Miracle-dz/UniFAR-FTUs huggingface dataset:
Scleral gene expression during recovery from myopia compared with expression during myopia development in tree shrew

Purpose During postnatal refractive development, the sclera receives retinally generated signals that regulate its biochemical properties. Hyperopic refractive error causes the retina to produce “GO” signals that, through the direct emmetropization pathway, cause scleral remodeling that increases the axial elongation rate of the eye, reducing the hyperopia. Myopia causes the retina to generate “STOP” signals that produce scleral remodeling, slowing the axial elongation rate and reducing the myopia. Our aim was to compare the pattern of gene expression produced in the sclera by the STOP signals with the GO gene expression signature we described previously. Methods The GO gene expression signature was produced by monocular –5 diopter (D) lens wear for 2 days (ML-2) or 4 days (ML-4); an additional “STAY” condition was examined after eyes had fully compensated for a –5 D lens after 11 days of lens wear (ML-11). After 11 days of −5 D lens wear had produced full refractive compensation, gene expression in the STOP condition was examined during recovery (without the lens) for 2 days (REC-2) or 4 days (REC-4). The untreated contralateral eyes served as a control in all groups. Two age-matched normal groups provided a comparison with the treated groups. Quantitative real-time PCR was used to measure mRNA levels for 55 candidate genes. Results The STAY group compensated fully for the lens (treated eye versus control eye, –5.1±0.2 D). Wearing the lens, the hyperopic signal for elongation had dissipated (–0.3±0.3 D). In the STOP groups, the refraction in the recovering eyes became less myopic relative to the control eyes (REC-2, +1.3±0.3 D; REC-4, +2.6±0.4 D). In the STAY group, three genes showed significant downregulation. However, many genes that were significantly altered in GO showed smaller, nonsignificant, expression differences in the same direction in STAY, suggesting the gene expression signature in STAY is a greatly weakened form of the GO signature. In the STOP groups, a different gene expression pattern was observed, characterized by mostly upregulation with larger fold differences after 4 days than after 2 days of recovery. Eleven of the 55 genes examined showed significant bidirectional GO/STOP regulation in the ML-2 and REC-2 groups, and 13 genes showed bidirectional regulation in the ML-4 and REC-4 groups. Eight of these genes (NPR3, CAPNS1, NGEF, TGFB1, CTGF, NOV, TIMP1, and HS6ST1) were bidirectionally regulated at both time points in the GO and STOP conditions. An additional 15 genes showed significant regulation in either GO or STOP conditions but not in both. Conclusions Many genes are involved in scleral remodeling and the control of axial length. The STOP (recovery) gene expression signature in the sclera involves some of the same genes, bidirectionally regulated, as the GO signature. However, other genes, regulated in GO, are not differentially regulated in STOP, and others show differential regulation only in STOP.
TR 14-014 Big Data Frequent Pattern Mining

Frequent pattern mining is an essential data mining task, with a goal of discovering knowledge in the form of repeated patterns. Many efficient pattern mining algorithms have been discovered in the last two decades, yet most do not scale to the type of data we are presented with today, the so-called “Big Data”. Scalable parallel algorithms hold the key to solving the problem in this context. In this chapter, we review recent advances in parallel frequent pattern mining, analyzing them through the Big Data lens. We identify three areas as challenges to designing parallel frequent pattern mining algorithms: memory scalability, work partitioning, and load balancing. With these challenges as a frame of reference, we extract and describe key algorithmic design patterns from the wealth of research conducted in this domain.
Effects of Treatment with Suppressive Combination Antiretroviral Drug Therapy and the Histone Deacetylase Inhibitor Suberoylanilide Hydroxamic Acid; (SAHA) on SIV-Infected Chinese Rhesus Macaques

Objectives Viral reservoirs–persistent residual virus despite combination antiretroviral therapy (cART)–remain an obstacle to cure of HIV-1 infection. Difficulty studying reservoirs in patients underscores the need for animal models that mimics HIV infected humans on cART. We studied SIV-infected Chinese-origin rhesus macaques (Ch-RM) treated with intensive combination antiretroviral therapy (cART) and 3 weeks of treatment with the histone deacetyalse inhibitor, suberoylanilide hydroxamic acid (SAHA). Methods SIVmac251 infected Ch-RM received reverse transcriptase inhibitors PMPA and FTC and integrase inhibitor L-870812 beginning 7 weeks post infection. Integrase inhibitor L-900564 and boosted protease inhibitor treatment with Darunavir and Ritonavir were added later. cART was continued for 45 weeks, with daily SAHA administered for the last 3 weeks, followed by euthanasia/necropsy. Plasma viral RNA and cell/tissue-associated SIV gag RNA and DNA were quantified by qRT-PCR/qPCR, with flow cytometry monitoring changes in immune cell populations. Results Upon cART initiation, plasma viremia declined, remaining <30 SIV RNA copy Eq/ml during cART, with occasional blips. Decreased viral replication was associated with decreased immune activation and partial restoration of intestinal CD4+ T cells. SAHA was well tolerated but did not result in demonstrable treatment-associated changes in plasma or cell associated viral parameters. Conclusions The ability to achieve and sustain virological suppression makes cART-suppressed, SIV-infected Ch-RM a potentially useful model to evaluate interventions targeting residual virus. However, despite intensive cART over one year, persistent viral DNA and RNA remained in tissues of all three animals. While well tolerated, three weeks of SAHA treatment did not demonstrably impact viral RNA levels in plasma or tissues; perhaps reflecting dosing, sampling and assay limitations.
Evaluating Unsupervised Dutch Word Embeddings as a Linguistic Resource

Word embeddings have recently seen a strong increase in interest as a result of strong performance gains on a variety of tasks. However, most of this research also underlined the importance of benchmark datasets, and the difficulty of constructing these for a variety of language-specific tasks. Still, many of the datasets used in these tasks could prove to be fruitful linguistic resources, allowing for unique observations into language use and variability. In this paper we demonstrate the performance of multiple types of embeddings, created with both count and prediction-based architectures on a variety of corpora, in two language-specific tasks: relation evaluation, and dialect identification. For the latter, we compare unsupervised methods with a traditional, hand-crafted dictionary. With this research, we provide the embeddings themselves, the relation evaluation task benchmark for use in further research, and demonstrate how the benchmarked embeddings prove a useful unsupervised linguistic resource, effectively used in a downstream task.
Snapin is Critical for Presynaptic Homeostatic Plasticity

The molecular mechanisms underlying the homeostatic modulation of presynaptic neurotransmitter release are largely unknown. We have previously used an electrophysiology-based forward genetic screen to assess the function of >400 neuronally expressed genes for a role in the homeostatic control of synaptic transmission at the neuromuscular junction of Drosophila melanogaster. This screen identified a critical function for dysbindin, a gene linked to schizophrenia in humans (Dickman and Davis, 2009). Biochemical studies in other systems have shown that Snapin interacts with Dysbindin, prompting us to test whether Snapin might be involved in the mechanisms of synaptic homeostasis. Here, we demonstrate that loss of snapin blocks the homeostatic modulation of presynaptic vesicle release following inhibition of postsynaptic glutamate receptors. This is true for both the rapid induction of synaptic homeostasis induced by pharmacological inhibition of postsynaptic glutamate receptors, and the long-term expression of synaptic homeostasis induced by the genetic deletion of the muscle-specific GluRIIA glutamate receptor subunit. Loss of snapin does not alter baseline synaptic transmission, synapse morphology, synapse growth, or the number or density of active zones, indicating that the block of synaptic homeostasis is not a secondary consequence of impaired synapse development. Additional genetic evidence suggests that snapin functions in concert with dysbindin to modulate vesicle release and possibly homeostatic plasticity. Finally, we provide genetic evidence that the interaction of Snapin with SNAP25, a component of the SNARE complex, is also involved in synaptic homeostasis.
Ultraviolet Signatures of Tidal Interaction in the Giant Spiral Galaxy M101

We present new evidence for the occurrence of tidal interactions in the disk of M101 during the last 108-109 yr. Recent imaging of the far-ultraviolet emission from M101 by the shuttle-borne Ultraviolet Imaging Telescope (UIT) reveals with unprecedented clarity a disk-wide pattern of multiple linear arm segments (“crooked arms”). The deep far-ultraviolet (FUV) image also shows a faint outer spiral arm with a (“curly tail”) feature that appears to loop around the supergiant H II region NGC 5471, linking this outlying starburst with the rest of the galaxy. These FUV-bright features most likely trace hot O- and B-type stars along with scattered light from associated nebular dust. Counterparts of the outermost “crooked arms” are evident in maps at visible wavelengths and in the 21 cm line of H I. The inner-disk FUV arms are most closely associated with Hα knots and the outer (downstream) sides of CO arms. Comparisons of the “crooked arm” and “curly tail” morphologies with dynamical simulations yield the greatest similitude, when the nonaxisymmetric forcing comes from a combination of external interactions with one or more companion galaxies and internal perturbations from massive objects orbiting within the disk. We speculate that NGC 5471 represents one of these “massive disturbers” within the disk, whose formation followed from a tidal interaction between M101 and a smaller galaxy.
A Generalized Unsharp Masking Algorithm

Enhancement of contrast and sharpness of an image is required in many applications. Unsharp masking is a classical tool for sharpness enhancement. We propose a generalized unsharp masking algorithm using the exploratory data model as a unified framework. The proposed algorithm is designed to address three issues: 1) simultaneously enhancing contrast and sharpness by means of individual treatment of the model component and the residual, 2) reducing the halo effect by means of an edge-preserving filter, and 3) solving the out-of-range problem by means of log-ratio and tangent operations. We also present a study of the properties of the log-ratio operations and reveal a new connection between the Bregman divergence and the generalized linear systems. This connection not only provides a novel insight into the geometrical property of such systems, but also opens a new pathway for system development. We present a new system called the tangent system which is based upon a specific Bregman divergence. Experimental results, which are comparable to recently published results, show that the proposed algorithm is able to significantly improve the contrast and sharpness of an image. In the proposed algorithm, the user can adjust the two parameters controlling the contrast and sharpness to produce the desired results. This makes the proposed algorithm practically useful.
A Half-Log Increase in BCR-ABL RNA Predicts a Higher Risk of Relapse in Patients with Chronic Myeloid Leukemia with an Imatinib-Induced Complete Cytogenetic Response

Purpose: Imatinib induces a complete cytogenetic response (CCR) in most chronic myeloid leukemia patients in chronic phase. Although CCR is usually durable, a minority of patients relapse. Biomarkers capable of predicting those CCR patients with a higher risk of relapse would improve therapeutic management. Experimental Design: To assess whether changes in BCR-ABL RNA levels are a prognostic biomarker predictive of relapse, we regularly monitored transcript levels [every 3 months (median)] in 90 patients with CCR during 49 months (median) of imatinib therapy. Results: Throughout follow-up, the 20 patients with eventual relapse had higher transcript levels than the durable responders. Major molecular response (MMR; >3-log reduction of BCR-ABL RNA) was attained by 76 patients (12 with subsequent relapse) and was a significant predictor of prolonged relapse-free survival (P = 0.0008). A minimal 0.5-log increase in transcripts (before relapse; experienced by 42 patients, 16 with subsequent relapse) conveyed a significantly shorter relapse-free survival (P = 0.0017). Loss of MMR (transcript increase to <2.5-log reduction, before relapse; experienced by 33 patients, 11 with subsequent relapse) was also predictive of shortened relapse-free survival (P = 0.0003). A complete molecular response (undetectable transcripts by nested PCR) was attained by 28 MMR patients (one with subsequent relapse) and conveyed a significantly prolonged relapse-free survival (P = 0.0052). Conclusions: In chronic myeloid leukemia patients with an imatinib-induced CCR, a minimal half-log increase in BCR-ABL RNA (including loss of MMR) is a significant risk factor for future relapse. The achievement of a complete molecular response imparts longer progression-free survival than the achievement of an MMR.
Neurotrophin, p75, and Trk Signaling Module in the Developing Nervous System of the Marine Annelid Platynereis dumerilii

In vertebrates, neurotrophic signaling plays an important role in neuronal development, neural circuit formation, and neuronal plasticity, but its evolutionary origin remains obscure. We found and validated nucleotide sequences encoding putative neurotrophic ligands (neurotrophin, NT) and receptors (Trk and p75) in two annelids, Platynereis dumerilii (Errantia) and Capitella teleta (Sedentaria, for which some sequences were found recently by Wilson, 2009). Predicted protein sequences and structures of Platynereis neurotrophic molecules reveal a high degree of conservation with the vertebrate counterparts; some amino acids signatures present in the annelid Trk sequences are absent in the basal chordate amphioxus, reflecting secondary loss in the cephalochordate lineage. In addition, expression analysis of NT, Trk, and p75 during Platynereis development by whole-mount mRNA in situ hybridization supports a role of these molecules in nervous system and circuit development. These annelid data corroborate the hypothesis that the neurotrophic signaling and its involvement in shaping neural networks predate the protostome-deuterostome split and were present in bilaterian ancestors.
A Comparison of Quiz Grading Criteria, Exam Question Type and Novelty, and their Effects on Exam Scores

A Comparison of Quiz Grading Criteria, Exam Question Type and Novelty, and their Effects on Exam scores by Samantha Dalfen Advisor: Daniel Fienup Students in higher education perform better on exams when they complete frequent quizzes on the assigned reading material; but little research has investigated the different ways quizzes can be administered and how these variations affect quiz and exam performance. One variable that influences how quizzes are administered is the grading criterion. The standard practice grading criterion consists of receiving a score for the quiz based on the number of correctly answered questions. A passing criterion consists of requiring a student to obtain a certain score to earn full credit for the quiz. Previous research has found that students, particularly those who are at risk for failing, do significantly better on exams when there is a low-passing criterion as compared to a higher-passing criterion. Currently, there is no research that compares the effects of quizzes with a standard practice criterion and quizzes with a passing criterion on exam scores. The present study sought to compare a low-passing criterion and a standard practice criterion for quizzes and their effects on exam scores. Furthermore, we manipulated the type of exam question and whether the question has been replicated from a previous quiz across both a lowpassing criterion and standard practice. This study replicated previous research demonstrating that students performed better on low-passing criterion exam questions. Additionally, students performed better on comprehension questions and replicated questions. Future research should
Implicit Approach–Avoidance Associations Predict Leisure-Time Exercise Independently of Explicit Exercise Motivation

Traditional models of exercise motivation presume that behavior is driven by rational decision-making processes. However, recent evidence suggests that automatic motivational processes also play a role in motivating exercise behavior. The current study examined whether regular exercise engagement is linked to implicit approach–avoidance memory associations, as well as explicit intentions and self-determined exercise motivation. A sample of 104 healthy adults completed self-reported measures of exercise intentions, self-determined exercise motivation, and levels of exercise engagement. Approach–avoidance associations were measured using a modified Recoding-Free Implicit Association Test. Overall, participants associated exercise more strongly with approach than with avoidance attributes in memory, indicating an approach bias for exercise cues. In addition, individuals who reported engaging in higher levels of leisure-time exercise displayed a significantly stronger approach bias for exercise than less active individuals. Furthermore, approach–avoidance associations explained unique variance in exercise behavior after controlling for the effects of explicit exercise intentions and self-determined exercise motivation. These findings suggest that increased engagement in leisure-time exercise is associated with an implicit cognitive bias to approach exercise-related cues in the environment. Moreover, these findings support current theoretical models that suggest that exercise is at least partly motivated by implicit motivational processes.
Nasal Continuous Positive Airway Pressure Inhibits Gastroesophageal Reflux in Newborn Lambs

Background Using esophageal pHmetry, nasal CPAP (nCPAP) has been shown to decrease acid gastroesophageal reflux (GER) in adult humans. Although both GER (mainly non-acid) and nCPAP use are very frequent in newborns, the effect of nCPAP on GER in early life is unknown. Having recently shown that the newborn lamb is a unique model for studying neonatal GER, our main objective was to assess the effect of nCPAP on GER in newborn lambs. Methods Eight newborn lambs, aged 2–3 days, were studied. Continuous esophageal pH-Impedance monitoring and polysomnography were performed for six hours during both spontaneous breathing and nCPAP application at 6 cmH2O (nCPAP6), in a randomized order. Results were compared in the two experimental conditions, as well as without CPAP during the following 6 hours. Results i) nCPAP6 virtually abolished GER [mean ±SD reflux number for 6 h = 9.1±8.6 without nCPAP6 vs. 0.6±1 with nCPAP6, P<0.05]; ii) GER number was also reduced during the 6 h-period following nCPAP6 application (18±16 without nCPAP6 vs. 7±8.1 with nCPAP6, P<0.05); iii) nCPAP6 decreased the depth and duration of lower esophageal sphincter relaxation. Conclusions nCPAP inhibits GER in the newborn lamb. Further clinical studies using different levels of nasal CPAP are needed to confirm this result in human infants.
Time-Varying MIMO Channels: Parametric Statistical Modeling and Experimental Results

Accurate characterization of multiple-input multiple-output (MIMO) fading channels is an important prerequisite for the design of multiantenna wireless-communication systems. In this paper, a single-bounce two-ring statistical model for the time-varying MIMO flat fading channels is proposed. In the model, both the base and mobile stations are surrounded by their own ring of scatterers. For the proposed model, a closed-form expression for the spatio-temporal cross-correlational function between any two subchannels is derived, assuming single-bounce scattering. The new analytical expression includes several key physical parameters of interest such as the mean angle-of-departure, the mean angle-of-arrival, the associated angle spreads, and the Doppler spread in a compact form. The model includes many existing correlation models as special cases. Its utility is demonstrated by a comparison with collected MIMO data in terms of the spatio-temporal correlations, level crossing rate, average fade duration, and the instantaneous mutual information.
Optimal parallel algorithms for string matching

Let WRAM [PRAM] be a parallel computer with p processors (RAM's) which share a common memory and are allowed simultaneous reads and writes [only simultaneous reads]. The only type of simultaneous writes allowed is a simultaneous AND: several processors may write O simultaneously into the same memory cell. Let t be the time bound of the computer. We design below families of parallel algorithms that solve the string matching problem with inputs of size n (n is the sum of lengths of the pattern and the text) and have the following performance in terms of p, t and n: 1. For WRAM: pt &equil; O(n) for for p ≤ n/log n. 2. For PRAM: pt &equil; O(n) for P ≤ n/log2n. 3. For WRAM: t &equil; constant for p &equil; nl+ε and any ε > O. 4. For WRAM: t &equil; O(log n/log log n) for p &equil; n. Similar families are also obtained for the problem of finding all initial palindromes of a given string.
INEX+DBPEDIA: a corpus for semantic search evaluation

This paper presents a new collection based on DBpedia and INEX for evaluating semantic search performance. The proposed corpus is used to calculate the impact of considering document's structure on the retrieval performance of the Lucene and BM25 ranking functions. Results show that BM25 outperforms Lucene in all the considered metrics and that there is room for future improvements, which may be obtained using a hybrid approach combining both semantic technology and information retrieval ranking functions.
A Lyapunov function for economic MPC without terminal conditions

We consider nonlinear economic model predictive control (MPC) without terminal constraints or costs. We show that under suitable conditions, consisting of strict dissipativity, the turnpike property and appropriate continuity properties, a practical Lyapunov function exists for the MPC closed loop. This Lyapunov function is given by the optimal value function of the optimal control problem with rotated stage costs originating from the dissipativity condition. Alternative sufficient conditions in terms of suitable controllability properties and finite time optimality of the closed loop trajectories during the transient phase are also discussed.
DELA: A Dynamic Online Ensemble Learning Algorithm

The present paper investigates the problem of prediction in the context of dynamically changing environment, where data arrive over time. A Dynamic on- line Ensemble Learning Algorithm (DELA) is introduced. The adaptivity concerns three levels: structural adaptivity, combination adaptivity and model adaptivity. In particular, the structure of the ensemble is sought to evolve in order to be able to deal with the problem of data drift. The proposed online ensemble is evaluated on the stagger data set to show its predictive power in presence of data drift.