Miracle-dz/UniFAR-FTUs huggingface dataset:
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures

Mobile genetic elements have significantly contributed to the shaping of mammalian genomes. The RTAnalyzer software tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome. More specifically, a sequence of interest is searched for in genomic databases using BLAST. Each hit, along with additional 5′ and 3′ sequences of pre-defined lengths, is saved. RTAnalyzer searches for specific L1 retrotransposition signatures (i.e. target site duplication, endonuclease cleavage site and poly(A)), and then calculates an overall retrotransposition score. This score represents the likelihood of a given sequence originating from a retrotransposition event involving the L1 machinery. RTAnalyzer may be used under GNU public license, and is available at http://www.riboclub. org/rtanalyzer.
Recommendations on the verification of local weather forecasts

The Library ECMWF Shinfield Park Reading, Berks RG2 9AX library@ecmwf.int Series: ECMWF Technical Memoranda A full list of ECMWF Publications can be found on our web site under: http://www.ecmwf.int/publications/library/ecpublications/ © Copyright 2003 European Centre for Medium Range Weather Forecasts Shinfield Park, Reading, Berkshire RG2 9AX, England
New Delay-Dependent Stability Criteria for Neural Networks With Time-Varying Delay

In this letter, a new method is proposed for stability analysis of neural networks (NNs) with a time-varying delay. Some less conservative delay-dependent stability criteria are established by considering the additional useful terms, which were ignored in previous methods, when estimating the upper bound of the derivative of Lyapunov functionals and introducing the new free-weighting matrices. Numerical examples are given to demonstrate the effectiveness and the benefits of the proposed method
Modulation Techniques to Reduce Leakage Current in Three-Phase Transformerless H7 Photovoltaic Inverter

Recently, reduced common-mode voltage (CMV) pulsewidth modulation (RCMV-PWM) methods have been proposed to reduce the leakage current in three-phase transformerless photovoltaic (PV) systems. However, most of these studies only focus on leakage current elimination and neglect the overall performance of the PV systems on issues such as cost, voltage linearity, dc-link current ripples, and harmonic distortion. In this paper, a three-phase transformerless inverter, adapted from the single-phase H5 topology, is investigated. Since the H5 topology has been conventionally developed for a single-phase system, its adaptation to the three-phase system requires the development of corresponding three-phase modulation techniques. Hence, modulation techniques are proposed based on conventional PWM. The performances of the proposed PWM, in terms of CMV, leakage current, voltage linearity, output current ripples, dc-link current ripples, and harmonic distortion are studied and discussed via simulation and experiment. It is proven that the proposed topology is able reduce the leakage current without sacrificing the overall performance of the system.
Bigrams and the Richness of the Stimulus

Recent challenges to Chomsky's poverty of the stimulus thesis for language acquisition suggest that children's primary data may carry "indirect evidence" about linguistic constructions despite containing no instances of them. Indirect evidence is claimed to suffice for grammar acquisition, without need for innate knowledge. This article reports experiments based on those of Reali and Christiansen (2005), who demonstrated that a simple bigram language model can induce the correct form of auxiliary inversion in certain complex questions. This article investigates the nature of the indirect evidence that supports this learning, and assesses how reliably it is available. Results confirm the original finding for one specific sentence type but show that the model's success is highly circumscribed. It performs poorly on inversion in related constructions in English and Dutch. Because other, more powerful statistical models have so far been shown to succeed only on the same limited subset of cases as the bigram model, it remains to be seen whether stimulus richness can be substantiated more generally.
Increased Efferent Cardiac Sympathetic Nerve Activity and Defective Intrinsic Heart Rate Regulation in Type 2 Diabetes

Elevated sympathetic nerve activity (SNA) coupled with dysregulated β-adrenoceptor (β-AR) signaling is postulated as a major driving force for cardiac dysfunction in patients with type 2 diabetes; however, cardiac SNA has never been assessed directly in diabetes. Our aim was to measure the sympathetic input to and the β-AR responsiveness of the heart in the type 2 diabetic heart. In vivo recording of SNA of the left efferent cardiac sympathetic branch of the stellate ganglion in Zucker diabetic fatty rats revealed an elevated resting cardiac SNA and doubled firing rate compared with nondiabetic rats. Ex vivo, in isolated denervated hearts, the intrinsic heart rate was markedly reduced. Contractile and relaxation responses to β-AR stimulation with dobutamine were compromised in externally paced diabetic hearts, but not in diabetic hearts allowed to regulate their own heart rate. Protein levels of left ventricular β1-AR and Gs (guanine nucleotide binding protein stimulatory) were reduced, whereas left ventricular and right atrial β2-AR and Gi (guanine nucleotide binding protein inhibitory regulatory) levels were increased. The elevated resting cardiac SNA in type 2 diabetes, combined with the reduced cardiac β-AR responsiveness, suggests that the maintenance of normal cardiovascular function requires elevated cardiac sympathetic input to compensate for changes in the intrinsic properties of the diabetic heart.
Neural circuitry of abdominal pain‐related fear learning and reinstatement in irritable bowel syndrome

Altered pain anticipation likely contributes to disturbed central pain processing in chronic pain conditions like irritable bowel syndrome (IBS), but the learning processes shaping the expectation of pain remain poorly understood. We assessed the neural circuitry mediating the formation, extinction, and reactivation of abdominal pain‐related memories in IBS patients compared to healthy controls (HC) in a differential fear conditioning paradigm.
Open Access Research

Research Issues in accelerometer methodology: the role of epoch length on estimates of physical activity and relationships with health outcomes in overweight, post-menopausal women Abstract Background: Current accelerometer technology allows for data collection using brief time sampling intervals (i.e., epochs). The study aims were to examine the role of epoch length on physical activity estimates and subsequent relationships with clinically-meaningful health outcomes in post-menopausal women. Methods: Data was obtained from the Woman On the Move through Activity and Nutrition Study (n = 102). Differences in activity estimates presented as 60s and 10s epochs were evaluated using paired t-tests. Relationships with health outcomes were examined using correlational and regression analyses to evaluate differences by epoch length. Results: Inactivity, moderate-and vigorous-intensity activity (MVPA) were significantly higher and light-intensity activity was significantly lower (all P < 0.001) when presented as 10s epochs. The correlation between inactivity and self-reported physical activity was stronger with 10s estimates (P < 0.03); however, the regression slopes were not significantly different. Conversely, relationships between MVPA and body weight, BMI, whole body and trunk lean and fat mass, and femoral neck bone mineral density was stronger with 60s estimates (all P < 0.05); however, regression slopes were similar. Conclusion: These findings suggest that although the use of a shorter time sampling interval may suggestively reduce misclassification error of physical activity estimates, associations with health outcomes did not yield strikingly different results. Additional studies are needed to further our understanding of the ways in which epoch length contributes to the ascertainment of physical activity in research studies. Background Waist-worn accelerometers provide a reliable and valid objective measure of free-living physical activity[1]. Accelerometers have been used in many research applications including validation of self-report physical activity measures, identification of psychosocial and environmental correlates of physical activity behavior, quantifica-tion of physical activity to examine relationships with
Beyond the nuclear starburst? Clustered star formation in major mergers

Recent simulation work has successfully captured the formation of the star clusters that have been observed in merging galaxies. These studies, however, tend to focus on studying extreme starbursts, such as the Antennae galaxies. We aim to establish whether there is something special occurring in these extreme systems or whether the mechanism for cluster formation is present in all mergers to a greater or lesser degree. We undertake a general study of merger-induced star formation in a sample of 5 pc resolution adaptive mesh refinement simulations of low redshift equal-mass mergers with randomly-chosen orbital parameters. We find that there is an enhanced mass fraction of very dense gas that appears as the gas density probability density function evolves during the merger. This finding has implications for the interpretation of some observations; a larger mass fraction of dense gas could account for the enhanced HCN/CO ratios seen in ULIRGs and predicts that αCO is lower in mergers, as for a given mass of H2, CO emission will increase in a denser environment. We also find that as the star formation rate increases, there is a correlated peak in the velocity dispersion of the gas, which we attribute to increasing turbulence driven by the interaction itself. Star formation tends to be clumpy: in some cases there is extended clumpy star formation, but even when star formation is concentrated within the inner kpc (i.e. what may be considered a nuclear starburst) it still often has a clumpy, rather than a smooth, distribution. We find no strong evidence for a clear bimodality in the Kennicutt-Schmidt relation for the average mergers simulated here. Instead, they are typically somewhat offset above the predicted quiescent relation during their starbursts.
Intragroup diffuse light in compact groups of galaxies – II. HCG 15, 35 and 51

This continuing study of intragroup light in compact groups of galaxies aims to establish new constraints to models of formation and evolution of galaxy groups, specially of compact groups, which are a key part in the evolution of larger structures, such as clusters. In this paper we present three additional groups (HCG 15, 35 and 51) using deep wide-field B- and R-band images observed with the LAICA camera at the 3.5-m telescope at the Calar Alto observatory (CAHA). This instrument provides us with very stable flat-fielding, a mandatory condition for reliably measuring intragroup diffuse light. The images were analysed with the OV_WAV package, a wavelet technique that allows us to uncover the intragroup component in an unprecedented way. We have detected that 19,15 and 26 per cent of the total light of HCG 15, 35 and 51, respectively, are in the diffuse component, with colours that are compatible with old stellar populations and with mean surface brightness that can be as low as 28.4 B mag arcsec -2 . Dynamical masses, crossing times and mass-to-light ratios were recalculated using the new group parameters. Also tidal features were analysed using the wavelet technique.
The Application of REDOR NMR to Understand the Conformation of Epothilone B

The structural information of small therapeutic compounds complexed in biological matrices is important for drug developments. However, structural studies on ligands bound to such a large and dynamic system as microtubules are still challenging. This article reports an application of the solid-state NMR technique to investigating the bioactive conformation of epothilone B, a microtubule stabilizing agent, whose analog ixabepilone was approved by the U.S. Food and Drug Administration (FDA) as an anticancer drug. First, an analog of epothilone B was designed and successfully synthesized with deuterium and fluorine labels while keeping the high potency of the drug; Second, a lyophilization protocol was developed to enhance the low sensitivity of solid-state NMR; Third, molecular dynamics information of microtubule-bound epothilone B was revealed by high-resolution NMR spectra in comparison to the non-bound epothilone B; Last, information for the macrolide conformation of microtubule-bound epothilone B was obtained from rotational-echo double-resonance (REDOR) NMR data, suggesting the X-ray crystal structure of the ligand in the P450epoK complex as a possible candidate for the conformation. Our results are important as the first demonstration of using REDOR for studying epothilones.
Gestational Age and Outcomes in Critical Congenital Heart Disease

Population-based cohort study to assess impact of GA on morbidity and mortality in preterm and term infants with CCHD. BACKGROUND AND OBJECTIVES: It is unknown how gestational age (GA) impacts neonatal morbidities in infants with critical congenital heart disease (CCHD). We aim to quantify GA-specific mortality and neonatal morbidity in infants with CCHD. METHODS: Cohort study using a database linking birth certificate, infant hospital discharge, readmission, and death records, including infants 22 to 42 weeks’ GA without chromosomal anomalies (2005–2012, 2 988 925 live births). The International Classification of Diseases, Ninth Revision diagnostic and procedure codes were used to define CCHD and neonatal morbidities (intraventricular hemorrhage, retinopathy, periventricular leukomalacia, chronic lung disease, necrotizing enterocolitis). Adjusted absolute risk differences (ARDs) with 95% confidence intervals (CIs) were calculated. RESULTS: We identified 6903 out of 2 968 566 (0.23%) infants with CCHD. The incidence of CCHD was highest at 29 to 31 weeks’ GA (0.9%) and lowest at 39 to 42 weeks (0.2%). Combined neonatal morbidity or mortality in infants with and without CCHD was 82.8% and 57.9% at <29 weeks and declined to 10.9% and 0.1% at 39 to 42 weeks’ GA. In infants with CCHD, being born at 34 to 36 weeks was associated with a higher risk of death or morbidity than being born at 37 to 38 weeks (adjusted ARD 9.1%, 95% CI 5.5% to 12.7%), and being born at 37 to 38 weeks was associated with a higher risk of death or morbidity than 39 to 42 weeks (adjusted ARD 3.2%, 95% CI 1.6% to 4.9%). CONCLUSIONS: Infants born with CCHD are at high risk of neonatal morbidity. Morbidity remains increased across all GA groups in comparison with infants born at 39 to 42 weeks. This substantial risk of neonatal morbidity is important to consider when caring for this patient population.
Effects of Benzoic Acid and Thymol on Growth Performance and Gut Characteristics of Weaned Piglets

A total of 144 weaned crossed pigs were used in a 42-d trial to explore the effects of different concentrations/combinations of benzoic acid and thymol on growth performance and gut characteristics in weaned pigs. Pigs were randomly allotted to 4 dietary treatments: i) control (C), basal diet, ii) C+1,000 mg/kg benzoic acid+100 mg/kg thymol (BT1), iii) C+1,000 mg/kg benzoic acid+200 mg/kg thymol (BT2) and, iv) C+2,000 mg/kg benzoic acid+100 mg/kg thymol (BT3). Relative to the control, pigs fed diet BT3 had lower diarrhoea score during the overall period (p<0.10) and improved feed to gain ratio between days 1 to 14 (p<0.05), which was accompanied by improved apparent total tract digestibility of ether extract, Ca and crude ash (p<0.05), and larger lipase, lactase and sucrose activities in the jejunum (p<0.05) at d 14 and d 42. Similarly, relative to the control, pigs fed diet BT3 had higher counts for Lactobacillus spp in digesta of ileum at d 14 (p<0.05), and pigs fed diets BT1, BT2, or BT3 also had higher counts of Bacillus spp in digesta of caecum at d 14 (p<0.05), and lower concentration of ammonia nitrogen in digesta of caecum at d 14 and d 42 (p<0.05). Finally, pigs fed diet BT3 had higher concentration of butyric acid in digesta of caecum at d 42 (p<0.05), and a larger villus height:crypt depth ratio in jejunum and ileum at d 14 (p<0.05) than pigs fed the control diet. In conclusion, piglets fed diet supplementation with different concentrations/combinations of benzoic acid and thymol could improve feed efficiency and diarrhoea, and improve gut microfloral composition. The combination of 2,000 mg/kg benzoic acid+100 mg/kg thymol produced better effects than other treatments in most measurements.
How sharp is the tropopause at midlatitudes?

Ten years of high‐resolution radiosonde data are contrasted with fifteen years of ECMWF reanalysis (ERA) data to explore the tropopause region above two midlatitude stations (Munich and Stuttgart) in Southern Germany. We present time‐averaged vertical profiles of several meteorological parameters relative to the tropopause. A strong mean inversion at the tropopause is evident from the radiosonde profiles with a vertical extension of about 2 km and a temperature increase of about 4 K. The impact of the tropopause definition on the strength of this inversion is discussed as well as the relevance of baroclinic eddies in forming it. The climatological profiles for Munich and Stuttgart do not differ significantly.
Algorithms of the Complex Tactile Information Processing

The t a c t i l e i n f o r m a t i o n p l a y s a n i m p o r t a n t r o l e f o r a n i n t e l l i g e n t r o b o t a c t i v i t y . The m a i n a d v a n t a g e o f t h e t a c t i l e i n f o r m a t i o n o v e r t h e o p t i c a l one l i e s i n i t s 3 -d c h a r a c t e r . The t a c t i l e i n f o r m a t i o n can b e used b o t h f o r a f i n e r p o s i t i o n i n g b e f o r e g r i p p i n g t h e o b j e c t and f o r t h e shape and d i m e n s i o n r e c o g n i t i o n by a s i m u l t a n e o u s h a n d l i n g t h e o b j e c t .
The “Silk Cursor”: investigating transparency for 3D target acquisition

This study investigates dynamic 3D target acquisition. The focus is on the relative effect of specific perceptual cues. A novel technique is introduced and we report on an experiment that evaluates its effectiveness. There are two aspects to the new technique. First, in contrast to normal practice, the tracking symbol is a volume rather than a point. Second, the surface of this volume is semi-transparent, thereby affording occlusion cues during target acquisition. The experiment shows that the volumehcclusion cues were effective in both monocular and stereoscopic conditions. For some tasks where stereoscopic presentation is unavailable or infeasible, the new techniaue offers an effective alternative.
2‐Aminoethylnitrate: pharmacological uses rediscovered and claimed as original

I am writing regarding an article I read recently which was published in your journal. The article, entitled ‘A new class of organic nitrates: investigations on bioactivation, tolerance and cross-tolerance phenomena’ was published by Schuhmacher et al. (2009). I happened to see this article while working as an undergraduate student researcher in a chemistry/biochemistry laboratory. The article presents the mononitrate compound 2-aminoethylnitrate as a modern marvel in the treatment of endothelial dysfunction that leads to cardiovascular disease(s). I was asked to synthesize this compound and as per my aspiration to understand the details and purpose of my assignment, I delved into a search for some useful references. During this process, I stumbled upon an article dating back to 1963 titled Anginal syndrome: Treatment with a long-acting nitrate (itramin tosylate) published by Batterman and Mouratoff (1963). This article addressed the use of 2-aminoethylnitrate in its p-toluenesulfonate salt form for the treatment of anginal syndrome. Not only had this idea been discussed in this article, but a number of clinical trials had also been performed relaying successful results. Also, some of the observations were confirmed by Kinnard et al., (1964). I found it quite intriguing that nearly the same information is presented in the article by Schuhmacher et al. (2009) who failed to mention, acknowledge or cite the earlier works which were published more than 40 years before their article. Upon discovering this, I brought this information to my mentor's attention who encouraged me to write to the editor to raise awareness of the issue. I was later surprised to also find a supportive and encouraging commentary written by Bauersachs (2009) in the same issue of British Journal of Pharmacology (BJP). Understandably, there was an attempt of undue, instant promotion of the use of 2-aminoethylnitrate as a modern breakthrough in which BJP became an inadvertent partner. I am concerned about the reputation of BJP and also the fact that this type of percolation of scientific errors must stop before they become a dogma and therefore have taken the initiative to bring this to your attention.
Interactive brains, social minds

To reveal the neural and behavioral dynamics of social interaction, single-person studies are increasingly complemented by research designs that simultaneously assess two or more interacting individuals. In this article, we review studies on neural mechanisms and markers of social interactions that use multi-person functional magnetic resonance imaging and electrophysiological recordings. We propose a terminology for investigating social interaction dynamics, show how forward models of action regulation may serve as a framework for investigating interpersonal action coordination and discuss different methodological approaches to studying functional brain connectivity.
Matrix Completion has No Spurious Local Minimum

Matrix completion is a basic machine learning problem that has wide applications, especially in collaborative filtering and recommender systems. Simple non-convex optimization algorithms are popular and effective in practice. Despite recent progress in proving various non-convex algorithms converge from a good initial point, it remains unclear why random or arbitrary initialization suffices in practice. We prove that the commonly used non-convex objective function for \textit{positive semidefinite} matrix completion has no spurious local minima --- all local minima must also be global. Therefore, many popular optimization algorithms such as (stochastic) gradient descent can provably solve positive semidefinite matrix completion with \textit{arbitrary} initialization in polynomial time. The result can be generalized to the setting when the observed entries contain noise. We believe that our main proof strategy can be useful for understanding geometric properties of other statistical problems involving partial or noisy observations.