Miracle-dz/UniFAR-FTUs huggingface dataset:
Purification of Highly Active Alphavirus Replication Complexes Demonstrates Altered Fractionation of Multiple Cellular Membranes

ABSTRACT Positive-strand RNA viruses replicate their genomes in membrane-associated structures; alphaviruses and many other groups induce membrane invaginations called spherules. Here, we established a protocol to purify these membranous replication complexes (RCs) from cells infected with Semliki Forest virus (SFV). We isolated SFV spherules located on the plasma membrane and further purified them using two consecutive density gradients. This revealed that SFV infection strongly modifies cellular membranes. We removed soluble proteins, the Golgi membranes, and most of the mitochondria, but plasma membrane, endoplasmic reticulum (ER), and late endosome markers were retained in the membrane fraction that contained viral RNA synthesizing activity, replicase proteins, and minus- and plus-strand RNA. Electron microscopy revealed that the purified membranes displayed spherule-like structures with a narrow neck. This membrane enrichment was specific to viral replication, as such a distribution of membrane markers was only observed after infection. Besides the plasma membrane, SFV infection remodeled the ER, and the cofractionation of the RC-carrying plasma membrane and ER suggests that SFV recruits ER proteins or membrane to the site of replication. The purified RCs were highly active in synthesizing both genomic and subgenomic RNA. Detergent solubilization destroyed the replication activity, demonstrating that the membrane association of the complex is essential. Most of the newly made RNA was in double-stranded replicative molecules, but the purified complexes also produced single-stranded RNA as well as released newly made RNA. This indicates that the purification established here maintained the functionality of RCs and thus enables further structural and functional studies of active RCs. IMPORTANCE Similar to all positive-strand RNA viruses, the arthropod-borne alphaviruses induce membranous genome factories, but little is known about the arrangement of viral replicase proteins and the presence of host proteins in these replication complexes. To improve our knowledge of alphavirus RNA-synthesizing complexes, we isolated and purified them from infected mammalian cells. Detection of viral RNA and in vitro replication assays revealed that these complexes are abundant and highly active when located on the plasma membrane. After multiple purification steps, they remain functional in synthesizing and releasing viral RNA. Besides the plasma membrane, markers for the endoplasmic reticulum and late endosomes were enriched with the replication complexes, demonstrating that alphavirus infection modified cellular membranes beyond inducing replication spherules on the plasma membrane. We have developed here a gentle purification method to obtain large quantities of highly active replication complexes, and similar methods can be applied to other positive-strand RNA viruses.
Too Crowded to Disclose! Exploring the Relationship Between Online Crowdedness and Self-Disclosure

Nowadays, people communicate with many others online. Of the online sites, product review pages have become an important communication medium on which consumers share information about a product. Drawing upon this trend, we examined the factors that affect reviewers’ self-disclosure behavior. Prior studies have found that privacy behaviors such as self-disclosure are affected by diverse contextual factors. In this study, we propose that online crowdedness is an important contextual factor for self-disclosure behavior. Using review data from the largest online apparel rental site in the U.S., we empirically explored the relationship between online crowdedness and self-disclosure behavior. The result shows that online crowdedness can discourage selfdisclosure behavior.
Mobile and Context-Aware GeoBI Applications: A Multilevel Model for Structuring and Sharing of Contextual Information

With the requirements for high performance results in the today’s mobile, global, highly competitive, and technology-based business world, business professionals have to get supported by convenient mobile decision support systems (DSS). To give an improved support to mobile business professionals, it is necessary to go further than just allowing a simple remote access to a Business Intelligence platform. In this paper, the need for actual context-aware mobile Geospatial Business Intelligence (GeoBI) systems that can help capture, filter, organize and structure the user mobile context is exposed and justified. Furthermore, since capturing, structuring, and modeling mobile contextual information is still a research issue, a wide inventory of existing research work on context and mobile context is provided. Then, step by step, we methodologically identify relevant contextual information to capture for mobility purposes as well as for BI needs, organize them into context-dimensions, and build a hierarchical mobile GeoBI context model which (1) is geo-spatial-extended, (2) fits with human perception of mobility, (3) takes into account the local context interactions and information-sharing with remote contexts, and (4) matches with the usual hierarchical aggregated structure of BI data.
Edge Estimation with Independent Set Oracles

We study the task of estimating the number of edges in a graph, where the access to the graph is provided via an independent set oracle. Independent set queries draw motivation from group testing and have applications to the complexity of decision versus counting problems. We give two algorithms to estimate the number of edges in an n-vertex graph, using (i) polylog(n) bipartite independent set queries or (ii) n2/3 polylog(n) independent set queries.
Visible Position Estimation in Whole Wrist Circumference Device towards Forearm Pose-aware Display

Smart watches allow instant access to information; however, the visual notiﬁcation is not always reachable depending on the forearm posture. Flexible and curved display technologies can enable full-wrist circumference displays that show information at the most visible positions using pose awareness. A prototype device is implemented with 10 LEDs and 10 accelerometers around the wrist. The most visible LED is estimated using a machine learning technique. The main idea is to utilize direct relationship between the raw acceleration signals and the position of the most visible LED, rather than assigning the position by particular classes of activities or forward-kinematic model-based estimation. Also, sensor reduction is attempted by introducing new features. A user study showed that the system allowed 89.9 % of the system’s judgment to ﬁt with the gap of 1 LED (18 mm) from the user’s expectations. The rotation-sensitive features proved to be informative, and a single sensor placed on the inside of the wrist achieved a performance level on par (F-measure 0.681) with the performance when all (10) sensors are used.
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.
Conditional random slope: A new approach for estimating individual child growth velocity in epidemiological research

Conditioning child growth measures on baseline accounts for regression to the mean (RTM). Here, we present the “conditional random slope” (CRS) model, based on a linear‐mixed effects model that incorporates a baseline‐time interaction term that can accommodate multiple data points for a child while also directly accounting for RTM.
CpxR-Dependent Thermoregulation of Serratia marcescens PrtA Metalloprotease Expression and Its Contribution to Bacterial Biofilm Formation

ABSTRACT PrtA is the major secreted metalloprotease of Serratia marcescens. Previous reports implicate PrtA in the pathogenic capacity of this bacterium. PrtA is also clinically used as a potent analgesic and anti-inflammatory drug, and its catalytic properties attract industrial interest. Comparatively, there is scarce knowledge about the mechanisms that physiologically govern PrtA expression in Serratia. In this work, we demonstrate that PrtA production is derepressed when the bacterial growth temperature decreases from 37°C to 30°C. We show that this thermoregulation occurs at the transcriptional level. We determined that upstream of prtA, there is a conserved motif that is directly recognized by the CpxR transcriptional regulator. This feature is found along Serratia strains irrespective of their isolation source, suggesting an evolutionary conservation of CpxR-dependent regulation of PrtA expression. We found that in S. marcescens, the CpxAR system is more active at 37°C than at 30°C. In good agreement with these results, in a cpxR mutant background, prtA is derepressed at 37°C, while overexpression of the NlpE lipoprotein, a well-known CpxAR-inducing condition, inhibits PrtA expression, suggesting that the levels of the activated form of CpxR are increased at 37°C over those at 30°C. In addition, we establish that PrtA is involved in the ability of S. marcescens to develop biofilm. In accordance, CpxR influences the biofilm phenotype only when bacteria are grown at 37°C. In sum, our findings shed light on regulatory mechanisms that fine-tune PrtA expression and reveal a novel role for PrtA in the lifestyle of S. marcescens. IMPORTANCE We demonstrate that S. marcescens metalloprotease PrtA expression is transcriptionally thermoregulated. While strongly activated below 30°C, its expression is downregulated at 37°C. We found that in S. marcescens, the CpxAR signal transduction system, which responds to envelope stress and bacterial surface adhesion, is activated at 37°C and able to downregulate PrtA expression by direct interaction of CpxR with a binding motif located upstream of the prtA gene. Moreover, we reveal that PrtA expression favors the ability of S. marcescens to develop biofilm, irrespective of the bacterial growth temperature. In this context, thermoregulation along with a highly conserved CpxR-dependent modulation mechanism gives clues about the relevance of PrtA as a factor implicated in the persistence of S. marcescens on abiotic surfaces and in bacterial host colonization capacity.
Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia

ABSTRACT Since 2000, cases of the neglected tropical disease Buruli ulcer, caused by infection with Mycobacterium ulcerans, have increased 100-fold around Melbourne (population 4.4 million), the capital of Victoria, in temperate southeastern Australia. The reasons for this increase are unclear. Here, we used whole-genome sequence comparisons of 178 M. ulcerans isolates obtained primarily from human clinical specimens, spanning 70 years, to model the population dynamics of this pathogen from this region. Using phylogeographic and advanced Bayesian phylogenetic approaches, we found that there has been a migration of the pathogen from the east end of the state, beginning in the 1980s, 300 km west to the major human population center around Melbourne. This move was then followed by a significant increase in M. ulcerans population size. These analyses inform our thinking around Buruli ulcer transmission and control, indicating that M. ulcerans is introduced to a new environment and then expands, rather than it being from the awakening of a quiescent pathogen reservoir. IMPORTANCE Buruli ulcer is a destructive skin and soft tissue infection caused by Mycobacterium ulcerans and is characterized by progressive skin ulceration, which can lead to permanent disfigurement and long-term disability. Despite the majority of disease burden occurring in regions of West and central Africa, Buruli ulcer is also becoming increasingly common in southeastern Australia. Major impediments to controlling disease spread are incomplete understandings of the environmental reservoirs and modes of transmission of M. ulcerans. The significance of our research is that we used genomics to assess the population structure of this pathogen at the Australian continental scale. We have then reconstructed a historical bacterial spread and modeled demographic dynamics to reveal bacterial population expansion across southeastern Australia. These findings provide explanations for the observed epidemiological trends with Buruli ulcer and suggest possible management to control disease spread.
Sub Auditory Communication and Facial EMG

Availability of speech related information in the facial EMG is discussed. The primary objective of this preliminary work is to investigate the use of facial EMG as a voiceless communication medium. Subjects were asked to utter the five English vowels with no acoustic output (sub-auditory). Three independent EMG signals were acquired from three facial muscles as subauditory EMG activations. In order to classify and recognize each vowel based on EMG, RMS of the recorded signals were estimated and used as parametric inputs to a neural network.
Facing the challenge of liquid phase crystallizing silicon on textured glass substrates

A major limitation in current liquid phase crystallized (LPC) silicon thin-film record solar cells are optical losses caused by their planar glass-silicon interface. In this study, silicon is grown on nanoimprinted periodically as well as on randomly textured glass substrates and successfully implemented into state-of-the-art LPC silicon thin-film solar cell stacks. By systematically varying every layer the whole sample stack is optimized regarding its anti-reflection ability. Compared to an optimized planar reference device, a reduction of reflection losses by -3.5% (absolute) on the random and by -9.4% (absolute) on the periodic texture has been achieved in the wavelength range of interest.
Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission.
Future-Oriented Thought Patterns Associated With Anxiety and Depression in Later Life: The Intriguing Prospects of Prospection

Anxiety and mood disorders in later life are the focus of an increasing amount of intervention research, however basic mechanisms and paradigms explaining etiology and maintenance warrant further exploration. Research on future-oriented thought patterns associated with anxiety and depression in this age group may prove useful, as these disorders are both characterized by a tendency to generate and fixate on threat-related future scenarios that may or may not materialize. Additionally, depression is associated with a reduced expectancy of positive future events. In this paper, we review the literature relevant to future thinking in anxiety and depression in older adults. We focus on the mental construction and anticipation of negative future events, and their underlying neurocognitive mechanisms. We then consider clinical and research implications of anxious and depressive future-oriented thought patterns for older adults. We believe that more research investigating future-oriented thought patterns associated with emotional disorders in later life could improve conceptualization, measurement, and perhaps potential treatments for late-life anxiety and depression.
Executive Function and Falls in Older Adults: New Findings from a Five-Year Prospective Study Link Fall Risk to Cognition

Background Recent findings suggest that executive function (EF) plays a critical role in the regulation of gait in older adults, especially under complex and challenging conditions, and that EF deficits may, therefore, contribute to fall risk. The objective of this study was to evaluate if reduced EF is a risk factor for future falls over the course of 5 years of follow-up. Secondary objectives were to assess whether single and dual task walking abilities, an alternative window into EF, were associated with fall risk. Methodology/Main Results We longitudinally followed 256 community-living older adults (age: 76.4±4.5 yrs; 61% women) who were dementia free and had good mobility upon entrance into the study. At baseline, a computerized cognitive battery generated an index of EF, attention, a closely related construct, and other cognitive domains. Gait was assessed during single and dual task conditions. Falls data were collected prospectively using monthly calendars. Negative binomial regression quantified risk ratios (RR). After adjusting for age, gender and the number of falls in the year prior to the study, only the EF index (RR: .85; CI: .74–.98, p = .021), the attention index (RR: .84; CI: .75–.94, p = .002) and dual tasking gait variability (RR: 1.11; CI: 1.01–1.23; p = .027) were associated with future fall risk. Other cognitive function measures were not related to falls. Survival analyses indicated that subjects with the lowest EF scores were more likely to fall sooner and more likely to experience multiple falls during the 66 months of follow-up (p<0.02). Conclusions/Significance These findings demonstrate that among community-living older adults, the risk of future falls was predicted by performance on EF and attention tests conducted 5 years earlier. The present results link falls among older adults to cognition, indicating that screening EF will likely enhance fall risk assessment, and that treatment of EF may reduce fall risk.
A 26 $\mu$ W 8 bit 10 MS/s Asynchronous SAR ADC for Low Energy Radios

This paper presents an asynchronous SAR ADC for flexible, low energy radios. To achieve excellent power efficiency for a relatively moderate resolution, various techniques are introduced to reduce the power consumption: custom-designed 0.5 fF unit capacitors minimize the analog power consumption while asynchronous dynamic logic minimizes the digital power consumption. The variability of the custom-designed capacitors is estimated by a specialized CAD tool and verified by chip measurements. An implemented 8-bit prototype in a 90 nm CMOS technology occupies 228 μm × 240 μm including decoupling capacitors, and achieves an ENOB of 7.77 bit at a sampling frequency of 10.24 MS/s. The power consumption equals 26.3 μW from a 1 V supply, thus resulting in an energy efficiency of 12 fJ/conversion-step. Moreover, the fully dynamic design, which is optimized for low-leakage, leads to a standby power consumption of 6 nW. In that way, the energy efficiency of this converter can be maintained down to very low sampling rates.
The Calculation of Inductor Sizes, for Heat Treatment of Aluminum Wires

Aluminum is efficient in using as a conducting material when producing wires and cables because of its high electrical conductivity and low specific gravity. Wires of different diameters are used for the production of the conductors, drawn from aluminum rods. Heat treatment of the wires is necessary for recovering the ductility of the conductors’ material. The progressive way of increasing the aluminum wires ductility is prolonged induction of heat treatment, which is based upon using an inductor with a ferromagnetic core, with one of its rods covering the circuit, drawn from the portion of the heated wire, and short-circuiting on the deflecting rollers. Calculations of basic dimensions, choosing the core material, and the inductors’ winding is determined by its weight, size and cost indicators. In this paper the initial data for calculations are; the performance of the heat treatment process, the power supply voltage and temperature, at which the ductile properties of aluminum are recovered. Keyword: Simulink/Matlab, Heat Treatment, Conductor, Cross Sectional Dimension.
Assessing the Perceived Predictability of Functions

How do we perceive the predictability of functions? We derive a rational measure of a function’s predictability based on Gaussian process learning curves. Using this measure, we show that the smoothness of a function can be more important to predictability judgments than the variance of additive noise or the number of samples. These patterns can be captured well by the learning curve for Gaussian process regression, which in turn crucially depends on the eigenvalue spectrum of the covariance function. Using approximate bounds on the learning curve, we model participants’ predictability judgments about sampled functions and find that smoothness is indeed a better predictor for perceived predictability than both the variance and the sample size. This means that it can sometimes be preferable to learn about noisy but smooth functions instead of deterministic complex ones.