Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of Trem2 Variant Associated with Triple Risk of Alzheimer’s Disease

Alzheimer’s disease is one of the main causes of dementia among elderly individuals and leads to the neurodegeneration of different areas of the brain, resulting in memory impairments and loss of cognitive functions. Recently, a rare variant that is associated with 3-fold higher risk of Alzheimer’s disease onset has been found. The rare variant discovered is a missense mutation in the loop region of exon 2 of Trem2 (rs75932628-T, Arg47His). The aim of this study was to investigate the evidence for potential structural and functional significance of Trem2 gene variant (Arg47His) through molecular dynamics simulations. Our results showed the alteration caused due to the variant in TREM2 protein has significant effect on the ligand binding affinity as well as structural configuration. Based on molecular dynamics (MD) simulation under salvation, the results confirmed that native form of the variant (Arg47His) might be responsible for improved compactness, hence thereby improved protein folding. Protein simulation was carried out at different temperatures. At 300K, the deviation of the theoretical model of TREM2 protein increased from 2.0 Å at 10 ns. In contrast, the deviation of the Arg47His mutation was maintained at 1.2 Å until the end of the simulation (t = 10 ns), which indicated that Arg47His had reached its folded state. The mutant residue was a highly conserved region and was similar to “immunoglobulin V-set” and “immunoglobulin-like folds”. Taken together, the result from this study provides a biophysical insight on how the studied variant could contribute to the genetic susceptibility to Alzheimer’s disease.
Role of mTOR, Bad, and Survivin in RasGAP Fragment N-Mediated Cell Protection

Partial cleavage of p120 RasGAP by caspase-3 in stressed cells generates an N-terminal fragment, called fragment N, which activates an anti-apoptotic Akt-dependent survival response. Akt regulates several effectors but which of these mediate fragment N-dependent cell protection has not been defined yet. Here we have investigated the role of mTORC1, Bad, and survivin in the capacity of fragment N to protect cells from apoptosis. Neither rapamycin, an inhibitor of mTORC1, nor silencing of raptor, a subunit of the mTORC1 complex, altered the ability of fragment N from inhibiting cisplatin- and Fas ligand-induced death. Cells lacking Bad, despite displaying a stronger resistance to apoptosis, were still protected by fragment N against cisplatin-induced death. Fragment N was also able to protect cells from Fas ligand-induced death in conditions where Bad plays no role in apoptosis regulation. Fragment N expression in cells did neither modulate survivin mRNA nor its protein expression. Moreover, the expression of cytoplasmic survivin, known to exert anti-apoptotic actions in cells, still occurred in UV-B-irradiated epidermis of mouse expressing a caspase-3-resistant RasGAP mutant that cannot produce fragment N. Additionally, survivin function in cell cycle progression was not affected by fragment N. These results indicate that, taken individually, mTOR, Bad, or Survivin are not required for fragment N to protect cells from cell death. We conclude that downstream targets of Akt other than mTORC1, Bad, or survivin mediate fragment N-induced protection or that several Akt effectors can compensate for each other to induce the pro-survival fragment N-dependent response.
Efficiency Analysis of Magnetic Resonance Wireless Power Transfer With Intermediate Resonant Coil

This letter presents an efficiency analysis of a magnetic resonance wireless power transfer (WPT) system with an intermediate resonant coil. A helical coil and a spiral coil with an additional capacitor are considered as resonant coils for the WPT system. The intermediate resonant coil is set up coaxially and perpendicular to both the Tx and Rx resonant coils in order to observe the efficiency change according to the directions. The power efficiency is calculated using the temporal coupled mode theory (CMT). Impedance matching conditions are also shown by using the CMT. Analysis results show that using an intermediate coil properly improves efficiency and extends the distance between the transmitter and receiver. Both calculated and measured efficiencies are in good agreement. It is also shown that the intermediate resonant system has a good efficiency and is superior to nonintermediate systems.
Melding structured abstracts and World Wide Web for retrieval of reusable components

Reusable Software Libraries (RSLs) often suffer from poor interfaces, too many formal standards, high levels of training required for their use, and most of all, a high cost to build and maintain. Hence, RSLs have largely failed to return the reuse benefits promised by their developers. This paper first describes an RSL implementation using the World Wide Web (WWW) browser Mosaic and shows how it meets most RSL needs, avoids most RSL pitfalls, and costs only a fraction of the cost for the average commercial RSL. Second, the paper describes a way to quickly assess the important aspects of a piece of software so programmers can decide whether or not to reuse it. Using the observation that when programmers discuss software they tend to convey the same key information in a somewhat predictable order, this paper describes a method to automatically mimic this activity using a Structured Abstract of reusable components. Structured Abstracts provide a natural, easy to use way for developers to (1) search for components, (2) quickly assess the component for use, and (3) submit components to the RSL.
Effects of the Emotion System on Adaptive Behavior

A central simplifying assumption in evolutionary behavioral ecology has been that optimal behavior is unaffected by genetic or proximate constraints. Observations and experiments show otherwise, so that attention to decision architecture and mechanisms is needed. In psychology, the proximate constraints on decision making and the processes from perception to behavior are collectively described as the emotion system. We specify a model of the emotion system in fish that includes sensory input, neuronal computation, developmental modulation, and a global organismic state and restricts attention during decision making for behavioral outcomes. The model further includes food competition, safety in numbers, and a fluctuating environment. We find that emergent strategies in evolved populations include common emotional appraisal of sensory input related to fear and hunger and also include frequency-dependent rules for behavioral responses. Focused attention is at times more important than spatial behavior for growth and survival. Spatial segregation of the population is driven by personality differences. By coupling proximate and immediate influences on behavior with ultimate fitness consequences through the emotion system, this approach contributes to a unified perspective on the phenotype, by integrating effects of the environment, genetics, development, physiology, behavior, life history, and evolution.
Content differences between print and online newspapers

iv Chapter 1: Introduction 1 Chapter 2: Literature Review 7 Gatekeeping 7 Broadening definitions 13 Framing 14 Television gatekeeping 15 Online gatekeeping 16 Trends in online newspapers 20 Shovelware 21 Interactivity and multimedia use 22 Local news online 25 Chapter 3: Method 29 Chapter 4: Results 36 Chapter 5: Conclusion 46 Limitations 49 Future research 51 References 54 Appendices 65 ii Appendix A: Print and online sample articles 66 Appendix B: Coding sheet 84 Appendix C: Coding instructions 85
Democratization: A Comparative Analysis of 170 Countries

1. Introduction: Debate on the Causes of Democratization 2. Resource Distribution Theory of Democratization 3. Measures of Democracy 4. Explanatory Variables 5. A review of Democratization 6. Correlation Analysis 7. Regression Analysis 8. Analysis of Single Countries 9. Conclusions
Case-based reasoning in 2 comparative effectiveness

3 research M. Markatou P. Kuruppumullage Don J. Hu F. Wang J. Sun R. Sorrentino S. Ebadollahi 4 A medical case, as defined by the medical field, is the fundamental 5 building block of medical knowledge. We combine the concept of 6 medical case with indirect evidence from similar patients so as to 7 enable the performance of CER (comparative effectiveness research) 8 treatment comparisons for personalization of medical care. We 9 propose that the vehicle by which this goal is achieved is provided 10 by the integration of case-based reasoning and CER considerations. 11 We discuss the challenges involved and propose a roadmap for 12 creating scientifically sound real-world evidence for assisting 13 personalized treatment decisions.
A multi sensor system to evaluate driving behavior in curves

Road constructions are supposed to have a direct effect on drivers behavior and thus on road safety. For example, the alignment will affect whether a curve is likely cut or not. This paper proposes a method which allows to record and to evaluate the driving behavior of road users with a little interactive effort. This is made possible by, first, an easy to install and nearly invisible multi sensor hardware to record data, and, second, as well an easy to use analysis program for offline analysis of the data.
DISCRETE WAVELET TRANSFORM BASED SPECTRUM SENSING IN COGNITIVE RADIOS USING EIGEN FILTER

In the developing world, the usage of Mobile phones and other data communication devices are unavoidable which results in the congestion of Spectrum. Recent studies have showed that nearly 70% of spectrum was unused most of the time. The band width becomes expensive due to shortage of frequencies. Therefore to use the spectrum effectively, we need to identify whether the spectrum is occupied or not. Cognitive Radio is a technology which helps us to use the spectrum effectively. Spectrum Sensing is one of the techniques in cognitive radio. Energy detection, Feature detection and Matched Filter detection are methods used for spectrum sensing. In the proposed method, Discrete Wavelet Transform (DWT) is used to identify the unused spectrum band in the RF spectrum. This will yield better results and fast sensing than the conventional method. Moreover, Eigen filter is used in the filter banks of wavelet to give high resolution outputs.
Social Deprivation, Inequality, and the Neighborhood-Level Incidence of Psychotic Syndromes in East London

Although urban birth, upbringing, and living are associated with increased risk of nonaffective psychotic disorders, few studies have used appropriate multilevel techniques accounting for spatial dependency in risk to investigate social, economic, or physical determinants of psychosis incidence. We adopted Bayesian hierarchical modeling to investigate the sociospatial distribution of psychosis risk in East London for DSM-IV nonaffective and affective psychotic disorders, ascertained over a 2-year period in the East London first-episode psychosis study. We included individual and environmental data on 427 subjects experiencing first-episode psychosis to estimate the incidence of disorder across 56 neighborhoods, having standardized for age, sex, ethnicity, and socioeconomic status. A Bayesian model that included spatially structured neighborhood-level random effects identified substantial unexplained variation in nonaffective psychosis risk after controlling for individual-level factors. This variation was independently associated with greater levels of neighborhood income inequality (SD increase in inequality: Bayesian relative risks [RR]: 1.25; 95% CI: 1.04–1.49), absolute deprivation (RR: 1.28; 95% CI: 1.08–1.51) and population density (RR: 1.18; 95% CI: 1.00–1.41). Neighborhood ethnic composition effects were associated with incidence of nonaffective psychosis for people of black Caribbean and black African origin. No variation in the spatial distribution of the affective psychoses was identified, consistent with the possibility of differing etiological origins of affective and nonaffective psychoses. Our data suggest that both absolute and relative measures of neighborhood social composition are associated with the incidence of nonaffective psychosis. We suggest these associations are consistent with a role for social stressors in psychosis risk, particularly when people live in more unequal communities.
Vesicle trafficking from a lipid perspective

The protein cargo transported by specific types of vesicles largely defines the different secretory trafficking pathways operating within cells. However, mole per mole the most abundant cargo contained within transport vesicles is not protein, but lipid. Taking a “lipid-centric” point-of-view, we examine the importance of lipid signaling, membrane lipid organization and lipid metabolism for vesicle transport during exocytosis in budding yeast. In fact, the essential requirement for some exocytosis regulatory proteins can be bypassed by making simple manipulations of the lipids involved. During polarized exocytosis the sequential steps required to generate post-Golgi vesicles and target them to the plasma membrane (PM) involves the interplay of several types of lipids that are coordinately linked through PI4P metabolism and signaling. In turn, PI4P levels are regulated by PI4P kinases, the Sac1p PI4P phosphatase and the yeast Osh proteins, which are homologs of mammalian oxysterol-binding protein (OSBP). Together these regulators integrate the transitional steps required for vesicle maturation directly through changes in lipid composition and organization.
Parallel Algorithms for Finding Cycles and Cutsets of Graphs

We rst present VLSI algorithms that run in O(n 2) steps for nding (and reporting) a fundamental set of cycles and a fundamental set of cutsets of an undirected graph on an nxn mesh of processors (SIMD). Both algorithms are decomposable and run in O(n 4 =k 2) steps for a graph with n vertices when the size of the mesh-connected computer is kxk and k < n. An idea similar to the one used in nding a fundamental set of cycles of an undirected graph yields an O(n 2) algorithm for generating shortest paths between all pairs of vertices of a graph on the same model. Then, we present a new and elegant cycle vector space algorithm that runs in O(n 2) steps and needs O(n) space for enumerating all the cycles of a planar graph with n vertices, where is the total number of simple cycles in the graph. Unlike backtrack algorithms, cycle vector space algorithms for this problem are suitable for parallelization. A parallel version of this algorithm along with a parallel version of Syslo's O(n) step algorithm for the same problem are given on an exclusive-read, exclusive-write parallel RAM model with p processors. The results of an implementation of our parallel algorithm on a mesh-connected SIMD computer are also presented.
Pesquisa Um guia básico e amplo sobre os diversos aspectos dessa nova ciência Bioinformática : Manual do Usuário

Do início até meados do século passado os geneticistas e químicos se questionaram sobre a natureza química domaterial genético. Das pesquisas desenvolvidas, surgiu a conclusãodeque o DNA era a molécula que armazenava a informação genética e, em 1953, sua estrutura química foi desvendada no clássico trabalho de Watson e Crick. Com a posterior descoberta do código genético e do fluxo da informação biológica, dos ácidos nucléicos para as proteínas, tais polímeros passarama constituir os principais objetos de estudo de uma nova ciência, a BiologiaMolecular. Logo surgirammétodos de seqüenciamentodesses polímeros, principalmente do DNA, que permitiam a investigação de suas seqüênciasmonoméricas constituintes.Desde então, mais de 18 bilhões dessas seqüências já foramproduzidas e estão disponíveis nos bancos dedadospúblicos.
Epstein-Barr virus genome level, T-cell clonality and the prognosis of angioimmunoblastic T-cell lymphoma.

BACKGROUND AND OBJECTIVES Angioimmunoblastic T-cell lymphoma (AILT) is a peripheral T-cell tumor of unknown etiology with variable biological and clinical presentations. Previous clonality studies have shown heterogeneous clonal restrictions of B- and T-cell populations in this tumor. AILT is characterized by the presence of increased numbers of Epstein-Barr virus (EBV) infected cells. The aim of this study was to clarify the correlation between clonality, EBV and prognosis. DESIGN AND METHODS Frozen material from 59 cases of AILT was used for DNA isolation and gene analysis by Southern blotting. A real-time polymerase chain reaction was used to quantify the amount of EBV-DNA in the tissue. Survival data were retrieved from clinical records. RESULTS Clonal T cells were found in 15/50 and clonal B-cells in 2/50 tumors, using Southern blot analysis. Bands of EBV-W were found in 10/50 tumors. Survival rate did not correlate with either T-cell clonality (p=0.84), or presence of EBV-infected cells (p=0.84). The EBV-DNA copy number in EBV-infected tissue did not correlate with disease progression (p=0.87). The survival rate and clinical status according to the international prognostic index (IPI) did not correlate with T-cell clonality status or EBV infection. INTERPRETATION AND CONCLUSIONS AILT remains a heterogeneous disease with clinical behavior that varies irrespective of the genomic parameters investigated.
Regional Distribution of Angiotensinogen in the Central Nervous System of the Rat: Effect of DOC-Salt Treatment

1. The distribution of angiotensinogen and endogenous renin-like activity were analysed in different areas of the central nervous system in normal and DOC-salt-treated hypertensive rats. 2. Angiotensinogen concentration and renin-like activity were significantly increased in the cerebral cortex, cerebellum, hypothalamus and brain stem of the DOC-salt-treated rats 30 days after the initiation of the experiment. 3. Influence of plasma contamination on the former results was evaluated by the determination of (a) plasma angiotensinogen concentration in control and treated animals and (b) blood content remaining in the different regions of the central nervous system, after saline perfusion of the brain, in a group of normal rats. 4. Plasma angiotensinogen concentration was significantly decreased in DOC-salt-treated rats, therefore blood contamination would tend to diminish the magnitude of increase in central nervous system angiotensinogen in these animals. 5. Present results have shown an increased concentration of angiotensinogen in some areas of the central nervous system in DOC-salt-treated rats. The results have also confirmed an enhanced activity of the endogenous renin-like enzyme in the same regions; this change seems to be mainly due to the increment in angiotensinogen. Increased formation of central angiotensin could be involved in the development of DOC-salt hypertension. The biosynthetic pathways of renin substrate as well as its endogenous regulation remain undetermined.
Representation of Perceptual Color Space in Macaque Posterior Inferior Temporal Cortex (the V4 Complex)

Abstract The lateral geniculate nucleus is thought to represent color using two populations of cone-opponent neurons [L vs M; S vs (L + M)], which establish the cardinal directions in color space (reddish vs cyan; lavender vs lime). How is this representation transformed to bring about color perception? Prior work implicates populations of glob cells in posterior inferior temporal cortex (PIT; the V4 complex), but the correspondence between the neural representation of color in PIT/V4 complex and the organization of perceptual color space is unclear. We compared color-tuning data for populations of glob cells and interglob cells to predictions obtained using models that varied in the color-tuning narrowness of the cells, and the color preference distribution across the populations. Glob cells were best accounted for by simulated neurons that have nonlinear (narrow) tuning and, as a population, represent a color space designed to be perceptually uniform (CIELUV). Multidimensional scaling and representational similarity analyses showed that the color space representations in both glob and interglob populations were correlated with the organization of CIELUV space, but glob cells showed a stronger correlation. Hue could be classified invariant to luminance with high accuracy given glob responses and above-chance accuracy given interglob responses. Luminance could be read out invariant to changes in hue in both populations, but interglob cells tended to prefer stimuli having luminance contrast, regardless of hue, whereas glob cells typically retained hue tuning as luminance contrast was modulated. The combined luminance/hue sensitivity of glob cells is predicted for neurons that can distinguish two colors of the same hue at different luminance levels (orange/brown).
Investors’ ‘Fear’ and ‘Greed’ Index: A Case of India Volatility Index (IVIX)

The aim of the paper is to explore the Indian derivatives market and show that why options are most important for the risk management and volatility estimate. The study demonstrated that investor prefer more options than the futures in hedging strategies. The inverse relation between Nifty index and India VIX occurs due to options trading; during the market weakness when investors are concerned about the moves of Nifty index they seek protection during the market panic. The great concern and nervousness of the investor allows them to buy options aggressively, consequently the aggressive buying result into high implied volatility of the Nifty index options. The empirical result evidences that there is an asymmetric relation between volatility and stock returns.
Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress

ABSTRACT The growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. In this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of Bradyrhizobium japonicum to drought. Desiccation of cells resulted in the differential expression of 15 to 20% of the 8,480 B. japonicum open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed genes. While 225 genes were universally up-regulated at all three incubation times in response to desiccation, an additional 43 and 403 up-regulated genes were common to the 4/24- and 24/72-h incubation times, respectively. Desiccating conditions resulted in the significant induction (>2.0-fold) of the trehalose-6-phosphate synthetase (otsA), trehalose-6-phosphate phosphatase (otsB), and trehalose synthase (treS) genes, which encode two of the three trehalose synthesis pathways found in B. japonicum. Gene induction was correlated with an elevated intracellular concentration of trehalose and increased activity of trehalose-6-phosphate synthetase, collectively supporting the hypothesis that this disaccharide plays a prominent and important role in promoting desiccation tolerance in B. japonicum. Microarray data also indicated that σ54- and σ24-associated transcriptional regulators and genes encoding isocitrate lyase, oxidative stress responses, the synthesis and transport of exopolysaccharides, heat shock response proteins, enzymes for the modification and repair of nucleic acids, and the synthesis of pili and flagella are also involved in the response of B. japonicum to desiccation. Polyethylene glycol-generated osmotic stress induced significantly fewer genes than those transcriptionally activated by desiccation. However, 67 genes were commonly induced under both conditions. Taken together, these results suggest that B. japonicum directly responds to desiccation by adapting to changes imparted by reduced water activity, such as the synthesis of trehalose and polysaccharides and, secondarily, by the induction of a wide variety of proteins involved in protection of the cell membrane, repair of DNA damage, stability and integrity of proteins, and oxidative stress responses.