studies are interpreted theologically in the context of Christian camps, providing particular relevance to faith communities and people of faith.
Categorizing Gigabytes: Experiments on the RCV1 Corpus

: This paper presents categorization results performed by means of HITEC categorizer tool on the new benchmark document collection of text categorization, the Reuters Corpus Volume 1 (RCV1). RCV1 is an archive of over 800,000 manually categorized newswire stories made available by Reuters in 2000 for research purposes. This collection was released to take place of the Reuters-21578 collection that has been used widespread in the text retrieval community. This paper inted to add some interesting result to the characterization of RCV1 and HITEC categorizer.
Sensor networks with mobile access: optimal random access and coding

We consider random access and coding schemes for sensor networks with mobile access (SENMA). Using an orthogonal code-division multiple access (CDMA) as the physical layer, an opportunistic ALOHA (O-ALOHA) protocol that utilizes channel state information is proposed. Under the packet capture model and using the asymptotic throughput as the performance metric, we show that O-ALOHA approaches the throughput equal to the spreading gain with an arbitrarily small power at each sensor. This result implies that O-ALOHA is close to the optimal centralized scheduling scheme for the orthogonal CDMA networks. When side information such as location is available, the transmission control is modified to incorporate either the distribution or the actual realization of the side information. Convergence of the throughput with respect to the size of the network is analyzed. For networks allowing sensor collaborations, we combine coding with random access by proposing two coded random access schemes: spreading code dependent and independent transmissions. In the low rate regime, the spreading code independent transmission has a larger random coding exponent (therefore, faster decay of error probability) than that of the spreading code dependent transmission. On the other hand, the spreading code dependent transmission gives higher achievable rate.
Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
Discovering the phase of a dynamical system from a stream of partial observations with a multi-map self-organizing architecture

—This paper presents a self-organizing architecture made of several maps, implementing a recurrent neural network to cope with partial observations of the phase of some dynamical system. The purpose of self-organization is to set up a distributed representation of the actual phase, although the observations received from the system are ambiguous (i.e. the same observation may correspond to distinct phases). The setting up of such a representation is illustrated by experiments, and then the paper concludes on extensions toward adaptive state representations for partially observable Markovian decision processes.
Interactive Grammar Repair

In order to make natural language understanding (NLU) systems truly useful, mechanisms must be provided to allow the end-user to recover from the limitations of the system, in particular, from the lack of grammar coverage. We are currently investigating methods of interactively extending semantic grammars through a variety of unsupervised learning methods, coupled with selected interactions with the end-user. In this paper we describe Gsg, an empathic computer system for the rapid deployment of NLU modules and their dynamic customization by non-expert end-users, and we explore some of the research questions that arise in the process of building it.
Quantifying left ventricular trabeculae function – application of image-based fractal analysis

The ventricular‐blood interface is geometrically complex due to the presence of ventricular trabeculae carneae (VTC). We introduce a new image‐based framework to quantify VTC function using high‐resolution computed tomography (CT) imaging and offer new insights into the active role of VTCs during ejection. High‐resolution Cine CT scans of a patient with normal cardiac function were acquired at a resolution of 0.77 mm per pixel at 10 phases of the cardiac cycle. The images were segmented and the VTC surface was obtained by triangulating the segmented data. Fractal dimension of the VTC surface was calculated for each cardiac phase as a function of scale size using the box‐counting algorithm. The fractal dimension, D corresponding to VTCs ranged between 2.05 and 2.2 and varied as a function of time during the cardiac cycle. Fractal dimension is highest at diastole and lowest at peak systole with the change being significantly different (P < 0.003). This variation of D when plotted against stroke volume (i.e., D‐V loop) revealed an active VTC role due to hysteresis in the loop. Physically the hysteresis in the D‐V loop indicates a new mechanical function of VTCs as structures that provide mechanical leverage during early systolic ejection through contraction. VTC relaxation is noted to occur during late diastole at larger ventricular volume. D‐V loop of VTCs quantifies VTC function. A new dynamic physical role of VTCs is suggested by way of mechanical leverage, as opposed to the traditionally accepted passive role.
Nebular Abundance Errors.

The errors inherent to the use of the standard "ionization correction factor" ("i_CF") method of calculating nebular conditions and relative abundances of H, He, N, O, Ne, S, and Ar in emission line nebulae have been investigated under conditions typical for planetary nebulae. The photoionization code CLOUDY was used to construct a series of model nebulae with properties spanning the range typical of PNe. Its radial "profiles" of bright, frequently observed optical emission lines were then summed over a variety of "apertures" to generate sets of emission line measurements. These resulting line ratios were processed using the i_CF method to "derive" nebular conditions and abundances. We find that for lines which are summed over the entire nebula the i_CF-derived abundances differ from the input abundances by less than 5% for He and O up to 25% or more for Ne, S, and Ar. For resolved observations, however, the discrepancies are often much larger and are systematically variable with radius. This effect is especially pronounced in low-ionization zones where nitrogen and oxygen are neutral or once-ionized such as in FLIERs, ansae and ionization fronts. We argue that the reports of stellar-enriched N in the FLIERs of several PNe are probably specious.