Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Transcriptome Analysis Reveals the Influence of Abscisic Acid on the Metabolism of Pigments, Ascorbic Acid and Folic Acid during Strawberry Fruit Ripening

A comprehensive investigation of abscisic acid (ABA) biosynthesis and its influence on other important phytochemicals is critical for understanding the versatile roles that ABA plays during strawberry fruit ripening. Using RNA-seq technology, we sampled strawberry fruit in response to ABA or nordihydroguaiaretic acid (NDGA; an ABA biosynthesis blocker) treatment during ripening and assessed the expression changes of genes involved in the metabolism of pigments, ascorbic acid (AsA) and folic acid in the receptacles. The transcriptome analysis identified a lot of genes differentially expressed in response to ABA or NDGA treatment. In particular, genes in the anthocyanin biosynthesis pathway were actively regulated by ABA, with the exception of the gene encoding cinnamate 4-hydroxylase. Chlorophyll degradation was accelerated by ABA mainly owing to the higher expression of gene encoding pheide a oxygenase. The decrease of β-carotene content was accelerated by ABA treatment and delayed by NDGA. A high negative correlation rate was found between ABA and β-carotene content, indicating the importance of the requirement for ABA synthesis during fruit ripening. In addition, evaluation on the folate biosynthetic pathway indicate that ABA might have minor function in this nutrient’s biosynthesis process, however, it might be involved in its homeostasis. Surprisingly, though AsA content accumulated during fruit ripening, expressions of genes involved in its biosynthesis in the receptacles were significantly lower in ABA-treated fruits. This transcriptome analysis expands our understanding of ABA’s role in phytochemical metabolism during strawberry fruit ripening and the regulatory mechanisms of ABA on these pathways were discussed. Our study provides a wealth of genetic information in the metabolism pathways and may be helpful for molecular manipulation in the future.
Adaptive Search Algorithms for Discrete Stochastic Optimization: A Smooth Best-Response Approach

This paper considers simulation-based optimization of the performance of a regime-switching stochastic system over a finite set of feasible configurations. Inspired by the stochastic fictitious play learning rules in game theory, we propose an adaptive random search algorithm that uses a smooth best-response sampling strategy and tracks the set of global optima, yet distributes the search so that most of the effort is spent on simulating the system performance at the global optima. The algorithm responds properly to the random unpredictable jumps of the global optimum even when the observations data are temporally correlated as long as a weak law of large numbers holds. Numerical examples show that the proposed scheme yields faster convergence and superior efficiency for finite sample lengths compared with several existing random search and pure exploration methods in the literature.
Position and Speed Estimation of Permanent Magnet Machine Sensorless Drive at High Speed Using an Improved Phase-Locked Loop

In conventional position sensorless permanent magnet (PM) machine drives, the rotor position is obtained from the phase-locked loop (PLL) with the regulation of spatial signal in estimated back electromotive force (EMF) voltages. Due to the sinusoidal distribution of back-EMF voltages, a small-signal approximation is assumed in the PLL in order to estimate the position. That is, the estimated position is almost equal to the actual position per sample instant. However, at high speed when the ratio of sampling frequency, f sample , over the rotor operating frequency, f e , is low, this approximation might not be valid during the speed and load transient. To overcome this limitation, a position estimation is proposed specifically for the high-speed operation of a PM machine drive. A discrete-time EMF voltage estimator is developed to obtain the machine spatial signal. In addition, an arctangent calculation is cascaded to the PLL in order to remove this small-signal approximation for better sensorless drive performance. By using the discrete-time EMF estimation and modified PLL, the drive is able to maintain the speed closed-loop at 36 krpm with only 4.2 sampling points per electrical cycle on a PM machine, according to experimental results.
Privacy-preserving multi-receiver signcryption scheme for heterogeneous systems

In recent years, secure communication and privacy-preserving are gaining popularity because of the advent of wireless network. Certificateless cryptography CLC and identity-based cryptography IBC have already been widely applied in the area of wireless network. Hence, to achieve secure communication from CLC to IBC, we present a heterogeneous signcryption scheme that enables a sender in the CLC to transmit a message to multi-receiver in the IBC. Our scheme has no restrictions on the system parameters and master keys; private key generator and key generating center generate their own system parameters and master key for the IBC users and the CLC user, separately. Considering privacy-preserving in heterogeneous communication, we show that our scheme can realize the anonymity of all receivers. Compared with other schemes, our scheme has more advantages, such as public verification and decryption fairness, which are attractive for wireless network applications. Moreover, our scheme has the indistinguishability against adaptive chosen ciphertext attacks, the existential unforgeability against adaptive chosen messages attacks, and anonymous indistinguishability of encryptions under selective-ID, chosen ciphertext attack in the random oracle model. Copyright © 2016 John Wiley & Sons, Ltd.
Cleaning up after a face tracker: False positive removal

Automatic person identification in TV series has gained popularity over the years. While most of the works rely on using face-based recognition, errors during tracking such as false positive face tracks are typically ignored. We propose a variety of methods to remove false positive face tracks and categorize the methods into confidence- and context-based. We evaluate our methods on a large TV series data set and show that up to 75% of the false positive face tracks are removed at the cost of 3.6% true positive tracks. We further show that the proposed method is general and applicable to other detectors or trackers.
Interactive graphics analysis of gastrointestinal electrical signals.

A suite of conversational correlation and spectral computer programs for the analysis of electrical data from the human and canine digestive tracts is described. The data being analyzed comprise electrical signals obtained from either the inside or outside walls of the stomach and small and large bowels. The basic rhythm is a low-frequency wave of about 0.05 Hz in the stomach and 0.2 Hz in the duodenum of man, and about 0.1 Hz in the stomach and 0.3 Hz in the duodenum of dogs. The interactive analysis allows the accurate investigation of changes in phase shifts and frequency spectra caused by drug stimulation and different types of vagotomy.
Second Language Vocabulary Acquisition: Reading and vocabulary development in a second language: A case study

Introduction Researchers in reading seldom have the opportunity to experience, as adults, an extended period of time learning to read. Although it is virtually impossible to have such an adult experience in one's first language, it is possible to find oneself in such a fortuitous situation in a second language (L2) context. This situation arose for the first author of this chapter when he spent 5 months in Brazil in 1990. Since he was not a speaker or reader of Portuguese, he took that opportunity to learn to read in Portuguese. This paper is a report of that case study, the outcomes after 5 months, and the records and reflections on the experience. As a case study, this report cannot make claims for statistical generalizations. There are, however, a number of important methodological advantages and research insights to this type of case study that cannot easily be explored experimentally (McCormick, 1993; Neuman & McCormick, 1995). As a research methodology, a small number of published case studies document the learning of a second or foreign language and second language (L2) teacher education (Bailey, 1980, 1983; Porter, Goldstein, Leatherman, & Conrad, 1990; Schmidt & Frota, 1986; Schumann, 1980; Schumann & Schumann, 1977; see Bailey, 1990, for a review of diary studies in teacher education). Few case studies, however, specifically address the development of L2 reading and vocabulary skills (see Parry, 1993). The research reported here represents an effort to explore L2 reading and vocabulary development through such a methodology.
Magnetic stimulation of the central and peripheral nervous systems

Since 1985, when the technique of transcranial magnetic stimulation (TMS) was first developed, a wide range of applications in healthy and diseased subjects has been described. Comprehension of the physiological basis of motor control and cortical function has been improved. Modifications of the basic technique of measuring central motor conduction time (CMCT) have included measurement of the cortical silent period, paired stimulation in a conditioning test paradigm, repetitive transcranial magnetic stimulation (rTMS), and peristimulus time histograms (PSTH). These methods allow dissection of central motor excitatory versus inhibitory interplay on the cortical motor neuron and its presynaptic connections at the spinal cord, and have proven to be powerful investigational techniques. TMS can be used to assess upper and lower motor neuron dysfunction, monitor the effects of many pharmacological agents, predict stroke outcome, document the plasticity of the motor system, and assess its maturation and the effects of aging, as well as perform intraoperative monitoring. The recent use of rTMS in the treatment of depression and movement disorders is novel, and opens the way for other potential therapeutic applications. © 2002 American Association of Electrodiagnostic Medicine. Muscle Nerve 25: 160–175, 2002 DOI 10.1002/mus.10038
(In)Formal and (Un)Productive: The Productivity Costs of Excessive Informality in Mexico

The laws that regulate relations between firms and workers in Mexico distinguish sharply between salaried and non-salaried workers, and they are at the root of the existence of informality. This paper provides a clear definition of informality, distinguishing it from illegality. Using Mexico's Economic Census, the paper shows that the majority of firms are informal but legal, that there are more small formal firms than large ones, and that some large firms are informal. It also shows that informality and illegality increased in the period 1998-2008. Using a simple model of monopolistic competition to measure the productivity losses due to distortions that misallocate resources, the paper finds that one peso of capital and labor allocated to formal and legal firms is worth 28 percent more than if allocated to illegal and informal firms, and 50 percent more than if allocated to legal and informal firms. The paper concludes arguing that the distortions in the labor market created by informality reduce total factor productivity.
Stochastic Variance Reduced Riemannian Eigensolver

We study the stochastic Riemannian gradient algorithm for matrix eigen-decomposition. The state-of-the-art stochastic Riemannian algorithm requires the learning rate to decay to zero and thus suffers from slow convergence and sub-optimal solutions. In this paper, we address this issue by deploying the variance reduction (VR) technique of stochastic gradient descent (SGD). The technique was originally developed to solve convex problems in the Euclidean space. We generalize it to Riemannian manifolds and realize it to solve the non-convex eigen-decomposition problem. We are the first to propose and analyze the generalization of SVRG to Riemannian manifolds. Specifically, we propose the general variance reduction form, SVRRG, in the framework of the stochastic Riemannian gradient optimization. It's then specialized to the problem with eigensolvers and induces the SVRRG-EIGS algorithm. We provide a novel and elegant theoretical analysis on this algorithm. The theory shows that a fixed learning rate can be used in the Riemannian setting with an exponential global convergence rate guaranteed. The theoretical results make a significant improvement over existing studies, with the effectiveness empirically verified.
Contour detection and image segmentation

This thesis investigates two fundamental problems in computer vision: contour detection and image segmentation. We present new state-of-the-art algorithms for both of these tasks. Our segmentation algorithm consists of generic machinery for transforming the output of any contour detector into a hierarchical region tree. In this manner, we reduce the problem of image segmentation to that of contour detection. Extensive experimental evaluation demonstrates that both our contour detection and segmentation methods significantly outperform competing algorithms. Our approach to contour detection couples multiscale local brightness, color, and texture cues to a powerful globalization framework using spectral clustering. The local cues, computed by applying oriented gradient operators at every location in the image, define an affinity matrix representing the similarity between pixels. From this matrix, we derive a generalized eigenproblem and solve for a fixed number of eigenvectors which encode contour information. Using a classifier to recombine this signal with the local cues, we obtain a large improvement over alternative globalization schemes built on top of similar cues. To produce high-quality image segmentations, we link this contour detector with a generic grouping algorithm consisting of two steps. First, we introduce a new image transformation called the Oriented Watershed Transform for constructing a set of initial regions from an oriented contour signal. Second, using an agglomerative clustering procedure, we form these regions into a hierarchy which can be represented by an Ultrametric Contour Map, the real-valued image obtained by weighting each boundary by its scale of disappearance. This approach outperforms existing image segmentation algorithms on measures of both boundary and segment quality. These hierarchical segmentations can optionally be further refined by user-specified annotations. While the majority of this work focuses on processing static images, we also develop extensions for video. In particular, we augment the set of static cues used for contour detection with a low-level motion cue to create an enhanced boundary detector. Using optical flow in conjunction with this detector enables the determination of occlusion boundaries and assignment of figure/ground labels in video.
Analysis of Phase 3 telavancin nosocomial pneumonia data excluding patients with severe renal impairment and acute renal failure

Objectives Telavancin is approved in Europe for the treatment of nosocomial pneumonia caused by methicillin-resistant Staphylococcus aureus when other alternatives are not suitable. The approved European prescribing information contraindicates the use of telavancin in patients with severe renal impairment (creatinine clearance <30 mL/min, including patients on haemodialysis) and pre-existing acute renal failure owing to the higher observed mortality in these patients. Data from the ATTAIN studies were reanalysed, excluding patients with these contraindicating conditions at baseline. (At the time of submission of this article, the European marketing authorization of telavancin for the treatment of nosocomial pneumonia was suspended pending evidence of a new European Medicines Agency-approved supplier. Clinigen Healthcare Ltd, Theravance's commercialization partner for telavancin in Europe, is in the process of seeking approval of a new manufacturing source.) Methods A post hoc analysis of data from two Phase 3 ATTAIN trials of telavancin for the treatment of Gram-positive nosocomial pneumonia assessing clinical outcomes and safety. Results The all-treated population for this analysis represented 84.2% (1266/1503) of the ATTAIN all-treated population. The cure rates in the clinically evaluable population were similar in the telavancin (82.5%, 231/280) and vancomycin (81.3%, 243/299) groups [treatment difference (95% CI): 1.3% (−5.0% to 7.6%)], and were consistent with the overall ATTAIN study results. The cure rate was higher in the telavancin than the vancomycin treatment group in microbiologically evaluable patients with only Gram-positive pathogens isolated at baseline [85.0% (130/153) versus 75.2% (109/145), respectively; treatment difference (95% CI): 9.7% (0.6%–18.8%)]. The incidences of adverse events were similar between treatment groups and consistent with the overall findings of the ATTAIN study. Conclusions This analysis demonstrated that in the subset of patients without severe renal impairment or pre-existing acute renal failure, clinical and safety outcomes were similar in the telavancin and vancomycin treatment groups.
The Proportion of Specific Viral Subpopulations in Attenuated Arkansas Delmarva Poultry Industry Infectious Bronchitis Vaccines Influences Vaccination Outcome

SUMMARY. We investigated the significance of differing proportions of specific subpopulations among commercial Arkansas (Ark) Delmarva poultry industry (DPI) vaccines with regard to vaccination outcome. Two ArkDPI-derived vaccines that contain a higher proportion of viruses with S1 genes that become selected during replication in chickens exhibited more rapid establishment of those selected subpopulations in chickens, produced significantly higher viral loads in tears, and induced higher antibody responses compared with two other ArkDPI vaccines with lower proportions of viruses that become selected in chickens. The presence of higher proportions of selected subpopulations was also associated with a significantly higher incidence of respiratory signs early after vaccination and in some cases more severe tracheal lesions. However, one of the ArkDPI-derived vaccines with a lower proportion of selected subpopulations, despite producing a lower viral load in tears, also induced a higher incidence of respiratory signs later after vaccination and more severe tracheal lesions. Furthermore, one of the ArkDPI-derived vaccines with a higher proportion of selected subpopulations, despite producing a higher viral loads in tears, resulted in less severe tracheal damage. These discrepancies suggest that infectious bronchitis virus (IBV) load in tears may not always predict degree of tracheal damage and that phenotypic characteristics other than S1 may also be involved in severity of vaccine reactions following ArkDPI vaccine administration. We observed lower antibody responses to the vaccines that produced lower viral loads, which might contribute to the persistence of Ark serotype IBV vaccines observed in commercial flocks.
Working-memory capacity protects model-based learning from stress

Significance The physiological response evoked by short-lived stressful events, referred to as acute stress, impacts human decision-making. Past studies assume that stress causes people to fall back, from more cognitive or deliberative modes of choice, to more primitive or automatic modes of choice because stress impairs peoples’ capacity to process information (working memory). We directly examined how acute stress affects choice in a laboratory decision-making task for which the working memory demands of the two forms of decision-making are well understood, finding that stress impaired use of sophisticated choice strategies that require working memory but did not affect use of simpler, more primitive strategies. Further, this impairment was exacerbated in individuals with smaller working memory capacity, which is related to general intelligence. Accounts of decision-making have long posited the operation of separate, competing valuation systems in the control of choice behavior. Recent theoretical and experimental advances suggest that this classic distinction between habitual and goal-directed (or more generally, automatic and controlled) choice may arise from two computational strategies for reinforcement learning, called model-free and model-based learning. Popular neurocomputational accounts of reward processing emphasize the involvement of the dopaminergic system in model-free learning and prefrontal, central executive–dependent control systems in model-based choice. Here we hypothesized that the hypothalamic-pituitary-adrenal (HPA) axis stress response—believed to have detrimental effects on prefrontal cortex function—should selectively attenuate model-based contributions to behavior. To test this, we paired an acute stressor with a sequential decision-making task that affords distinguishing the relative contributions of the two learning strategies. We assessed baseline working-memory (WM) capacity and used salivary cortisol levels to measure HPA axis stress response. We found that stress response attenuates the contribution of model-based, but not model-free, contributions to behavior. Moreover, stress-induced behavioral changes were modulated by individual WM capacity, such that low-WM-capacity individuals were more susceptible to detrimental stress effects than high-WM-capacity individuals. These results enrich existing accounts of the interplay between acute stress, working memory, and prefrontal function and suggest that executive function may be protective against the deleterious effects of acute stress.
Evaluation of the prevalence and prospective clinical impact of the JAK2 V617F mutation in coronary patients

The JAK2 V617F mutation is not only found in the majority of patients with myeloproliferative neoplasms (MPN), including essential thrombocythemia (ET), but also has been reported in individuals without overt MPN. A close relation of the JAK2 V617F mutation to atherothrombotic events has been described, at least in patients with MPN. The prevalence of the JAK2 V617F mutation and its clinical impact in coronary patients is unknown. To address this issue, DNA samples from 1,589 subjects undergoing coronary angiography with up to 11 years of follow up were genotyped using allele‐specific real‐time PCR assays. Prevalence of the JAK2 V617F mutation was 1.32% (n = 21) in coronary patients. Two JAK2 V617F positive patients showed baseline platelet counts indicative for ET and a third patient developed ET during follow up, finally resulting in a percentage of 0.188% of ET cases. This corresponds to an up to fivefold accumulation of ET cases in coronary patients compared with the general population. Our study showed no impact of the JAK2 V617F mutation on future atherothrombotic events or overall survival (HR = 1.04 [0.33–3.27]; P = 0.949 and HR = 0.35 [0.05–2.46]; P = 0.288, respectively). Therefore, our data suggest that JAK2 V617F positive coronary patients are not at increased risk for future atherothrombotic complications. Routine mutation screening in coronary patients is, therefore, not warranted. However, number of ET cases appears to be accumulated in coronary patients. For this reason, we recommend JAK2 V617F testing only in coronary patients showing abnormal blood cell counts for further clarification. Am. J. Hematol. 89:295–301, 2014. © 2013 Wiley Periodicals, Inc.