Miracle-dz/UniFAR-FTUs huggingface dataset:
RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods

Abstract RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.
Direct torque control using space vector modulation and dynamic performance of the drive, via a fuzzy logic controller for speed regulation

This paper presents a method of controlling the Torque of an asynchronous motor that is fed by a PWM-Inverter. The control method that is used is a modified direct torque control (DTC) scheme with constant switching frequency, using space vector modulation (SVM). In this scheme a closed loop of torque control is applied. Small and rapid changes on motor's torque are achieved by applying an appropriate voltage vector, which is responsible for the jerky movement of the stator's flux vector. The voltage vector can be of any magnitude and angle and is produced using Space Vector Pulse Width Modulation. The modified method of DTC using SVM improves the electrical magnitudes of asynchronous machine, such as reduction of current and flux ripple and also fading out the edges of torque ripple which are occurred during the sector changes of stator flux vector. Another point of this paper is the presentation of speed control in dynamic situations. The production of the reference torque value is achieved by using a fuzzy logic speed controller. The response of the fuzzy PI is compared to the response of a classic PI speed controller. Results, shows that the fuzzy PI speed controller has a better response in a wide range area of motor speed. Combining the characteristics of DTC-SVM scheme and the fuzzy logic speed controller we can have a high performance vector controlled asynchronous motor drive.
Energy-Efficient Intrusion Detection and Mitigation for Networked Control Systems Security

This paper proposes an energy-efficient security-aware architecture for wireless control systems to be used in factory automation. We face deception attacks that corrupt commands and measurements in a smart way and with intermittent behavior to produce the highest damage without being discovered. The intrusion is hard to distinguish from normal disturbance. Furthermore, protection against attacks is energy-consuming and it would be desirable to activate protection only when needed. We propose packet-based selective encryption to reduce energy consumption, and to detect when an attack starts and ends. Since energy consumption depends also on packet transmission rate, especially during attacks, we also propose to adapt it according to instantaneous control performance.
Accelerating Markov Chain Monte Carlo with Active Subspaces

The Markov chain Monte Carlo (MCMC) method is the computational workhorse for Bayesian inverse problems. However, MCMC struggles in high-dimensional parameter spaces, since its iterates must sequentially explore the high-dimensional space. This struggle is compounded in physical applications when the nonlinear forward model is computationally expensive. One approach to accelerate MCMC is to reduce the dimension of the state space. Active subspaces are part of an emerging set of tools for subspace-based dimension reduction. An active subspace in a given inverse problem indicates a separation between a low-dimensional subspace that is informed by the data and its orthogonal complement that is constrained by the prior. With this information, one can run the sequential MCMC on the active variables while sampling independently according to the prior on the inactive variables. However, this approach to increase efficiency may introduce bias. We provide a bound on the Hellinger distance between the true posterio.
Une géographie sociale dans le triangle des rapports hommes, sociétés, espaces (A social geography in the triangle of the relationships between men, societies, spaces)

Ce projet de geographie sociale prend en compte l'etre humain considere dans son double processus de socialisation et de spatialisation. Ses objets de recherche concernent le rapport tant individuel que collectif a l'espace et les formes geographiques qu'il engendre. Il accorde un grand credit aux representations, ainsi qu 'aux dimensions politiques, economiques et ideologiques des constructions geographiques.
Content and transformation effect matching for automated home video editing

While camcordcrs havc bccome a commodity home appliance, few watch the recorded vidcos or sharc thcm with friends and relatives duc to the difficulty of turning thc raw footagc into a compclling vidco story. Previous works on Automated Video Editing (AVE) dcvelopcd an automatic solution for vidco contcnt selection and video-music matching. Howcvcr, to automatically apply vidco transformation effects, such a fastislow motion, thresholding, binariration and watercolor, has not been solved or even addressed. In this paper, we proposed several automatic video effect and contcnt matching schemes, which facilitate generating more compelling and intcrcsting AVE rcsults.
Adaptive thresholding based EMD for delineation of QRS complex in ECG signal analysis

Analyzing the patterns of ECG signals is a vital step in detecting abnormal conditions of the heart. Early detection of cardiac arrhythmia could avoid sudden cardiac death. Artifacts like power line interference and muscle contraction degrades the quality of the recorded ECG signals. In this paper, empirical mode decomposition (EMD) technique used to remove undesirable frequency components in denoising the ECG signals. An adaptive thresholding has been embedded with an EMD algorithm to improve the performance of the proposed method to detect the QRS (Q wave, R wave, S wave) complex. The performance of the proposed method is evaluated in terms of Sensitivity (Se) that results 99.87%, positive predictivity (Pp) of 99.76%, detection error (Er) of 0.41%. The proposed method is found to be more accurate to detect QRS complex in mit-db database compared to cudb database in ECG signal analysis.
Early responsiveness of women with osteoporosis to teriparatide after therapy with alendronate or risedronate.

BACKGROUND Anabolic responsiveness to teriparatide can be blunted or delayed in patients previously treated with alendronate. The extent of this effect is different for other antiresorptives. This study evaluated the early anabolic effects of teriparatide in postmenopausal women with osteoporosis previously treated with alendronate or risedronate. METHODS Patients treated for at least 24 months with alendronate or risedronate discontinued their bisphosphonate and received teriparatide for 12 months. The primary endpoint was a comparison of changes from baseline in N-terminal propeptide of type 1 collagen after 3 months between prior bisphosphonate groups. We also examined changes in other bone turnover markers, bone mineral density (BMD), and relationships between early changes in bone turnover markers and 12-month areal and volumetric BMD. RESULTS In the prior risedronate group, the N-terminal propeptide of type 1 collagen increase was significantly greater after 3 months of teriparatide than in the prior alendronate group (mean +/- se, 86.0 +/- 5.6 vs. 61.2 +/- 5.3 ng/ml, respectively; P < 0.001). Findings were similar for the other bone turnover markers. The changes in areal BMD and trabecular spine volumetric BMD were also greater in the prior risedronate group (P < 0.05). Early changes in bone turnover markers correlated with changes in trabecular spine volumetric BMD at 12 months (Spearman r = 0.45). Teriparatide was well tolerated. CONCLUSION This nonrandomized but prospective study suggests that there may be differences in anabolic responsiveness to teriparatide as a function of the type of prior bisphosphonate exposure.
A decision-theoretic approach to data mining

In this paper, we develop a decision-theoretic framework for evaluating data mining systems, which employ classification methods, in terms of their utility in decision-making. The decision-theoretic model provides an economic perspective on the value of "extracted knowledge", in terms of its payoff to the organization, and suggests a wide range of decision problems that arise from this point of view. The relation between the quality of a data mining system and the amount of investment that the decision maker is willing to make is formalized. We propose two ways by which independent data mining systems can be combined and show that the combined data mining system can be used in the decision-making process of the organization to increase payoff. Examples are provided to illustrate the various concepts, and several ways by which the proposed framework can be extended are discussed.
Mapping of DSP algorithms on the MONTIUM architecture

In battery operated mobile devices there is a growing need for flexible high-performance architectures due to the limited amount of available energy and the increasing demand of processing power. Course grained reconfigurable architectures could be the key to more energy-efficient, yet programmable systems. In this paper a course-grained reconfigurable architecture, called MONTIUM, is presented. Several mappings of commonly used digital signal processing algorithms are shown to demonstrate the flexibility of this architecture.
The detection of monosynaptic connexions from inspiratory bulbospinal neurones to inspiratory motoneurones in the cat.

Simultaneous recordings were made of the discharges of inspiratory bulbospinal neurones and phrenic or external intercostal alpha‐motoneurones in the anaesthetized cat. The connexions between these neurones were studied by the construction of cross‐correlation histograms from their discharges. Peaks observed in the cross‐correlation histograms were divided into three groups on the basis of their time courses: narrow, medium‐width and high‐frequency oscillations (h.f.o.). Narrow peaks were defined as having half‐widths less than 1.1 ms and medium‐width peaks as having half‐widths greater than this, while h.f. o. was characterized by periodic waves in the range 60‐120 Hz. H.f. o. peaks were interpreted as being derived from the well known periodic synchronization of medullary inspiratory neurones in this frequency range. The time courses and latencies of the medium‐width peaks could be quantitatively explained by a simple model representing excitation of the motoneurones by bulbospinal neurones whose discharges showed synchronization within +/‐ 1 ms of the reference spike, together with temporal dispersion in bulbospinal axons having a distribution of conduction velocities given by the measurements of this study. Such an explanation was essential for some of the medium‐width peaks, whose latencies were short compared to the conduction times to the spinal cord for their own axons, but for other medium‐width peaks oligosynaptic excitation of the motoneurones from the identified bulbospinal neurones was another possible explanation. The narrow peaks were of appropriate durations for monosynaptic connexions and were all at appropriate latencies (0.6‐2.4 ms after the calculated arrival time of the bulbospinal impulse in the segment concerned). It is concluded from the observations of narrow peaks that monosynaptic excitation exists between inspiratory bulbospinal neurones and both phrenic and external intercostal motoneurones. However, because of the existence of presynaptic synchronization, as shown by the presence of the medium‐width peaks, such a conclusion is predicated upon being able to discriminate against such an effect. The model showed that this restriction applies just as much to the measurements of excitatory post‐synaptic potentials (e.p.s.p.s) by spike‐triggered averaging as it does to cross‐correlation measurements. We suggest that the discrimination against presynaptic synchronization here was possible only because the long conduction distance created temporal dispersion in the synchronized presynaptic impulses.
Detection of aspiration in enterally fed patients: a requiem for bedside monitors of aspiration.

BACKGROUND Pulmonary aspiration of gastric and oropharyngeal contents is common in enterally fed patients. Detection of early aspiration in these patients has relied on clinical impression, the coloring of enteral feedings with dyes, and less commonly the detection of elevated glucose in tracheal aspirates. The potential benefits, risks, and clinical use of bedside monitors of aspiration are under increasing scrutiny. METHODS Literature review. Although this review reflects the opinions of the authors, recommendations of an expert consensus panel (North American Summit on Aspiration, which included one author, J. P. Maloney) were also used to guide recommendations. The specific recommendations of that panel are presented elsewhere. RESULTS No large prospective clinical trials have been done to evaluate the use and safety of bedside monitors for aspiration. Clinical impression remains a poor "gold standard" of aspiration diagnosis in enterally fed patients. The coloring of enteral feedings with blue dyes (chiefly FD&C Blue No.1) is ubiquitous in hospitals despite evidence that it is not sensitive and potentially harmful. Cases of absorption of blue dye from enteral feedings in patients with critical illness have raised concern about the safety of the blue dye method, particularly in light of apparent toxic effects of these dyes on mitochondria. The glucose detection method has not been embraced; it too has little use and is labor intensive. CONCLUSIONS Use of colored dyes in enteral feedings and glucose detection methods should be abandoned. Nonrecumbent positioning is an evidenced-based method for aspiration prevention that needs to be re-emphasized. Novel bedside methods of detecting early aspiration are needed to supplement preventative strategies.
Social Semantic Web Fosters Idea Brainstorming

Generating and identifying promising ideas represent important challenges for any Enterprise that is focused on knowledge-intensive activities. The generation of new ideas, especially high-quality creative ideas, is vital to business success. Brainstorming is a didactic method that can be exploited to sustain the development of high order skills considered fundamental to foster innovation. On the other side, brain-storming sessions produce new ideas that have to be evaluated and possibly selected. In this paper the Social Semantic Web is exploited in order to deﬁne an approach for brainstorming that overcomes the limitations of the existing systems supporting groups in generating ideas. The Semantic Web-based structures organize, correlate and simplify the search for user-generated contents (e.g. ideas). Meanwhile, user-generated contents are analysed in order to elicit non-asserted correlations between them that are used to enrich the aforementioned structures.
Veto Bargaining and Coalition Formation: A Theory of Presidential Policymaking with Application to Venezuela

This paper reports a work in progress. We extend a simple, complete-information model of executive-legislative bargaining over policy devised for the U.S. to fit the case of Venezuela. We first deal with two major differences between the two systems: Venezuelan presidents have a weaker veto than their U.S. counterparts, and Venezuelan presidents can initiate bills. Two main predictions follow from the model’s assumptions: no veto should ever occur, and no executive-sponsored bill should ever be defeated; the logic behind both hypotheses is anticipation. The evidence from Venezuela (1959-1995) falsifies both predictions, suggesting that some of the model’s assumptions are too restrictive. We make tentative suggestions of what a more complete model should look like. We then address a third difference between the presidential systems of Venezuela and the U.S.: Venezuelan presidents often make post-election coalitions to improve their support in the assembly. We find strong evidence of one effect of this legislative strategy: coalition cabinets have better support for their programs in the legislature.
Neural Network-Based Passive Filtering for Delayed Neutral-Type Semi-Markovian Jump Systems

This paper investigates the problem of exponential passive filtering for a class of stochastic neutral-type neural networks with both semi-Markovian jump parameters and mixed time delays. Our aim is to estimate the states by designing a Luenberger-type observer, such that the filter error dynamics are mean-square exponentially stable with an expected decay rate and an attenuation level. Sufficient conditions for the existence of passive filters are obtained, and a convex optimization algorithm for the filter design is given. In addition, a cone complementarity linearization procedure is employed to cast the nonconvex feasibility problem into a sequential minimization problem, which can be readily solved by the existing optimization techniques. Numerical examples are given to demonstrate the effectiveness of the proposed techniques.
Towards context-aware adaptable web services

In this paper, we present a context framework that facilitates the development and deployment of context-aware adaptable Web services. Web services are provided with context information about clients that may be utilized to provide a personalized behavior. Context is extensible with new types of information at any time without any changes to the underlying infrastructure. Context processing is done by Web services, context plugins, or context services. Context plugins and context services pre- and post-process Web service messages based on the available contextinformation. Both are essential for automatic context processing and automatic adaption of Web services to new context types without the necessity to adjust the Web services themselves. We implemented the context framework within the ServiceGlobe system, our open and distributed Web service platform.
Blood pressure changes in patients with chronic heart failure undergoing slow breathing training

Abstract Background. Slow breathing training (SBT) has been proposed as a new non-pharmacological treatment able to induce favorable effects in patients with chronic heart failure (CHF). However, no information is available regarding its effects on orthostatic blood pressure (BP) changes in these patients, an issue of practical relevance given the reported BP-lowering effect of SBT. The aim of this study is to evaluate the influence of SBT on BP and whether SBT induces orthostatic hypotension (OH) or changes in quality of life (QoL) in CHF patients. Methods. The analysis was performed as part of an ongoing crossover open trial aimed at assessing the clinical effectiveness of SBT in treated patients with CHF. The patients underwent 10–12 weeks of SBT with the RESPeRATE device and 10–12 week follow-up under usual care. Patients were randomly divided into two groups: group I began with SBT, followed by usual care; group II began with usual care, followed by SBT. Patients undergoing SBT were asked to perform each day two separate 15 min sessions of device-guided SBT at a breathing frequency of 6 breaths/min. In all patients, before the enrollment and after each study phase, clinical data collection and BP measurements in sitting, supine and standing position were performed. OH was defined as a decrease of ≥ 20 mmHg in systolic blood pressure (SBP) or ≥ 10 mmHg in diastolic blood pressure (DBP) within 3 min of standing. QoL was assessed three times at the beginning, and after each phase of the study by the Minnesota Living with Heart Failure (MLHF) questionnaire. Results. Forty patients (two equal groups) completed the study, with the following baseline characteristics: 32 males/eight females, age 63.3 ± 13.4 years, 25 with ischemic CHF, 37 in New York Heart Association class II and three in class III, left ventricular ejection fraction 30.8 ± 6.7%, mean BP 138.7 ± 16.5/83.1 ± 11.5 mmHg, 23 with arterial hypertension and four with a history of stroke. There were no significant differences between the groups in clinical characteristics, SBP and DBP at rest, while seated and before and after standing up. OH prevalence was low and did not change during the study (10% vs 10%). No significant difference in average SBP and DBP changes secondary to body position were found when comparing the two study phases. Decrease in MLHF score was observed in group I during SBT (p = 0.002), but not in group II. Conclusions. Our data indicate that SBT is safe, does not affect the prevalence of OH in CHF patients and shows a non-significant tendency to improve QoL. These results should be confirmed in a larger sample of patients to support the safety of SBT and its possible benefits as a novel component of cardiorespiratory rehabilitation programs in CHF.
The Board of Regents of the University of Wisconsin System Evaluating the Labor Market Performance of Veterans Using a Matched Comparison Group Design Author ( s ) :

The effect of active-duty service on civilian earnings is estimated using the Reserve Components Surveys, permitting a matched comparison between reservists who are veterans and reservists without active-duty service. Estimated treatment effects control for selection by the military and individuals, due in part to identical active-duty and reserve entrance requirements. The average impact of active-duty service on civilian earnings is 3 percent among the reservist population, reflecting effects of essentially zero for enlisted personnel and 1O percent for officers. Among white enlisted personnel veteran effects are negative but small, while averaging about 5 percent among African-Americans. Wage penalties resulting from Vietnam-era service are larger for white draftees than volunteers, while African-American draftees and volunteers realized gains.
True random number generation based on environmental noise measurements for military applications

True random number generators can significantly contribute to the development of high security cryptographic schemes, such as those required for use in military applications. This article presents some the results of an innovative method for the generation of truly random number sequences, based on environmental noise measurements. The statistical properties of different noise types have been studied. Based on this study, an efficient random number generator has been developed that uses signals from the built in microphone that is ubiquitous most current personal computers and other personal information processing systems. Statistical measures have been determined that measure the randomness qualities of the output sequence. These measures have been studied for different input noise properties. The merit of the proposed generator in terms of the rate at which random numbers are produced has also been assessed.