Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Blind Areas in Information Spreading

Recently, contagion-based (disease, information, etc.) spreading on social networks has been extensively studied. In this paper, other than traditional full interaction, we propose a partial interaction based spreading model, considering that the informed individuals would transmit information to only a certain fraction of their neighbors due to the transmission ability in real-world social networks. Simulation results on three representative networks (BA, ER, WS) indicate that the spreading efficiency is highly correlated with the network heterogeneity. In addition, a special phenomenon, namely Information Blind Areas where the network is separated by several information-unreachable clusters, will emerge from the spreading process. Furthermore, we also find that the size distribution of such information blind areas obeys power-law-like distribution, which has very similar exponent with that of site percolation. Detailed analyses show that the critical value is decreasing along with the network heterogeneity for the spreading process, which is complete the contrary to that of random selection. Moreover, the critical value in the latter process is also larger than that of the former for the same network. Those findings might shed some lights in in-depth understanding the effect of network properties on information spreading.
Examination of the validity of the atlas-informed approach to functional parcellation: a resting functional MRI study

With the advancement in MRI, functional parcellation (FP) of brain structure(s) has become an important topic. However, the large number of voxels is a major obstacle. A-priori partitioning of the brain into several regions of interest (ROIs) is the main data-reduction strategy to simplify brain informatics. This study aims to examine the validity of ROI-based approach to FP by exploring the concordance of the relative distance structures between voxel-wise (raw data) and atlas-informed analyses. Structural and resting state functional MRI (rfMRI) scans of 26 right-handed healthy individuals were selected from the Rockland dataset. Four target regions were included in the analyses, that is, left and right thalamus and amygdala. For each voxel in the target region, four classes of correlation maps (sampling strategies) were constructed from the rfMRI: whole brain, cortex, 150 ROIs, and 70 ROIs (ROIs are informed by anatomical atlases). The relative distance metric between two different voxels was defined as the mean absolute difference of their associated correlation maps. Considering all the possible pairs of voxels in a target region, the relative distance structure was derived and stored in a matrix (distance map). For every target region, the distance maps were very similar across the four classes of sampling strategies, with the grand mean correlation coefficient reaching 0.95. The results confirm the validity of previous ROI-based analyses of rfMRI data in FP. The rationale and limitation are discussed and an analytic strategy of whole-brain FP is proposed.
Ionotropic and Metabotropic Mechanisms of Allosteric Modulation of α7 Nicotinic Receptor Intracellular Calcium

The pharmacological targeting of the α7 nicotinic acetylcholine receptor (α7) is a promising strategy in the development of new drugs for neurologic diseases. Because α7 receptors regulate cellular calcium, we investigated how the prototypical type II–positive allosteric modulator PNU120596 affects α7-mediated calcium signaling. Live imaging experiments show that PNU120596 augments ryanodine receptor-driven calcium-induced calcium release (CICR), inositol-induced calcium release (IICR), and phospholipase C activation by the α7 receptor. Both influx of calcium through the α7 nicotinic acetylcholine receptor (nAChR) channel as well as the binding of intracellular G proteins were involved in the effect of PNU120596 on intracellular calcium. This is evidenced by the findings that chelation of extracellular calcium, expression of α7D44A or α7345–348A mutant subunits, or blockade of calcium store release compromised the ability of PNU120596 to increase intracellular calcium transients generated by α7 ligand activation. Spatiotemporal stochastic modeling of calcium transient responses corroborates these results and indicates that α7 receptor activation enables calcium microdomains locally and to lesser extent in the distant cytosol. From the model, allosteric modulation of the receptor activates CICR locally via ryanodine receptors and augments IICR through enhanced calcium influx due to prolonged α7 nAChR opening. These findings provide a new mechanistic framework for understanding the effect of α7 receptor allosteric modulation on both local and global calcium dynamics.
A novel method for assessing the severity of levodopa-induced dyskinesia using wearable sensors

Patients with Parkinson's disease often experience significant changes in the severity of dyskinesia when they undergo titration of their medications. Dyskinesia is marked by involuntary jerking movements that occur randomly in a burst-like fashion. The burst-like nature of such movements makes it difficult to estimate the clinical scores of severity of dyskinesia using wearable sensors. Clinical observations are generally made over intervals of 15-30 s. On the other hand, techniques designed to estimate the severity of dyskinesia based on the analysis of wearable sensor data typically use data segments of approximately 5 s. Consequently, some data segments might include dyskinetic movements, whereas others might not. Herein, we propose a novel method suitable to automatically select data segments from the training dataset that are marked by dyskinetic movements. The proposed method also aggregates results derived from the testing dataset using a machine learning algorithm to estimate the severity of dyskinesia from wearable sensor data. Results obtained from the analysis of sensor data collected from seven subjects with Parkinson's disease showed a marked improvement in the accuracy of the estimation of clinical scores of dyskinesia.
A Meta-Analysis of Multiple Matched Copy Number and Transcriptomics Data Sets for Inferring Gene Regulatory Relationships

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
Is the environment in kindergarten associated with the vegetables served and eaten? The BRA Study

Aim: The aim of the present study was to explore the associations between the economic, political, sociocultural and physical environments in kindergartens, along with the frequency and variety of vegetables served, and the amount of vegetables eaten. Method: The BRA Study collected data through two paper-based questionnaires answered by the kindergarten leader and pedagogical leader of each selected kindergarten, and a five-day vegetable diary from kindergartens (n = 73) in Vestfold and Buskerud Counties, Norway. The questionnaires assessed environmental factors, and the frequency and variety of vegetables served. The non-parametric Mann–Whitney U and Kruskal–Wallis tests were used to explore the associations between factors in the kindergarten environments and vegetables served and eaten. Results: Kindergartens that included expenditures for food and beverages in the parental fees served a larger variety of vegetables (p = 0.046). A higher frequency of served vegetables (p = 0.014) and a larger amount (p = 0.027) of vegetables eaten were found in kindergartens where parents paid a monthly fee of 251 NOK or more. Similarly, the amount of vegetables eaten was higher (p = 0.017) in kindergartens where the employees paid a monthly fee to eat at work. Furthermore, a larger amount (p = 0.046) of vegetables was eaten in kindergartens that had written guidelines for food and beverages that were offered. Conclusions: This study indicates that the economic environment in a kindergarten seems to be positively associated with the vegetables served and eaten there. This is of high relevance for public health policy as vegetable consumption is an important factor in reducing the risk of non-communicable diseases.
Motor Imagery Shapes Abstract Concepts

The concepts of "good" and "bad" are associated with right and left space. Individuals tend to associate good things with the side of their dominant hand, where they experience greater motor fluency, and bad things with their nondominant side. This mapping has been shown to be flexible: Changing the relative fluency of the hands, or even observing a change in someone else's motor fluency, results in a reversal of the conceptual mapping, such that good things become associated with the side of the nondominant hand. Yet, based on prior studies, it is unclear whether space-valence associations were determined by the experience of fluent versus disfluent actions, or by the mere expectation of fluency. Here, we tested the role of expected fluency by removing motor execution and perceptual feedback altogether. Participants were asked to imagine themselves performing a psychomotor task with one of their hands impaired, after which their implicit space-valence mapping was measured. After imagining that their right hand was impaired, right-handed participants showed the "good is left" association typical of left-handers. Motor imagery can change people's implicit associations between space and emotional valence. Although asymmetric motor experience may be necessary to establish body-specific associations between space and valence initially, neither motoric nor perceptual experience is needed to change these associations subsequently. The mere expectation of fluent versus disfluenct actions can drive fluency-based effects on people's implicit spatialization of "good" and "bad. " These results suggest a reconsideration of the mechanisms and boundary conditions of fluency effects.
Excess Success for Psychology Articles in the Journal Science

This article describes a systematic analysis of the relationship between empirical data and theoretical conclusions for a set of experimental psychology articles published in the journal Science between 2005–2012. When the success rate of a set of empirical studies is much higher than would be expected relative to the experiments' reported effects and sample sizes, it suggests that null findings have been suppressed, that the experiments or analyses were inappropriate, or that the theory does not properly follow from the data. The analyses herein indicate such excess success for 83% (15 out of 18) of the articles in Science that report four or more studies and contain sufficient information for the analysis. This result suggests a systematic pattern of excess success among psychology articles in the journal Science.
Transient Oral Human Cytomegalovirus Infections Indicate Inefficient Viral Spread from Very Few Initially Infected Cells

ABSTRACT Cytomegalovirus (CMV) is acquired by the oral route in children, and primary infection is associated with abundant mucosal replication, as well as the establishment of latency in myeloid cells that results in lifelong infection. The efficiency of primary CMV infection in humans following oral exposure, however, is unknown. We consistently detected self-limited, low-level oral CMV shedding events, which we termed transient CMV infections, in a prospective birth cohort of 30 highly exposed CMV-uninfected infants. We estimated the likelihood of transient oral CMV infections by comparing their observed frequency to that of established primary infections, characterized by persistent high-level shedding, viremia, and seroconversion. We developed mathematical models of viral dynamics upon initial oral CMV infection and validated them using clinical shedding data. Transient infections comprised 76 to 88% of oral CMV shedding events. For this high percentage of transient infections to occur, we identified two mathematical prerequisites: a very small number of initially infected oral cells (1 to 4) and low viral infectivity (<1.5 new cells infected/cell). These observations indicate that oral CMV infection in infants typically begins with a single virus that spreads inefficiently to neighboring cells. Thus, although the incidence of CMV infection is high during infancy, our data provide a mechanistic framework to explain why multiple CMV exposures are typically required before infection is successfully established. These findings imply that a sufficiently primed immune response could prevent CMV from establishing latent infection in humans and support the achievability of a prophylactic CMV vaccine. IMPORTANCE CMV infects the majority of the world's population and is a major cause of birth defects. Developing a vaccine to prevent CMV infection would be extremely valuable but would be facilitated by a better understanding of how natural human CMV infection is acquired. We studied CMV acquisition in infants and found that infections are usually brief and self-limited and are successfully established relatively rarely. Thus, although most people eventually acquire CMV infection, it usually requires numerous exposures. Our analyses indicate that this is because the virus is surprisingly inefficient, barely replicating well enough to spread to neighboring cells in the mouth. Greater knowledge of why CMV infection usually fails may provide insight into how to prevent it from succeeding.
Development of cell-specific and organelle-specific delivery systems by surface modification of lipid-based pharmaceutical nanocarriers

Objective The use of lipid-based pharmaceutical nanocarriers, such as lipid-core polymeric micelles and liposomes have improved the pharmacokinetic and pharmacodynamic properties of many pharmaceuticals, especially in chemotherapy. These delivery systems have not only helped in increasing the solubility of poorly soluble chemotherapeutic drugs but have also acted as reservoir of large molecular weight active pharmaceutical ingredients (API) like proteins. The objective of the thesis was to explore surface modification options to further enhance the delivery of pro-apoptotic small molecules for cell-specific delivery and proteins for intracellular delivery. The thesis has been divided into two sections. Section a The purpose of this study was to enhance the delivery of new pro-apoptotic small molecule, N-{[(2-hydroxy-5-nitrophenyl)amino]carbonothioyl}-3,5-dimethylbenzamide (DM-PIT-1), which is the non-lipid antagonist of phopshatidylinositol-3.4. 5-triphopshate and inhibitor of the PI3-kinase pathway. Micelle-forming PEG2000-PE was used to solubilize DM-PIT-1, which has an aqueous solubility of 30 uM. To further improve the delivery of the micellar DM-PIT-1, cancer-targeting anti-nucleosomal mAb2C5 antibodies and/or Tumor necrosis factor-Related Apoptosis Inducing Ligand (TRAIL) were attached to the surface of polymeric micelles. Methods. Plain micelles and surface-modified micelles (mAb2C5 and TRAIL) loaded with DMPIT-1 were prepared and characterized by dynamic light scattering. Drug Abstract
Tyrosine phosphorylation switching of a G protein

Heterotrimeric G protein complexes are molecular switches relaying extracellular signals sensed by G protein–coupled receptors (GPCRs) to downstream targets in the cytoplasm, which effect cellular responses. In the plant heterotrimeric GTPase cycle, GTP hydrolysis, rather than nucleotide exchange, is the rate-limiting reaction and is accelerated by a receptor-like regulator of G signaling (RGS) protein. We hypothesized that posttranslational modification of the Gα subunit in the G protein complex regulates the RGS-dependent GTPase cycle. Our structural analyses identified an invariant phosphorylated tyrosine residue (Tyr166 in the Arabidopsis Gα subunit AtGPA1) located in the intramolecular domain interface where nucleotide binding and hydrolysis occur. We also identified a receptor-like kinase that phosphorylates AtGPA1 in a Tyr166-dependent manner. Discrete molecular dynamics simulations predicted that phosphorylated Tyr166 forms a salt bridge in this interface and potentially affects the RGS protein–accelerated GTPase cycle. Using a Tyr166 phosphomimetic substitution, we found that the cognate RGS protein binds more tightly to the GDP-bound Gα substrate, consequently reducing its ability to accelerate GTPase activity. In conclusion, we propose that phosphorylation of Tyr166 in AtGPA1 changes the binding pattern with AtRGS1 and thereby attenuates the steady-state rate of the GTPase cycle. We coin this newly identified mechanism “substrate phosphoswitching. ”
Epidemiology, Risk Factors and Genotypes of HBV in HIV-Infected Patients in the Northeast Region of Colombia: High Prevalence of Occult Hepatitis B and F3 Subgenotype Dominance

Introduction Chronic hepatitis B virus (HBV) infection is an increasing cause of morbidity and mortality in human immunodeficiency virus (HIV)-infected individuals. HIV-positive patients are commonly co-infected with HBV due to shared routes of transmission. Objectives Our aim was to determine the risk factors, prevalence, genotypes, and mutations of the Surface S gene of HBV, and occult hepatitis B infection (OBI) among patients infected with HIV in a northeastern Colombian city. Methods A cross-sectional study was conducted with 275 HIV-positive patients attending an outpatient clinic in Bucaramanga, Colombia during 2009–2010. Blood samples were collected and screened for serological markers of HBV (anti-HBs, anti-HBc and HBsAg) through ELISA assay. Regardless of their serological profile, all samples were tested for the HBV S gene by nested-PCR and HBV genotypes were determined by phylogenetic inference. Clinical records were used to examine demographic, clinical, virological, immunological and antiretroviral therapy (ART) variables of HIV infection. Results Participants were on average 37±11 years old and 65.1% male. The prevalence of HIV-HBV coinfection was 12% (95%CI 8.4–16.4) of which 3.3% had active HBV infection and 8.7% OBI. The prevalence of HIV-HBV coinfection was associated with AIDS stage and ART treatment. Sequence analysis identified genotype F, subgenotype F3 in 93.8% of patients and genotype A in 6.2% of patients. A C149R mutation, which may have resulted from failure in HBsAg detection, was found in one patient with OBI. Conclusions The present study found a high prevalence of HIV-HBV coinfection with an incidence of OBI 2.6-fold higher compared to active HBV infection. These findings suggest including HBV DNA testing to detect OBI in addition to screening for HBV serological markers in HIV patients.
Hydration kinetics of fly ash-portland cement paste with low water to cementitious powder ratio

Fly ash is widely used as a supplementary cementitious material in high performance concrete because of its benefits in enhancing both fresh and long-term concrete properties and as it promotes eco-friendly construction. In the past, many investigations have been carried out mainly to elucidate the pozzolanic reaction of fly ash and its effect on the microstructure of the fly ash-cement paste. Although the effect of fly ash on hydration has been established experimentally, the quantitative influence of fly ash on the kinetics of cement hydration is not well understood. In particular, for modern high-performance concretes with low w/b ratios, the effect of the fly ash on the cement hydration may be different. To predict the performance of fly ash concrete accurately throughout its service life, a more quantitative understanding of the effect of fly ash on cement hydration in low w/b ratio cementitious mixtures is needed.
CD8 and CD4 Epitope Predictions in RV144: No Strong Evidence of a T-Cell Driven Sieve Effect in HIV-1 Breakthrough Sequences from Trial Participants

The modest protection afforded by the RV144 vaccine offers an opportunity to evaluate its mechanisms of protection. Differences between HIV-1 breakthrough viruses from vaccine and placebo recipients can be attributed to the RV144 vaccine as this was a randomized and double-blinded trial. CD8 and CD4 T cell epitope repertoires were predicted in HIV-1 proteomes from 110 RV144 participants. Predicted Gag epitope repertoires were smaller in vaccine than in placebo recipients (p = 0.019). After comparing participant-derived epitopes to corresponding epitopes in the RV144 vaccine, the proportion of epitopes that could be matched differed depending on the protein conservation (only 36% of epitopes in Env vs 84–91% in Gag/Pol/Nef for CD8 predicted epitopes) or on vaccine insert subtype (55% against CRF01_AE vs 7% against subtype B). To compare predicted epitopes to the vaccine, we analyzed predicted binding affinity and evolutionary distance measurements. Comparisons between the vaccine and placebo arm did not reveal robust evidence for a T cell driven sieve effect, although some differences were noted in Env-V2 (0.022≤p-value≤0.231). The paucity of CD8 T cell responses identified following RV144 vaccination, with no evidence for V2 specificity, considered together both with the association of decreased infection risk in RV 144 participants with V-specific antibody responses and a V2 sieve effect, lead us to hypothesize that this sieve effect was not T cell specific. Overall, our results did not reveal a strong differential impact of vaccine-induced T cell responses among breakthrough infections in RV144 participants.
Optimal Relay Selection for Secure Cooperative Communications With an Adaptive Eavesdropper

Optimal relay selection is investigated for secure cooperative communications against an adaptive eavesdropper that can perform eavesdropping if the eavesdropping link has good channel quality or perform jamming otherwise. A number of decode-and-forward relays are available for legitimate communications, among which one relay can be selected to help. For legitimate communications, three cases for availability of the eavesdropping channel information are considered: full channel knowledge, partial channel knowledge, and statistical channel knowledge. An optimal relay selection scheme is proposed for each case. For the first and third cases, exact secrecy outage probability expressions in closed form are derived, and for the second case, an approximate secrecy outage probability is derived, which is tight in the high main-to-eavesdropper ratio regime. Moreover, secrecy diversity order for the proposed relay selection scheme in each case is also derived, which is shown to be a full secrecy diversity. Finally, numerical results are given to verify the theoretical analysis derived in this paper.