Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into DNA hydroxymethylation in the honeybee from in-depth analyses of TET dioxygenase

In mammals, a family of TET enzymes producing oxidized forms of 5-methylcytosine (5mC) plays an important role in modulating DNA demethylation dynamics. In contrast, nothing is known about the function of a single TET orthologue present in invertebrates. Here, we show that the honeybee TET (AmTET) catalytic domain has dioxygenase activity and converts 5mC to 5-hydroxymethylcytosine (5hmC) in a HEK293T cell assay. In vivo, the levels of 5hmC are condition-dependent and relatively low, but in testes and ovaries 5hmC is present at approximately 7–10% of the total level of 5mC, which is comparable to that reported for certain mammalian cells types. AmTET is alternatively spliced and highly expressed throughout development and in adult tissues with the highest expression found in adult brains. Our findings reveal an additional level of flexible genomic modifications in the honeybee that may be important for the selection of multiple pathways controlling contrasting phenotypic outcomes in this species. In a broader context, our study extends the current, mammalian-centred attention to TET-driven DNA hydroxymethylation to an easily manageable organism with attractive and unique biology.
HAEMATOLOGICAL PARAMETERS ALTERED IN TUBERCULOSIS

Wah Medical College, Wah Cantt, *Army Medical College, Rawalpindi, Pakistan Background: Tuberculosis is a chronic granulomatous inflammation highly prevalent in developing countries resulting in high mortality rate. The study was conducted to investigate the change in haematological parameters with effective anti-tuberculosis therapy. Methods: A total of 45 active tuberculous patients and 45 age and sex matched healthy controls were enrolled for study by convenient non-probability sampling. Patients were taken from Military Hospital, Rawalpindi, whereas controls were taken from community. All the subjects underwent blood sampling for complete blood picture. The samples were taken in ethylene diamine tetraacetic acid (EDTA) treated tube and were analysed in KX-21 Sysmex ® automated haematology analyser. Differential leukocyte count was done manually by microscopy of Leishman’s stained blood films. Statistical analysis was done and p<0.05 was considered significant. Results: Haemoglobin and lymphocyte were significantly different in cases and controls at time of diagnosis. Haemoglobin concentration, neutrophil, monocyte and lymphocyte count were significantly different, whereas total leukocyte counts were not significantly different. Change in platelet count among cases and controls were statistically significant. Monocyte Lymphocyte (M/L) ratio and Lymphocyte Neutrophil (L/N) ratio were also significantly different. Conclusion: Haemoglobin concentration, platelet count, lymphocyte count, and neutrophil count alter with chronic inflammatory process and revert to normal with effective therapy. These parameters can be used as indicators in the assessment of response to chemotherapy.
Dynamics and thermodynamics of a non-local PNJL model with running coupling

A non-local covariant extension of the two-flavor Nambu and Jona-Lasinio (NJL) model is constructed, with built-in constraints from the running coupling of QCD at high-momentum and instanton physics at low-momentum scales. Chiral low-energy theorems and basic current algebra relations involving pion properties are shown to be reproduced. The momentum-dependent dynamical quark mass derived from this approach is in agreement with results from Dyson-Schwinger equations and lattice QCD. At finite temperature, inclusion of the Polyakov loop and its gauge invariant coupling to quarks reproduces the dynamical entangle-ment of the chiral and deconfinement crossover transitions as in the (local) PNJL model, but now without the requirement of introducing an artificial momentum cutoff. Steps beyond the mean-field approximation are made including mesonic correlations through quark-antiquark ring summations. Various quantities of interest (pressure, energy density, speed of sound etc.) are calculated and discussed in comparison with lattice QCD thermodynamics at zero chemical potential. The extension to finite quark chemical potential and the phase diagram in the (T, µ)-plane are also discussed.
On exponential decay for linear porous-thermo-elasticity system

Abstract We study the problem of exponential decaying for solutions of porous-thermoelasticity system, when time t → ∞. For sufficiently small values of the parameter of intensity of elasticity-porosity interactions the exponential decaying is established. In the considerations we apply the idea of compact decoupling for the system of equations. The exponential decaying property is proved first for the corresponding decoupled system, which is simpler to handle, then the property is derived for the original system.
Three-Dimensional Video Compression using Motion Estimation-Compensation and Discrete Wavelet Transform

Internet data almost double every year. The need of multimedia communication is less storage space and fast transmission. So, the large volume of video data has become the reason for video compression. The aim of this paper is to achieve temporal compression for three-dimensional (3D) videos using motion estimation-compensation and wavelets. Instead of performing a two-dimensional (2D) motion search, as is common in conventional video codec’s, the use of a 3D motion search has been proposed, that is able to better exploit the temporal correlations of 3D content. This leads to more accurate motion prediction and a smaller residual. The discrete wavelet transform (DWT) compression scheme has been added for better compression ratio. The DWT has a high-energy compaction property thus greatly impacted the field of compression. The quality parameters peak signal to noise ratio (PSNR) and mean square error (MSE) have been calculated. The simulation results shows that the proposed work improves the PSNR from existing work.
Adaptive Predictive Control Using Neural Network for a Class of Pure-Feedback Systems in Discrete Time

In this paper, adaptive neural network (NN) control is investigated for a class of nonlinear pure-feedback discrete-time systems. By using prediction functions of future states, the pure-feedback system is transformed into an n-step-ahead predictor, based on which state feedback NN control is synthesized. Next, by investigating the relationship between outputs and states, the system is transformed into an input-output predictor model, and then, output feedback control is constructed. To overcome the difficulty of nonaffine appearance of the control input, implicit function theorem is exploited in the control design and NN is employed to approximate the unknown function in the control. In both state feedback and output feedback control, only a single NN is used and the controller singularity is completely avoided. The closed-loop system achieves semiglobal uniform ultimate boundedness (SGUUB) stability and the output tracking error is made within a neighborhood around zero. Simulation results are presented to show the effectiveness of the proposed control approach.
Double-blind comparison of ziprasidone and risperidone in the treatment of Chinese patients with acute exacerbation of schizophrenia

Background: The aim of the study was to evaluate the efficacy and safety of ziprasidone versus risperidone in Chinese subjects with acute exacerbation of schizophrenia. Methods: In patients meeting the Chinese Classification of Mental Disorders criteria for schizophrenia and with a Positive and Negative Syndrome Scale (PANSS) total score ≥60 were randomly assigned to six weeks of double-blind treatment with ziprasidone 40–80 mg twice daily or risperidone 1–3 mg bid, flexibly dosed. Noninferiority was demonstrated if the upper limit of the two-sided 95% confidence interval (CI) for the difference in PANSS total score improvement from baseline in the evaluable population was smaller than the prespecified noninferiority margin of 10 units. Results: The intent-to-treat population comprised 118 ziprasidone-treated and 121 risperidone-treated subjects. Improvement (reduction) from baseline to week 6 in PANSS total score was (−35.6 [95% CI: −38.6, −32.6]) for ziprasidone and (−37.1 [95% CI: −39.9, −34.4]) for risperidone. Noninferiority was demonstrated in the evaluable population with a difference score of 1.5 [95% CI: −2.5, 5.5]. Mean prolactin levels decreased at week 6 compared with baseline for ziprasidone (−3.5 ng/mL), but significantly increased for risperidone (61.1 ng/mL; P < 0.001). More risperidone-treated subjects (14.9%) than ziprasidone-treated subjects (4.2%) reported weight gain ≥7%. Akathisia and somnolence in the ziprasidone group and akathisia and insomnia in the risperidone group were the most common side effects. Treatment-related/treatment-emergent adverse events were reported by 79.7% and 71.1% of ziprasidone-treated and risperidone-treated subjects, respectively. Conclusion: In Chinese subjects, ziprasidone was as effective as risperidone, with less weight gain and less prolactin elevation.
Molecular character ization of digestate identifies microorganisms that correlate to reactor perf ormance

We conducted a time-course analysis of thermophilic anaerobic digestion of dairy manure and wheat distillery thin stillage, both individually and in combination. Sequencing of universal chaperonin targets provided a phylogenetic survey of both Bacteria and Archaea in the digestate, along with an appraisal of the diversity of the reactor microbiome. A total of 1129 bacterial operational taxonomic units (OTU) were detected in the reactors, with OTU related to Clostridium and Acetovibrio becoming numerically dominant by day 7 and day 21 respectively. Archaeal communities were less diverse, with 19 OTU detected representing both acetoclastic and hydrogenotrophic methanogens. Regardless of the input material or the initial microbial community distribution, the same organisms came to dominate the reactors, reflecting the strong selective pressures present in the digesters. Quantitative PCR was used to correlate OTU to reactor performance measures. Bacterial and Archaeal OTU were identified with significant correlations to acetate levels and methane production, suggesting important roles in various aspects of the methane production pathway.
Transinformation for active object recognition

This article develops an analogy between object recognition and the transmission of information through a channel based on the statistical representation of the appearances of 3D objects. This analogy provides a means to quantitatively evaluate the contribution of individual receptive field vectors, and to predict the performance of the object recognition process. Transinformation also provides a quantitative measure of the discrimination provided by each viewpoint, thus permitting the determination of the most discriminant viewpoints. As an application, the article develops an active object recognition algorithm which is able to resolve ambiguities inherent in a single-view recognition algorithm.
Optimization of Test Cases using Soft Computing Techniques : A Critical Review

Software testing is the key technology for evaluating the fault detecting capability quantitatively. Software testing is very labor-intensive and expensive process. It is a core activity in quality assurance. Test cases minimization, selection, prioritization forms common thread of optimization. Test case optimization is a multi-objective optimization, peculiar nature and NP-Complete problem. However, by applying appropriate test case optimization techniques, these efforts can be reduced considerably. Moreover, by using the multi-objective optimization of test cases with test data adequacy criteria and automation of testing process will help in improving the overall quality of the software. Present paper gives the insight into existing single objective test cases optimization techniques such as Genetic Algorithms, Ant Colony Optimization, Hybrid Genetic, Intelligent Search Agent Techniques, Particle Swan Optimization, Graph based Intelligent Techniques, Hybridization of Soft Computing techniques devised by various researchers or practionners by using single parameter like number of defect detecting capability, cost, efforts, coveragebility of requirement/ code and quality of the results. In addition to this, it highlights some research issues relating to above. Key-Words: Multi-Objective Optimization, Soft Computing Techniques, Test Cases, Test Data Adequacy
Strati cation of Anisotropy in the Paci c Upper Mantle

Based on the use of broad-band (25 sec 150 sec) Rayleigh wave group speeds to estimate the 2 component of azimuthal anisotropy, we present evidence for a strati cation of anisotropy in the uppermost mantle at large-scales across the Paci c basin. We con rm previous surface wave studies that established that the fast-axis directions of azimuthal anisotropy for intermediate and long period Rayleigh waves approximately align with present-day plate motions. At shorter periods (25 sec 50 sec), however, fast-axes align nearer to the paleoor fossil spreading direction which di ers from present-day plate motion in the old Paci c. These observations, together with the age dependence of the amplitude of azimuthal anisotropy, imply that azimuthal anisotropy in the Paci c upper lithosphere (< 100 km depth) is xed or \fossilized", on average, re ecting the strain conditions extant during the early evolution of the lithosphere rather than the current ambient ow direction. In the deeper lithosphere and asthenosphere, anisotropic fast axis directions align nearer to present-day plate motions, apparently having re-oriented to conform to the current conditions of ow. The anisotropy of the shallow lithosphere may be xed because the shear strains that can produce a change in anisotropy occur at increasing depths as the plate ages. 2
Accelerated aging-related transcriptome changes in the female prefrontal cortex

Human female life expectancy is higher than that of males. Intriguingly, it has been reported that women display faster rates of age‐related cognitive decline and a higher prevalence of Alzheimer’s disease (AD). To assess the molecular bases of these contradictory trends, we analyzed differences in expression changes with age between adult males and females, in four brain regions. In the superior frontal gyrus (SFG), a part of the prefrontal cortex, we observed manifest differences between the two sexes in the timing of age‐related changes, that is, sexual heterochrony. Intriguingly, age‐related expression changes predominantly occurred earlier, or at a faster pace, in females compared to men. These changes included decreased energy production and neural function and up‐regulation of the immune response, all major features of brain aging. Furthermore, we found that accelerated expression changes in the female SFG correlated with expression changes observed in AD, as well as stress effects in the frontal cortex. Accelerated aging‐related changes in the female SFG transcriptome may provide a link between a higher stress exposure or sensitivity in women and the higher prevalence of AD.
Log-Double-Uniform Jump-Diffision Model for Stock Price Dynamics ( Working Paper )

where a < 0 < b and 0 < p < 1 represents the probability of downword jumps and q = 1 − p is the probability of upward jumps. The set indicator function is I{S} for set S. The mean of Q is μj = 1 2 (pa + qb) and the variance of Q is σ j = pq 4 (b − a) + pa2+qb2 12 . The third central moment of Q is M (3) j ≡ E[(q − μj)] = pq 4 (b − a)(aq + bp) and The fourth central moment of Q is M (4) j ≡ E[(q−μj)] = μj +p/5(a−5aμj+10aμj−10aμj)+q/5(b−5bμj+10bμj−10bμj ). According to the Itô stochastic chain rule [5] for jump-diffusions, the log-return process ln(S(t)) satisfies the constant coefficient SDE
Thalamic reticular nucleus induces fast and local modulation of arousal state

During low arousal states such as drowsiness and sleep, cortical neurons exhibit rhythmic slow wave activity associated with periods of neuronal silence. Slow waves are locally regulated, and local slow wave dynamics are important for memory, cognition, and behaviour. While several brainstem structures for controlling global sleep states have now been well characterized, a mechanism underlying fast and local modulation of cortical slow waves has not been identified. Here, using optogenetics and whole cortex electrophysiology, we show that local tonic activation of thalamic reticular nucleus (TRN) rapidly induces slow wave activity in a spatially restricted region of cortex. These slow waves resemble those seen in sleep, as cortical units undergo periods of silence phase-locked to the slow wave. Furthermore, animals exhibit behavioural changes consistent with a decrease in arousal state during TRN stimulation. We conclude that TRN can induce rapid modulation of local cortical state. DOI: http://dx.doi. org/10.7554/eLife.08760. 001
Differential Roles of ATM- and Chk2-Mediated Phosphorylations of Hdmx in Response to DNA Damage

ABSTRACT The p53 tumor suppressor plays a major role in maintaining genomic stability. Its activation and stabilization in response to double strand breaks (DSBs) in DNA are regulated primarily by the ATM protein kinase. ATM mediates several posttranslational modifications on p53 itself, as well as phosphorylation of p53's essential inhibitors, Hdm2 and Hdmx. Recently we showed that ATM- and Hdm2-dependent ubiquitination and subsequent degradation of Hdmx following DSB induction are mediated by phosphorylation of Hdmx on S403, S367, and S342, with S403 being targeted directly by ATM. Here we show that S367 phosphorylation is mediated by the Chk2 protein kinase, a downstream kinase of ATM. This phosphorylation, which is important for subsequent Hdmx ubiquitination and degradation, creates a binding site for 14-3-3 proteins which controls nuclear accumulation of Hdmx following DSBs. Phosphorylation of S342 also contributed to optimal 14-3-3 interaction and nuclear accumulation of Hdmx, but phosphorylation of S403 did not. Our data indicate that binding of a 14-3-3 dimer and subsequent nuclear accumulation are essential steps toward degradation of p53's inhibitor, Hdmx, in response to DNA damage. These results demonstrate a sophisticated control by ATM of a target protein, Hdmx, which itself is one of several ATM targets in the ATM-p53 axis of the DNA damage response.
An ontology for internal and external business processes

In this paper we introduce our multi metamodel process ontology (m3po), which is based on various existing reference models and languages from the workflow and choreography domain. This ontology allows the extraction of arbitrary choreography interface descriptions from arbitrary internal workflow models. We also report on an initial validation: we translate an IBM Websphere MQ Workflow model into the m3po ontology and then extract an Abstract BPEL model from the ontology.
Suppression of Latent Transforming Growth Factor (TGF)-β1 Restores Growth Inhibitory TGF-β Signaling through microRNAs

Cancer cells secreting excess latent TGF-β are often resistant to TGF-β induced growth inhibition. We observed that RNAi against TGF-β1 led to apoptotic death in such cell lines with features that were, paradoxically, reminiscent of TGF-β signaling activity and that included transiently enhanced SMAD2 and AKT phosphorylation. A comprehensive search in Hela cells for potential microRNA drivers of this mechanism revealed that RNAi against TGF-β1 led to induction of pro-apoptotic miR-34a and to a globally decreased oncomir expression. The reduced levels of the oncomirs miR-18a and miR-24 accounted for the observed derepression of two TGF-β1 processing factors, thrombospondin-1, and furin, respectively. Our data suggest a novel mechanism in which latent TGF-β1, thrombospondin 1, and furin form a microRNA-mediated regulatory feedback loop. For cells with high levels of latent TGF-β, this provides a potentially widespread mechanism of escape from TGF-β-mediated growth arrest at the earliest point in the signaling pathway, TGF-β processing.
Event trigger identification for biomedical events extraction using domain knowledge

MOTIVATION In molecular biology, molecular events describe observable alterations of biomolecules, such as binding of proteins or RNA production. These events might be responsible for drug reactions or development of certain diseases. As such, biomedical event extraction, the process of automatically detecting description of molecular interactions in research articles, attracted substantial research interest recently. Event trigger identification, detecting the words describing the event types, is a crucial and prerequisite step in the pipeline process of biomedical event extraction. Taking the event types as classes, event trigger identification can be viewed as a classification task. For each word in a sentence, a trained classifier predicts whether the word corresponds to an event type and which event type based on the context features. Therefore, a well-designed feature set with a good level of discrimination and generalization is crucial for the performance of event trigger identification. RESULTS In this article, we propose a novel framework for event trigger identification. In particular, we learn biomedical domain knowledge from a large text corpus built from Medline and embed it into word features using neural language modeling. The embedded features are then combined with the syntactic and semantic context features using the multiple kernel learning method. The combined feature set is used for training the event trigger classifier. Experimental results on the golden standard corpus show that >2.5% improvement on F-score is achieved by the proposed framework when compared with the state-of-the-art approach, demonstrating the effectiveness of the proposed framework.
Increased risks of parkinsonism in the 3 years after chronic renal failure

Aims: Movement disorders are one of the central nervous system complications in uremic patients. Asterixis, multifocal myoclonus, and restless leg syndrome are well‐documented in this category. Acute parkinsonism, however, is only reported in rare series with a small number of cases. In this study, we investigated the risk for parkinsonism during a 3‐year follow‐up period after a diagnosis of uremia.
Part 3: Evidence evaluation process: 2010 International Consensus on Cardiopulmonary Resuscitation and Emergency Cardiovascular Care Science With Treatment Recommendations.

Peter T. Morley, Chair; Dianne L. Atkins; John E. Billi; Leo Bossaert; Clifton W. Callaway; Allan R. de Caen; Charles D. Deakin; Brian Eigel; Mary Fran Hazinski; Robert W. Hickey; Ian Jacobs; Monica E. Kleinman; Rudolph W. Koster; Mary E. Mancini; William H. Montgomery; Laurie J. Morrison; Vinay M. Nadkarni; Jerry P. Nolan; Robert E. O’Connor; Jeffrey M. Perlman; Michael R. Sayre; Tanya I. Semenko; Michael Shuster; Jasmeet Soar; Jonathan Wyllie; David Zideman
3DVAR and Cloud Analysis with WSR-88D Level-II Data for the Prediction of the Fort Worth, Texas, Tornadic Thunderstorms. Part I: Cloud Analysis and Its Impact

Abstract In this two-part paper, the impact of level-II Weather Surveillance Radar-1988 Doppler (WSR-88D) reflectivity and radial velocity data on the prediction of a cluster of tornadic thunderstorms in the Advanced Regional Prediction System (ARPS) model are studied. Radar reflectivity data are used primarily in a cloud analysis procedure that retrieves the amount of hydrometeors and adjusts in-cloud temperature, moisture, and cloud fields, while radial velocity data are analyzed through a three-dimensional variational (3DVAR) scheme that contains a mass divergence constraint in the cost function. In Part I, the impact of the cloud analysis and modifications to the scheme are examined while Part II focuses on the impact of radial velocity and the mass divergence constraint. The case studied is that of the 28 March 2000 Fort Worth, Texas, tornado outbreaks. The same case was studied by Xue et al. using the ARPS Data Analysis System (ADAS) and an earlier version of the cloud analysis procedure with WSR-88.