Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro circularization of RNA

ABSTRACT Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
Analytical treatment of randomly birefringent periodically spun fibers

Spun fibers are increasingly used in telecommunication systems because their polarization-mode dispersion (PMD) is lower than that in unspun fibers. In this paper, we investigate the effects of a periodic spin on the PMD of fibers with randomly varying birefringence. Numerical simulations show that when the spin period is of the same order as or larger than the beat length, the mean differential group delay of a spun fiber depends on the model used for the random birefringence. We then carry out a general theoretical analysis using the second Wai-Menyuk model, which is the only model of fiber birefringence to date that is consistent with polarization optical time domain reflectometry data. Finally, we consider some particular regimes by means of a perturbative approach.
The Left Posterior Superior Temporal Gyrus Participates Specifically in Accessing Lexical Phonology

Impairments in phonological processing have been associated with damage to the region of the left posterior superior temporal gyrus (pSTG), but the extent to which this area supports phonological processing, independent of semantic processing, is less clear. We used repetition priming and neural repetition suppression during functional magnetic resonance imaging (fMRI) in an auditory pseudoword repetition task as a semantics-free model of lexical (whole-word) phonological access. Across six repetitions, we observed repetition priming in terms of decreased reaction time and repetition suppression in terms of reduced neural activity. An additional analysis aimed at sublexical phonology did not show significant effects in the areas where repetition suppression was observed. To test if these areas were relevant to real word production, we performed a conjunction analysis with data from a separate fMRI experiment which manipulated word frequency (a putative index of lexical phonological access) in picture naming. The left pSTG demonstrated significant effects independently in both experiments, suggesting that this area participates specifically in accessing lexical phonology.
Texture-Directed Mobile GPU Power Management for Closed-Source Games

Power consumption and battery life constrain the developments of the mobile platforms. Among the mobile applications, games are the most demanding applications in terms of both computational cost and consumed energy. The power consumption spent on GPU to accelerate the rendering speed keeps increasing rapidly. Most of the GPU power saving techniques using the prediction-based GPU DVFS policies. We propose the Texture-Directed Mobile GPU DVFS policy based on the observation that GPU workloads and texture operations in CPU are strongly positively correlated when playing games. The proposed policy utilizes the texture operations collected from the front-end of the graphic pipeline to scale the GPU frequency. The evaluation results show that, compared with the prediction-based policy, our policy saves more power in the tested games with competitive performance. Up to 43.75% GPU power consumption is saved in the games whose scenes change drastically. About 7.16% power is saved on average in games whose scenes change gently.
Online Energy Harvesting Prediction in Environmentally Powered Wireless Sensor Networks

The increasing popularity of micro-scale power-scavenging techniques for wireless sensor networks (WSNs) is paving the way to energy-autonomous sensing systems. To sustain perpetual operations, however, environmentally powered devices must adapt their workload to the stochastic nature of ambient sources. Energy prediction models, which estimate the future expected energy intake, are effective tools to support the development of proactive power management strategies. In this paper, we present profile energy prediction model (Pro-Energy), an energy prediction model for multi-source energy-harvesting WSNs that leverages past energy observations to forecast future energy availability. We then propose Pro-Energy with variable-length timeslots (Pro-Energy-VLT), an extension of Pro-Energy that combines our energy predictor with timeslots of variable lengths to adapt to the dynamics of the power source. To assess the performance of our proposed solutions, we use real-life solar and wind traces, as well as publicly available traces of solar irradiance and wind speed. A comparative performance evaluation shows that Pro-Energy significantly outperforms the state-of-the-art energy predictors, by improving the prediction accuracy of up to 67%. Moreover, by adapting the granularity of the prediction timeslots to the dynamics of the energy source, Pro-Energy-VLT further improves the prediction accuracy, while reducing the memory footprint and the energy overhead of energy forecasting.
Engineering basic algorithms of an in-memory text search engine

Inverted index data structures are the key to fast text search engines. We first investigate one of the predominant operation on inverted indexes, which asks for intersecting two sorted lists of document IDs of different lengths. We explore compression and performance of different inverted list data structures. In particular, we present Lookup, a new data structure that allows intersection in expected time linear in the smaller list. Based on this result, we present the algorithmic core of a full text data base that allows fast Boolean queries, phrase queries, and document reporting using less space than the input text. The system uses a carefully choreographed combination of classical data compression techniques and inverted-index-based search data structures. Our experiments show that inverted indexes are preferable over purely suffix-array-based techniques for in-memory (English) text search engines. A similar system is now running in practice in each core of the distributed data base engine TREX of SAP.
Chlorinated Pool Attendance, Atopy, and the Risk of Asthma during Childhood

The pool chlorine hypothesis postulates that the rise in childhood asthma in the developed world could result at least partly from the increasing exposure of children to toxic gases and aerosols contaminating the air of indoor chlorinated pools. To further assess this hypothesis, we explored the relationships between childhood asthma, atopy, and cumulated pool attendance (CPA). We studied 341 schoolchildren 10–13 years of age who attended at a variable rate the same public pool in Brussels (trichloramine in air, 0.3–0.5 mg/m3). Examination of the children included a questionnaire, an exercise-induced bronchoconstriction (EIB) test, and the measurement of exhaled nitric oxide (eNO) and total and aeroallergen-specific serum IgE. CPA by children (range, 0–1,818 hr) emerged among the most consistent predictors of asthma (doctor diagnosed or screened with the EIB test) and of elevated eNO, ranking immediately after atopy and family history of asthma or hay fever. Although the risk of elevated eNO increased with CPA [odds ratio (OR) = 1.30; 95% confidence interval (CI), 1.10–1.43] independently of total or specific serum IgE, the probability of developing asthma increased with CPA only in children with serum IgE > 100 kIU/L (OR for each 100-hr increase in CPA = 1.79; 95% CI, 1.07–2.72). All these effects were dose related and most strongly linked to pool attendance before 6–7 years of age. Use of indoor chlorinated pools especially by young children interacts with atopic status to promote the development of childhood asthma. These findings further support the hypothesis implicating pool chlorine in the rise of childhood asthma in industrialized countries.
Surprise and Error: Common Neuronal Architecture for the Processing of Errors and Novelty

According to recent accounts, the processing of errors and generally infrequent, surprising (novel) events share a common neuroanatomical substrate. Direct empirical evidence for this common processing network in humans is, however, scarce. To test this hypothesis, we administered a hybrid error-monitoring/novelty-oddball task in which the frequency of novel, surprising trials was dynamically matched to the frequency of errors. Using scalp electroencephalographic recordings and event-related functional magnetic resonance imaging (fMRI), we compared neural responses to errors with neural responses to novel events. In Experiment 1, independent component analysis of scalp ERP data revealed a common neural generator implicated in the generation of both the error-related negativity (ERN) and the novelty-related frontocentral N2. In Experiment 2, this pattern was confirmed by a conjunction analysis of event-related fMRI, which showed significantly elevated BOLD activity following both types of trials in the posterior medial frontal cortex, including the anterior midcingulate cortex (aMCC), the neuronal generator of the ERN. Together, these findings provide direct evidence of a common neural system underlying the processing of errors and novel events. This appears to be at odds with prominent theories of the ERN and aMCC. In particular, the reinforcement learning theory of the ERN may need to be modified because it may not suffice as a fully integrative model of aMCC function. Whenever course and outcome of an action violates expectancies (not necessarily related to reward), the aMCC seems to be engaged in evaluating the necessity of behavioral adaptation.
Predictable Mobile Routing for Spacecraft Networks

In predictable mobile networks, network nodes move in a predictable way and therefore have dynamically changing but predictable connectivity. We have developed a model that formalizes predictable dynamic topologies as sequences of static snapshots. We use this model to design and evaluate a predictable mobile-routing protocol based on link-state routing, whose performance is superior to its static and ad hoc counterparts. Our routing protocol accounts for occurrences of additional, unpredictable changes, as well as their interaction with predictable changes. We evaluate our protocol using simulations based on randomly generated topologies and spacecraft-network scenarios. In both cases, we show that our protocol outperforms traditional routing protocols and is well suited for routing in next-generation space networks.
The Role of Neurokinin-1 Receptor in the Microenvironment of Inflammation and Cancer

The recent years have witnessed an exponential increase in cancer research, leading to a considerable investment in the field. However, with few exceptions, this effort has not yet translated into a better overall prognosis for patients with cancer, and the search for new drug targets continues. After binding to the specific neurokinin-1 (NK-1) receptor, the peptide substance P (SP), which is widely distributed in both the central and peripheral nervous systems, triggers a wide variety of functions. Antagonists against the NK-1 receptor are safe clinical drugs that are known to have anti-inflammatory, analgesic, anxiolytic, antidepressant, and antiemetic effects. Recently, it has become apparent that SP can induce tumor cell proliferation, angiogenesis, and migration via the NK-1 receptor, and that the SP/NK-1 receptor complex is an integral part of the microenvironment of inflammation and cancer. Therefore, the use of NK-1 receptor antagonists as a novel and promising approach for treating patients with cancer is currently under intense investigation. In this paper, we evaluate the recent scientific developments regarding this receptor system, its role in the microenvironment of inflammation and cancer, and its potentials and pitfalls for the usage as part of modern anticancer strategies.
Simian Immunodeficiency Virus SIVmac239 Infection of Major Histocompatibility Complex-Identical Cynomolgus Macaques from Mauritius

ABSTRACT Nonhuman primates are widely used to study correlates of protective immunity in AIDS research. Successful cellular immune responses have been difficult to identify because heterogeneity within macaque major histocompatibility complex (MHC) genes results in quantitative and qualitative differences in immune responses. Here we use microsatellite analysis to show that simian immunodeficiency virus (SIV)-susceptible cynomolgus macaques (Macaca fascicularis) from the Indian Ocean island of Mauritius have extremely simple MHC genetics, with six common haplotypes accounting for two-thirds of the MHC haplotypes in feral animals. Remarkably, 39% of Mauritian cynomolgus macaques carry at least one complete copy of the most frequent MHC haplotype, and 8% of these animals are homozygous. In stark contrast, entire MHC haplotypes are rarely conserved in unrelated Indian rhesus macaques. After intrarectal infection with highly pathogenic SIVmac239 virus, a pair of MHC-identical Mauritian cynomolgus macaques mounted concordant cellular immune responses comparable to those previously reported for a pair of monozygotic twins infected with the same strain of human immunodeficiency virus. Our identification of relatively abundant SIV-susceptible, MHC-identical macaques will facilitate research into protective cellular immunity.
Lung function decline in bronchial asthma.

STUDY OBJECTIVE We evaluated the longitudinal changes in lung function and the factors associated with FEV(1) changes over time in a sample of asthmatic subjects. SETTING FEV(1) measures were recorded every 3 months over a 5-year follow-up period. To compare all subjects independently of body size, FEV(1) values were normalized for the subject's height at the third power. We evaluated the possible effect of age, baseline FEV(1), disease duration, and FEV(1) variability on the rate of change of FEV(1). PATIENTS We studied 142 subjects with asthma diagnosed on the basis of validated clinical and functional criteria. RESULTS FEV(1) showed a linear decay with aging in each subject. For a subject 1.65 m in height, the median overall FEV(1) decay was 40.9 mL/yr. FEV(1) decay slopes were significantly influenced by age and sex, being steeper in younger male subjects. A significant interaction was found between age and baseline FEV(1): the FEV(1) decay was significantly higher among younger asthmatics with a poorer baseline functional condition. A longer disease duration was associated with a lower FEV(1) slope. FEV(1) variability was strongly associated with an increased rate of FEV(1) decline. CONCLUSIONS FEV(1) decline in patients with bronchial asthma is significantly influenced by baseline FEV(1), disease duration, and FEV(1) variability. Moreover, the rate of FEV(1) decline seems to increase in younger subjects only when the baseline function is poorer.
Correlation between hormones , cytokines , MMP 2 and α-fetoprotein among hyperlipidemic obese children 1

Childhood obesity and its complications have become a very serious public health concern and threat. Obesity confers increased risk for cardiovascular diseases as a result of accumulation of visceral fat, which alters metabolism and insulin sensitivity. The objective of this study is to identify, correlate and validate certain biomarkers for detecting obesity in Egyptian children. Thirty patients and twenty healthy volunteers as control were enrolled in this study. All subjects were prepubertal (7-12 years) and of both sex. Anthropometric measurements; body mass index (BMI), waist and hip circumferences and abdominal skin fold thickness (ASFT) were taken into consideration. Leptin, matrix metalloproteinase -2 (MMP2), interlukin-10 (IL-10), alpha-fetoprotein (AFP) and tumor necrosis factor-α (TNF-α) were evaluated. Lipid profile; cholesterol, high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and triglycerides (TG) were also tested. The work was extended to measure liver function enzymes; aspartate and alanine aminotransferases (ASL&ALT). The results revealed significant elevation (p<0.05) of all the selected parameters in obese children as compared to healthy individuals, while HDL-C showed significant decrease. The pearson’s correlation test (2-tailed) revealed significant (p<0.01) positive correlation between BMI and the selected parameters. In conclusion, these biomarkers succeeded for detecting children who may be at risk of being overweight or obese. Strong association between obesity and the selected biomarkers were observed.
Growing Hidden Markov Models: An Incremental Tool for Learning and Predicting Human and Vehicle Motion

Modeling and predicting human and vehicle motion is an active research domain. Owing to the difficulty in modeling the various factors that determine motion (e.g. internal state, perception) this is often tackled by applying machine learning techniques to build a statistical model, using as input a collection of trajectories gathered through a sensor (e.g. camera, laser scanner), and then using that model to predict further motion. Unfortunately, most current techniques use offline learning algorithms, meaning that they are not able to learn new motion patterns once the learning stage has finished. In this paper, we present an approach where motion patterns can be learned incrementally, and in parallel with prediction. Our work is based on a novel extension to hidden Markov models, called growing hidden Markov models, which gives us the ability to learn incrementally both the parameters and the structure of the model. The proposed approach has been evaluated using synthetic and real trajectory data. In our experiments our approach consistently learned motion models that were more compact and accurate than those produced by two other state-of-the-art techniques.
Breakthrough Technologies Monitoring MesoScale Ordering of Cellulose in Intact Plant Cell Walls Using Sum Frequency Generation Spectroscopy

Sum frequency generation (SFG) vibration spectroscopy can selectively detect crystalline cellulose without spectral interference from cell wall matrix components. Here, we show that the cellulose SFG spectrum is sensitive to cellulose microfibril alignment and packing within the cell wall. SFG intensity at 2,944 cm correlated well with crystalline cellulose contents of various regions of the Arabidopsis (Arabidopsis thaliana) inflorescence, while changes in the 3,320/2,944 cm intensity ratio suggest subtle changes in cellulose ordering as tissues mature. SFG analysis of two cellulose synthase mutants (irx1/cesa8 and irx3/cesa7) indicates a reduction in cellulose content without evidence of altered cellulose structure. In primary cell walls of Arabidopsis, cellulose exhibited a characteristic SFG peak at 2,920 and 3,320 cm, whereas in secondary cell walls, it had peaks at 2,944 and 3,320 cm. Starch (amylose) gave an SFG peak at 2,904 cm (CH methine) whose intensity increased with light exposure prior to harvest. Selective removal of matrix polysaccharides from primary cell walls by acid hydrolysis resulted in an SFG spectrum resembling that of secondary wall cellulose. Our results show that SFG spectroscopy is sensitive to the ordering of cellulose microfibrils in plant cell walls at the meso scale (nm to mm) that is important for cell wall architecture but cannot be probed by other spectroscopic or diffraction techniques.
Disease stage and plasma levels of cytokines in Huntington's disease: A 2‐year follow‐up study

It has been shown that plasma levels of cytokines are elevated in Huntington’s disease (HD) gene expansion carriers when compared with controls and are higher in advanced disease stages. To test the hypothesis that plasma cytokines may serve as a biomarker of disease progression, levels of proinflammatory and anti-inflammatory cytokines were measured in different disease stages at baseline and during a 2year follow-up.
Combining Optimality Theory and a Cognitive Architecture

Optimality Theory (OT) has had a lot of attention from the linguistics research community but also still largely lacks cognitive grounding. We used the ACT-R cognitive architecture to gain greater insight into the cognitive grounding issues that OT needs to address, most notably the GEN process and the learning of the constraint ranking. A generic ACT-R 5.0 model was developed guided by OT principles. The generic model was instantiated in two specific models, one for syllabification and one for past tense formation. Realistic perception data was used to train the models, both were successful in learning the correct constraint ranking for their domain. This result partly bridges the gap between Optimality Theory and ACT-R, providing OT with a better cognitive grounding and ACT-R with better linguistic capabilities.
Lossless Convexification of Non-Convex Control Bound and Pointing Constraints of the Soft Landing Optimal Control Problem

Planetary soft landing problem is one of the benchmark problems of optimal control theory and it is gaining a renewed interest due to the increased focus on the exploration of planets in the solar system, such as Mars. The soft landing problem with all relevant constraints can be posed as a finite horizon optimal control problem with state and control constraints. The realtime generation of fuel optimal paths to a prescribed location on a planet’s surface is a challenging problem due to the constraints on the fuel, the control inputs, and the states. The main difficulty in solving this constrained problem is the existence of non-convex constraints on the control input, which are due to a nonzero lower bound on the control input magnitude and a non-convex constraint on the its direction. This paper introduces a convexification of the control constraints that is proven to be lossless, that is, an optimal solution of the soft landing problem can be obtained via solution of the proposed convex relaxation of the problem. The lossless convexification enables the use of interior point methods of convex optimization to obtain optimal solutions of the original non-convex optimal control problem. ∗B. Açıkmeşe is with Department Aerospace Engineering and Engineering Mechanics at The University of Texas, Austin, TX 78712, USA. Email: behcet@austin.utexas. edu. J. M. Carson is with the Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., Pasadena, CA 91109, USA. Email: jmcarson@jpl.nasa. gov. L. Blackmore is with SpaceX Company, 1 Rocket Rd. Hawthorne, CA 90250, USA. Email: lars.blackmore@spacex.com. † c ©2012 California Institute of Technology. Government sponsorship acknowledged.