Miracle-dz/UniFAR-FTUs huggingface dataset:
Enlightenment of Yeast Mitochondrial Homoplasmy: Diversified Roles of Gene Conversion

Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within a cell (“homoplasmy”) during vegetative cell growth or through a few sexual generations. Heteroplasmy is strongly associated with mitochondrial diseases, diabetes and aging. Recent studies revealed that the yeast cell has the machinery to homogenize mtDNA, using a common DNA processing pathway with gene conversion; i.e., both genetic events are initiated by a double-stranded break, which is processed into 3′ single-stranded tails. One of the tails is base-paired with the complementary sequence of the recipient double-stranded DNA to form a D-loop (homologous pairing), in which repair DNA synthesis is initiated to restore the sequence lost by the breakage. Gene conversion generates sequence diversity, depending on the divergence between the donor and recipient sequences, especially when it occurs among a number of copies of a DNA sequence family with some sequence variations, such as in immunoglobulin diversification in chicken. MtDNA can be regarded as a sequence family, in which the members tend to be diversified by a high frequency of spontaneous mutagenesis. Thus, it would be interesting to determine why and how double-stranded breakage and D-loop formation induce sequence homogenization in mitochondria and sequence diversification in nuclear DNA. We will review the mechanisms and roles of mtDNA homoplasmy, in contrast to nuclear gene conversion, which diversifies gene and genome sequences, to provide clues toward understanding how the common DNA processing pathway results in such divergent outcomes.
Fumarates Promote Cytoprotection of Central Nervous System Cells against Oxidative Stress via the Nuclear Factor (Erythroid-Derived 2)-Like 2 Pathway

Oxidative stress is central to the pathology of several neurodegenerative diseases, including multiple sclerosis, and therapeutics designed to enhance antioxidant potential could have clinical value. The objective of this study was to characterize the potential direct neuroprotective effects of dimethyl fumarate (DMF) and its primary metabolite monomethyl fumarate (MMF) on cellular resistance to oxidative damage in primary cultures of central nervous system (CNS) cells and further explore the dependence and function of the nuclear factor (erythroid-derived 2)-like 2 (Nrf2) pathway in this process. Treatment of animals or primary cultures of CNS cells with DMF or MMF resulted in increased nuclear levels of active Nrf2, with subsequent up-regulation of canonical antioxidant target genes. DMF-dependent up-regulation of antioxidant genes in vivo was lost in mice lacking Nrf2 [Nrf2(−/−)]. DMF or MMF treatment increased cellular redox potential, glutathione, ATP levels, and mitochondrial membrane potential in a concentration-dependent manner. Treating astrocytes or neurons with DMF or MMF also significantly improved cell viability after toxic oxidative challenge in a concentration-dependent manner. This effect on viability was lost in cells that had eliminated or reduced Nrf2. These data suggest that DMF and MMF are cytoprotective for neurons and astrocytes against oxidative stress-induced cellular injury and loss, potentially via up-regulation of an Nrf2-dependent antioxidant response. These data also suggest DMF and MMF may function through improving mitochondrial function. The clinical utility of DMF in multiple sclerosis is being explored through phase III trials with BG-12, which is an oral therapeutic containing DMF as the active ingredient.
miRVaS: a tool to predict the impact of genetic variants on miRNAs

Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
A complete resolution of the Keller maximum clique problem

A d-dimensional Keller graph has vertices which are numbered with each of the 4d possible d-digit numbers (d-tuples) which have each digit equal to 0, 1, 2, or 3. Two vertices are adjacent if their labels differ in at least two positions, and in at least one position the difference in the labels is two modulo four. Keller graphs are in the benchmark set of clique problems from the DIMACS clique challenge, and they appear to be especially difficult for clique algorithms. The dimension seven case was the last remaining Keller graph for which the maximum clique order was not known. It has been claimed in order to resolve this last case it might take a "high speed computer the size of a major galaxy". This paper describes the computation we used to determine that the maximum clique order for dimension seven is 124.
Flexible Object Adaptation for Java-like Languages

To realize object adaptability with a clear conceptual framework, a role model Epsilon was proposed. The novelty of Epsilon model is its ability to change object’s behavior dynamically. However, such kind of flexibility also easily brings type-unsafety and other unreliabilities. This paper proposes a small core language that formalizes some key concepts of object adaptation, which is informally described in the Epsilon model. In , three kinds of objects, context instances, role instances, and class instances exist at run-time. A role instance is a member of a context instance where how role instances are collaborating with each other is encapsulated. A class instance can dynamically assume a role by binding itself with a role instance, and can also throw the role away. Their relationship can change during computation, and ’s type system assures that the computation does not go wrong, even though some exceptional cases concerning downcasting exist. This formalization clarifies the essential features of the object adaptation incorporated in Epsilon model and provides a solid base for program analysis and language processor implementation.
Psychometric Properties of the Procrastination Assessment Scale-Student (PASS) in a Student Sample of Sabzevar University of Medical Sciences

Background: Procrastination is a common behavior which affects different aspects of life. The procrastination assessment scale-student (PASS) evaluates academic procrastination apropos its frequency and reasons. Objectives: The aims of the present study were to translate, culturally adapt, and validate the Farsi version of the PASS in a sample of Iranian medical students. Patients and Methods: In this cross-sectional study, the PASS was translated into Farsi through the forward-backward method, and its content validity was thereafter assessed by a panel of 10 experts. The Farsi version of the PASS was subsequently distributed among 423 medical students. The internal reliability of the PASS was assessed using Cronbach’s alpha. An exploratory factor analysis (EFA) was conducted on 18 items and then 28 items of the scale to find new models. The construct validity of the scale was assessed using both EFA and confirmatory factor analysis. The predictive validity of the scale was evaluated by calculating the correlation between the academic procrastination scores and the students’ average scores in the previous semester. Results: The corresponding reliability of the first and second parts of the scale was 0.781 and 0.861. An EFA on 18 items of the scale found 4 factors which jointly explained 53.2% of variances: The model was marginally acceptable (root mean square error of approximation [RMSEA] =0.098, standardized root mean square residual [SRMR] =0.076, χ2 /df =4.8, comparative fit index [CFI] =0.83). An EFA on 28 items of the scale found 4 factors which altogether explained 42.62% of variances: The model was acceptable (RMSEA =0.07, SRMR =0.07, χ2/df =2.8, incremental fit index =0.90, CFI =0.90). There was a negative correlation between the procrastination scores and the students’ average scores (r = -0.131, P =0.02). Conclusions: The Farsi version of the PASS is a valid and reliable tool to measure academic procrastination in Iranian undergraduate medical students.
X---------------------------------------------------------------------------------------------------------A DOUBLE INPUT BUCK BOOST CONVERTER FOR WIND ENERGY SYSTEM WITH POWER SHARING CONTROL

-The simulation of a nonlinear controller with power sharing control capabilities for a wind energy system double input buck boost–buck boost converter is presented. A multiple-input DC–DC converter is useful to obtain the regulated output voltage from input power source such as a wind array. Double input DC-DC buck boost converter principle of operation and the equations describing the converter circuit are reviewed. Wind energy system combining two Photo Voltaic (PV) panels based double input buck boost – buck boost converter is simulated. Finally, various simulation results for a buck boost– buck boost converter operating under the proposed controller are reported to verify the operation of the designed controller.
At the Edge of Trading : Analyzing High Frequency Time-Series Data in Real-Time using Computational Intelligence

Advances in computing have profoundly changed our society. It has provided us with the ability to capture and process massive volumes of meaningful data. We never before have had the amount of financial data available for analysis nor have had the processing power to analysis a complete market in real-time. This in conjunction with the advances in computational methods, we have been recently equipped to examine financial data in real-time and more efficiently than anytime previously. This paper examines the scientific and commercial relevance exposed as a result of the convergence of four advanced and diverse fields of; (i) model-driven trading, (ii) computational intelligence, (iii) the availability of high frequency market data, and (iv) the evolution of enabling technologies; such as available 64-bit processors, high performance data managers and grid computing. We will demonstrate the unique power of this technology convergence by analyzing quote depth, which is still not commercially available in historic form, in real-time and identifying important non-seasonal patterns. We will examine the BIDASK depth of the NASDAQ cash equity market by loading and committing inhomogeneous time-series market data into cache memory. We will then applying the dataset to a continuously adaptive and biologically-inspired computational method that will conduct high speed pattern recognition. The resultant patterns will indicate market anomalies and will form stylized facts that in turn can be used to supply a paradigm for modeldriven trading. Because of the technology barriers to entry and a high level of domain specific knowledge required the method described here has not been attempted by any known large non-bank entities and is truly ground breaking. Index Terms – High frequency market data, computational intelligence (CI), neural networks, Kohonen self-organizing feature maps (SOM), market depth, efficient market hypothesis (EMH), behavioral finance, market-microstructure, modeldriven trading, automated trading, program trading, and algorithmic trading.
An ‘In the Wild’ Experiment on Presence and Embodiment using Consumer Virtual Reality Equipment

Consumer virtual reality systems are now becoming widely available. We report on a study on presence and embodiment within virtual reality that was conducted `in the wild', in that data was collected from devices owned by consumers in uncontrolled settings, not in a traditional laboratory setting. Users of Samsung Gear VR and Google Cardboard devices were invited by web pages and email invitation to download and run an app that presented a scenario where the participant would sit in a bar watching a singer. Each participant saw one of eight variations of the scenario: with or without a self-avatar; singer inviting the participant to tap along or not; singer looking at the participant or not. Despite the uncontrolled situation of the experiment, results from an in-app questionnaire showed tentative evidence that a self-avatar had a positive effect on self-report of presence and embodiment, and that the singer inviting the participant to tap along had a negative effect on self-report of embodiment. We discuss the limitations of the study and the platforms, and the potential for future open virtual reality experiments.
On the Relationship between My Avatar and Myself

What is the relationship between avatars and the people they represent in terms of appearance and behavior? In this paper, we hypothesize that people (balancing motives of self-verification and self-enhancement) customize the image of their avatars to bear similarity to their real selves, but with moderate enhancements. We also hypothesize that virtual-world behavior (due to deindividuation in computer-mediated communication environments) is less restrained by normal inhibitions than real-world behavior. Lastly, we hypothesize that people with more attractive avatars than their real selves will be somewhat more confident and extraverted in virtual worlds than they are in the real world. We examine these issues using data collected from Second Life residents using an in-world intercept method that involved recruiting respondents’ avatars from a representative sample of locations. Our quantitative data indicate that, on average, people report making their avatars similar to themselves, but somewhat more attractive. And, compared to real-world behavior, respondents indicate that their virtual-world behavior is more outgoing and risk-taking and less thoughtful/more superficial. Finally, people with avatars more attractive than their real selves state that they are more outgoing, extraverted, risk-taking, and loud than their real selves (particularly if they reported being relatively low on these traits in the real world). Qualitative data from open-ended questions corroborate our hypotheses.
X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations

The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ∼500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.
Essential Role for the C5a Receptor in Regulating the Effector Phase of Synovial Infiltration and Joint Destruction in Experimental Arthritis

A characteristic feature of rheumatoid arthritis is the abundance of inflammatory cells in the diseased joint. Two major components of this infiltrate are neutrophils in the synovial fluid and macrophages in the synovial tissue. These cells produce cytokines including tumor necrosis factor α and other proinflammatory mediators that likely drive the disease through its effector phases. To investigate what mechanisms underlie the recruitment of these cells into the synovial fluid and tissue, we performed expression analyses of chemoattractant receptors in a related family that includes the anaphylatoxin receptors and the formyl-MetLeuPhe receptor. We then examined the effect of targeted disruption of two abundantly expressed chemoattractant receptors, the receptors for C3a and C5a, on arthritogenesis in a mouse model of disease. We report that genetic ablation of C5a receptor expression completely protects mice from arthritis.
Galaxy Halo Masses from Galaxy-Galaxy Lensing

We present measurements of the extended dark halo profiles of bright early-type galaxies at redshifts 0.1 < z < 0.9 obtained via galaxy-galaxy lensing analysis of images taken at the Canada-France-Hawaii Telescope using the UH8K CCD mosaic camera. Six 0. °5 × 0. °5 fields were observed for a total of 2 hr each in I and V, resulting in catalogs containing ~20,000 galaxies per field. We used V-I color and I magnitude to select bright early-type galaxies as the lens galaxies, yielding a sample of massive lenses with fairly well-determined redshifts and absolute magnitudes M ~ M* ± 1. We paired these with faint galaxies lying at angular distances 20′′ < θ < 60′′, corresponding to physical radii of 26 < r < 77 h-1 kpc (z = 0.1) and 105 < r < 315 h-1 kpc (z = 0.9), and computed the mean tangential shear γT(θ) of the faint galaxies. The shear falls off with radius roughly as γT ∝ 1/θ as expected for flat rotation curve halos. The shear values were weighted in proportion to the square root of the luminosity of the lens galaxy. This is optimal if the halo mass at a given radius varies as M ∝ , as is the case at smaller radii, and in this context our results give a value for the average mean rotation velocity of an L* galaxy halo at r ~ 50-200 h-1 kpc of v* = 238 km s-1 for a flat lambda (Ωm0 = 0.3,Ωλ0 = 0.7) cosmology (v* = 269 km s-1 for Einstein-de Sitter) and with little evidence for evolution with redshift. These halo masses are somewhat (2-3 times) lower than a simple perfectly flat rotation curve extrapolation from smaller scale dynamical measurements. They are also considerably lower than the masses of halos found from the best-studied X-ray halos. They do, however, agree extremely well with the masses of halos of the same abundance in lambda-CDM simulations. We find a mass-to-light ratio of M/LB ≃ 121 ± 28h(r/100 h-1 kpc) (for L* galaxies) and these halos constitute Ω ≃ 0.04 ± 0.01(r/100 h-1 kpc) of closure density.
Effects of an Essentialism Manipulation on the Neural Processing of Racial Minorities

Racial minorities are increasingly growing in the United States and the racial category “multiracial” is one of the fastest growing racial minorities. Racial essentialism is the belief that race has an underlying property and is innate and biological. Many people with essentialist beliefs do not normally categorize individuals with a multiracial background as multiracial. The current study assessed how an essentialism manipulation affects the neural processing of minority race targets by White participants. Participants completed a categorization task and passive task looking at ambiguous and monoracial faces while connect to EEG. For the passive task, results revealed gradient by race by condition interactions for the N170, P2, and N4 components as well as race by gradient interactions for the P1, N2, P3, N3, and LPP components. Additionally, the category chosen for the target affected neural processing in the N3 component for the categorization condition. These findings demonstrate the need for continued research of the perception of multiracial individuals and continued attempts to reduce attentional bias.
Directional measures of postural sway as predictors of balance instability and accidental falls

Abstract Despite the obvious advantages and popularity of static posturography, universal standards for posturographic tests have not been developed thus far. Most of the center-of-foot pressure (COP) indices are strongly dependent on an individual experimental design, and are susceptible to distortions, which makes results of their analysis incomparable. In this research, we present a novel approach to the analysis of the COP trajectory based on the directional features of postural sway. Our novel output measures: the sway directional indices (DI) and sway vector (SV) were applied to assess the postural stability in the group of young able-bodied subjects. Towards this aim, the COP trajectories were recorded in 100 students standing still for 60 s, with eyes open (EO) and then, with eyes closed (EC). Each record was subdivided then into 20, 30 and 60 s samples. Interclass correlation coefficients were calculated from the samples. The controlled variables (visual conditions) uniquely affected the output measures, but only in case of proper signal pretreatment (low-pass filtering). In filtering below 6 Hz, the DI and SV provided a unique set of descriptors for postural control. Both sway measures were highly independent of the trial length and the sampling frequency, and were unaffected by the sampling noise. Directional indices of COP filtered at 6 Hz showed high to very high reliability, with ICC range of 0.7-0.9. Results of a single 60 s trial are sufficient to reach acceptable reliability for both DI and SV. In conclusion, the directional sway measures may be recommended as the primary standard in static posturography.
Border collision bifurcations in two-dimensional piecewise smooth maps

Recent investigations on the bifurcations in switching circuits have shown that many atypical bifurcations can occur in piecewise smooth maps that cannot be classified among the generic cases like saddle-node, pitchfork, or Hopf bifurcations occurring in smooth maps. In this paper we first present experimental results to establish the need for the development of a theoretical framework and classification of the bifurcations resulting from border collision. We then present a systematic analysis of such bifurcations by deriving a normal form - the piecewise linear approximation in the neighborhood of the border. We show that there can be eleven qualitatively different types of border collision bifurcations depending on the parameters of the normal form, and these are classified under six cases. We present a partitioning of the parameter space of the normal form showing the regions where different types of bifurcations occur. This theoretical framework will help in explaining bifurcations in all systems, which can be represented by two-dimensional piecewise smooth maps.