Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Geranylgeranyltransferase I Is Involved in Specific Aspects of Abscisic Acid and Auxin Signaling in Arabidopsis1

Arabidopsis (Arabidopsis thaliana) mutants lacking a functional ERA1 gene, which encodes the β-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects that establish roles for protein prenylation in abscisic acid (ABA) signaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsis GGB gene, which encodes the β-subunit of protein geranylgeranyltransferase type I (PGGT I). Stomatal apertures of ggb plants were smaller than those of wild-type plants at all concentrations of ABA tested, suggesting that PGGT I negatively regulates ABA signaling in guard cells. However, germination of ggb seeds in response to ABA was similar to the wild type. Lateral root formation in response to exogenous auxin was increased in ggb seedlings compared to the wild type, but no change in auxin inhibition of primary root growth was observed, suggesting that PGGT I is specifically involved in negative regulation of auxin-induced lateral root initiation. Unlike era1 mutants, ggb mutants exhibited no obvious developmental phenotypes. However, era1 ggb double mutants exhibited more severe developmental phenotypes than era1 mutants and were indistinguishable from plp mutants lacking the shared α-subunit of PFT and PGGT I. Furthermore, overexpression of GGB in transgenic era1 plants partially suppressed the era1 phenotype, suggesting that the relatively weak phenotype of era1 plants is due to partial redundancy between PFT and PGGT I. These results are discussed in the context of Arabidopsis proteins that are putative substrates of PGGT I.
Biomarkers in Relation to Cognitive Reserve in Patients with Mild Cognitive Impairment – Proof of Concept

Background: The concept of the cognitive reserve (CR) posits that factors such as education enable compensation for the effect of brain pathology. Consequently, pathology should be more pronounced in individuals with higher CR before becoming clinically apparent. Biomarkers such as total tau (t-tau) and β-amyloid 42 (Aβ42) may be surrogates for pathology in relation to CR in patients with neurodegenerative disease. Objective: To examine the applicability of biomarkers as surrogates for pathology in relation to the CR in patients with mild cognitive impairment (MCI) either converting to dementia or remaining stable at follow-up. Method: Comparisons of baseline t-tau, Aβ42, educational years and global cognition for MCI patients either converting to dementia (n = 57) or remaining stable (n = 91) were made. Patients converting to dementia were grouped on the basis of educational level and compared considering biomarkers and neuropsychological tests. Results: Stable MCI patients were better educated, performed better cognitively, had higher Aβ42 levels and lower levels of t-tau. Converting MCI patients with higher education had lower levels of Aβ42 and performed equally in neuropsychological tests compared to those with lower education. Conclusion: Our results suggest that highly educated MCI patients subsequently converting to dementia display more amyloid pathology.
Multiple Functions of Thioredoxins

Abstract Reduced thioredoxins from microbial and plant cells, both of cytoplasmic or chloroplast origin, are interchangeable in stimulating such diverse enzyme activities as ribonucleoside diphosphate reductase (E. coli) , PAPS sulfotransferase (Synechococcus), and fructose-1,6-bis-phosphatase (from spinach) in vitro. It is suggested that reduced thioredoxins are unspecific, multifunctional cellular proteins while in contrast the oxidized froms require specific enzymes for their reduction.
Image-based Participating Media

Light transport inside participating media, like fog or water, involves complex interaction phenomena, which make traditional 3D rendering approaches challenging and computationally expensive. To circumvent this, we propose an image-based method which adds perceptually plausible participating media effects to a single, clean high dynamic range image. We impose no prior requirements on the input image, and show that the underconstrained nature of the problem (where variables like depth or reflectance properties of the objects are obviously unknown) can be overcome with relatively little unskilled user input, similar to other image-editing techniques. We additionally validate the visual correctness of the results by means of psychophysical tests.
RHO GTPases in the control of cell morphology, cell polarity, and actin localization in fission yeast

The fission yeast Schizosaccharomyces pombe undergoes morphogenetic changes during both vegetative and sexual cell cycles that require asymmetric cell growth and actin cytoskeleton reorganisations. Different complex signal transduction pathways participate in S. pombe morphogenesis. The Rho family of GTPases are present in all eukaryotic cells, from yeast to mammals, and their role as key regulators in the signalling pathways that control actin organisation and morphogenetic processes is well known. In this review, we will briefly summarize the role of the Rho GTPases in the establishment and maintenance of cell polarity and growth of S. pombe. As in other fungi, S. pombe morphogenesis is closely related to cell wall biosynthesis, and Rho GTPases are critical modulators of this process. They provide the coordinated regulation of cell wall biosynthetic enzymes and actin organisation required to maintain cell integrity and polarised growth. Microsc. Res. Tech 47:51–60, 1999. © 1999 Wiley‐Liss, Inc.
Nonwearable Gaze Tracking System for Controlling Home Appliance

A novel gaze tracking system for controlling home appliances in 3D space is proposed in this study. Our research is novel in the following four ways. First, we propose a nonwearable gaze tracking system containing frontal viewing and eye tracking cameras. Second, our system includes three modes: navigation (for moving the wheelchair depending on the direction of gaze movement), selection (for selecting a specific appliance by gaze estimation), and manipulation (for controlling the selected appliance by gazing at the control panel). The modes can be changed by closing eyes during a specific time period or gazing. Third, in the navigation mode, the signal for moving the wheelchair can be triggered according to the direction of gaze movement. Fourth, after a specific home appliance is selected by gazing at it for more than predetermined time period, a control panel with 3 × 2 menu is displayed on laptop computer below the gaze tracking system for manipulation. The user gazes at one of the menu options for a specific time period, which can be manually adjusted according to the user, and the signal for controlling the home appliance can be triggered. The proposed method is shown to have high detection accuracy through a series of experiments.
Cooperation enforcement scheme based on reputation for delay tolerant networks

Delay tolerant networks (DTNs) benefit diverse applications where the condition suffers significant delays and disruptions. In DTNs, bundles, the in-transit messages, can be sent immediately over an existing link or be buffered until an opportunistic link appears. The opportunistic data transferring in DTNs relies on the hypothesis that each individual forwards bundles honestly. The hypothesis that all the nodes behave rationally to share their resources for the global connectivity is considered as a utopia, and might easily be impaired in the presence of selfish individuals. To address this problem, we propose a cooperation enforcement scheme based on reputation. For the unique features of DTNs, a protocol of bundle propagation is presented to cope with the detection of misbehavior, and a design of reputation manager is proposed to distinguish selfish individuals. The performance evaluation demonstrates the efficiency of our proposal.
Effect of locally injected medications on healing of pad wounds in dogs.

OBJECTIVE To ascertain the effects of locally injected immunostimulant and tripeptide-copper complex (TCC) on improving healing of pad wounds. DESIGN Wounds in pads of large dogs were injected with either medication or physiologic saline solution (controls). Healing was evaluated. ANIMALS 12 mature English Pointers. PROCEDURE Full-thickness 6 x 8-mm wounds in metatarsal and third and fourth digital pads were injected with immunostimulant or TCC at 0, 3, and 6 days after wounding. Wounds on control dogs were injected with physiologic saline solution. Using planimetric measurements at 0, 3, 6, 14, and 21 days, rates of healing were evaluated. Biopsy of the digital pad wounds at 3, 6, and 14 days was used to evaluate collagen content by hydroxyproline analysis. Biopsy specimens were also evaluated for type-I and type-III collagen, using Sirius red differential staining. RESULTS Effect on healing rate and hydroxyproline content was best during the first week for immunostimulant. Immunostimulant- and TCC-injected wounds had more type-I collagen than did controls at 6 days; TCC-injected wounds had the most type-I collagen. At 14 days, the amount of type-I collagen in TCC-injected wounds was significantly greater than that in other wounds. CONCLUSIONS Tested medications had positive effects on healing of pad wounds. CLINICAL RELEVANCE Intralesional injection of medications helps ensure their presence for enhancement of wound healing. The benefit could be lost with topical use in a bandage if the bandage is lost or becomes wet.
Taming Wildcards in Java ’ s Type System ∗ Technical Report ( incomplete )

Wildcards have become an important part of Java’s type system since their introduction 7 years ago. Yet there are still many open problems with Java’s wildcards. For example, there are no known sound and complete algorithms for subtyping (and consequently type checking) Java wildcards, and in fact subtyping is suspected to be undecidable because wildcards are a form of bounded existential types. Furthermore, some Java types with wildcards have no joins, making inference of type arguments for generic methods particularly difficult. Although there has been progress on these fronts, we have identified significant shortcomings of the current state of the art, along with new problems that have not been addressed. In this paper, we illustrate how these shortcomings reflect the subtle complexity of the problem domain, and then present major improvements to the current algorithms for wildcards by making slight restrictions on the usage of wildcards. Our survey of existing Java programs suggests that realistic code should already satisfy our restrictions without any modifications. We present a simple algorithm for subtyping which is both sound and complete with our restrictions, an algorithm for lazily joining types with wildcards which addresses some of the shortcomings of prior work, and techniques for improving the Java type system as a whole. Lastly, we describe various extensions to wildcards that would be compatible with our algorithms.
Scale-free primordial cosmology

The large-scale structure of the universe suggests that the physics underlying its early evolution is scale-free. This was the historic motivation for the Harrison-Zel’dovich-Peebles spectrum and for ination. Based on a hydrodynamical approach, we identify scale-free forms for the background equation-of-state for both inationary and cyclic scenarios and use these forms to derive predictions for the spectral tilt and tensor-to-scalar ratio of primordial density perturbations. For the case of ination,
Postnatal development of baroreflex sensitivity in infancy

Baroreflex sensitivity (BRS) using spontaneous sequence analysis in the time domain is not fully applicable in infancy, as the time delay for heart period to change (heart period delay, HPD) after an arterial pressure change is unknown. We estimated and compared HPD and BRS in the frequency (BRSsp, HPDsp) and time domains (BRSseq, HPDseq) from systolic blood pressure (SBP) and heart period fluctuations. Continuous SBP, using photoplethysmography, and heart period measurements were performed on 30 term infants at 2–4 weeks, 2–3 months and 5–6 months postnatal age. Cross‐spectral analysis between SBP and heart period fluctuations was used to estimate BRSsp and HPDsp. Spontaneous sequence analysis was used to estimate BRS using a fixed beat delay of 1–12 beats (BRSseq) or a variable delay identified by a novel method accounting for epoch–epoch variability in HPD (BRSseqvar). HPDsp averaged 3.4 s (∼7 beats); BRSsp averaged 11.4 ms mmHg−1. BRSseq and BRSseqvar were consistently lower than BRSsp (P < 0.05), but the three BRS estimates were strongly correlated using a HPD of ∼5–6 beats. BRSseqvar resulted in the average estimate (8.9 ms mmHg−1) closest to BRSsp and overall had the strongest correlation with BRSsp (R2= 0.61; P < 0.001). All three BRS estimates increased progressively with postnatal age, with BRSsp averaging 6.4, 10.5 and 16.0 ms mmHg−1 at 2–4 weeks, 2–3 months and 5–6 months, respectively (P < 0.05). Accounting for the HPD of infancy provides estimates of BRS in the time domain that closely parallel spectral estimates, and provides a novel analytical tool to assess normal development and dysfunction of the baroreflex in infants.
Output feedback neural network adaptive robust control of a class of SISO nonlinear systems

Through the use of high-gain observer to estimate the unmeasurable system states, neural networks (NN) and adaptive robust control (ARC) method are integrated to design performance oriented output feedback control laws for a class of single-input-single-output (SISO) nth-order nonlinear systems in normal form. Multi-layer neural networks (MLNN) with the estimated states as inputs are used to approximate all unknown but repeatable nonlinear functions in the system. A controlled learning is achieved through the use of discontinuous projections with fictitious bounds in the tuning laws for NN weights. Certain robust control terms are constructed to effectively attenuate various model uncertainties and estimation errors for a guaranteed output tracking transient performance and a guaranteed final tracking accuracy in general. In addition, asymptotic output tracking is achieved in the ideal case. Experimental results on the output feedback control of a linear motor drive system are obtained to illustrate the proposed algorithm.
NCI-H295R, a Human Adrenal Cortex-Derived Cell Line, Expresses Purinergic Receptors Linked to Ca2+-Mobilization/Influx and Cortisol Secretion

Purinergic receptor expression and involvement in steroidogenesis were examined in NCI-H295R (H295R), a human adrenal cortex cell line which expresses all the key enzymes necessary for steroidogenesis. mRNA/protein for multiple P1 (A2A and A2B), P2X (P2X5 and P2X7), and P2Y (P2Y1, P2Y2, P2Y6, P2Y12, P2Y13, and P2Y14) purinergic receptors were detected in H295R. 2MeS-ATP (10–1000 µM), a P2Y1 agonist, induced glucocorticoid (GC) secretion in a dose-dependent manner, while other extracellular purine/pyrimidine agonists (1–1000 µM) had no distinct effect on GC secretion. Extracellular purines, even non-steroidogenic ones, induced Ca2+-mobilization in the cells, independently of the extracellular Ca2+ concentration. Increases in intracellular Ca2+ concentration induced by extracellular purine agonists were transient, except when induced by ATP or 2MeS-ATP. Angiotensin II (AngII: 100 nM) and dibutyryl-cyclic AMP (db-cAMP: 500 µM) induced both GC secretion and Ca2+-mobilization in the presence of extracellular Ca2+ (1.2 mM). GC secretion by AngII was reduced by nifedipine (10–100 µM); whereas the Ca2+ channel blocker did not inhibit GC secretion by 2MeS-ATP. Thapsigargin followed by extracellular Ca2+ exposure induced Ca2+-influx in H295R, and the cells expressed mRNA/protein of the component molecules for store-operated calcium entry (SOCE): transient receptor C (TRPC) channels, calcium release-activated calcium channel protein 1 (Orai-1), and the stromal interaction molecule 1 (STIM1). In P2Y1-knockdown, 2MeS-ATP-induced GC secretion was significantly inhibited. These results suggest that H295R expresses a functional P2Y1 purinergic receptor for intracellular Ca2+-mobilization, and that P2Y1 is linked to SOCE-activation, leading to Ca2+-influx which might be necessary for glucocorticoid secretion.
Local dominant binary patterns for recognition of multi-view facial expressions

In this paper, a novel framework is proposed for automatic recognition of facial expressions. However, the face images for the proposed problem are captured at multiple view angle (i.e., multi-view facial expressions). The proposed scheme introduces a local dominant binary pattern (LDBP). Unlike uniform LBP based features, the LDBP uses fewer feature dimension without affecting the recognition performances. The LDBP is computed by improvising LBP with dominant orientations of neighborhood pixels. The eigen-value analysis of structure tensor representation of expressive face images determines the dominant directions of gray value changes in local neighbors of pixels. We use SVM for view-specific classification of multi-view facial expressions. The proposed model is experimented with the benchmark datasets of both near-frontal (CK+ and JAFEE) and multi-view (KDEF, SFEW and LFPW) face images. The datasets include faces from posed as well as spontaneous expressions. The proposed scheme outperforms state-of-the-arts by approximately 1% for the near-frontal facial expressions and by at least 3% for multi-view facial expressions on an average.
Extraction of relevant information from document images using measures of visual attention

This paper describes an approach to attention based layout segmentation using general principles of the human visual perception to achieve this goal. The text is considered as texture in different resolution levels. A new measure of attractiveness is introduced. The segmentation is generic and not limited to specific document classes and models. The resulting regions of interest may be used for further interpretation. The overall speed of browsing and searching large volumes of scanned documents can be increased considerably.
Efficient Self-Join Algorithm in Interval-based Temporal Data Models

Interval-based temporal data model is a popular data model in temporal databases. It uses time intervals for representing the period of validity of a tuple, leading to unavoidable self-joins when combining tuples for objects. It requires k + 1-way self-join for k conjunctive conditions. Join operations are one of the most expensive operations in databases and they are even more serious in temporal databases because of growing data. There are many join algorithms for temporal databases. However, they focus on joining different inputs rather than an identical input, leading to multiple scans for the identical input. Advanced 2way join algorithms avoid a quadratic disk I/O complexity, but they are affected by the number of self-joins and partition sizes. In this paper, we address the problem of self-joins in the interval-based temporal data model and introduce a stream-based self-join algorithm. The proposed algorithm shows that it achieves a single relation scan for k-way self-join and its performance is not affected by partition sizes.
Resting-State Functional Connectivity Differences in Premature Children

We examine the coherence in the spontaneous brain activity of sleeping children as measured by the blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) signals. The results are described in terms of resting-state networks (RSN) and their properties. More specifically, in this study we examine the effect of severe prematurity on the spatial location of the visual, temporal, motor, basal ganglia, and the default mode networks, the temporal response properties of each of these networks, and the functional connectivity between them. Our results suggest that the anatomical locations of the RSNs are well developed by 18 months of age and their spatial locations are not distinguishable between premature and term born infants at 18 months or at 36 months, with the exception of small spatial differences noted in the basal ganglia area and the visual cortex. The two major differences between term and pre-term children were present at 36 but not 18 months and include: (1) increased spectral energy in the low frequency range (0.01–0.06 Hz) for pre-term children in the basal ganglia component, and (2) stronger connectivity between RSNs in term children. We speculate that children born very prematurely are vulnerable to injury resulting in weaker connectivity between resting-state networks by 36 months of age. Further work is required to determine whether this could be a clinically useful tool to identify children at risk of developmental delay related to premature birth.
BCI meeting 2005-workshop on clinical issues and applications

This paper describes the outcome of discussions held during the Third International BCI Meeting at a workshop charged with reviewing and evaluating the current state of and issues relevant to brain-computer interface (BCI) clinical applications. These include potential BCI users, applications, validation, getting BCIs to users, role of government and industry, plasticity, and ethics.
Combination of amniotic epithelial cells with NDGA promotes the survival of transplanted AECs in spinal cord-injured rats

Abstract Our previous research has shown that seeding amniotic epithelial cells (AECs) in chemically extracted acellular muscle scaffold (CEAMC) better promotes the functional recovery of spinal cord injury (SCI) than scaffold alone. However, the massive death of transplanted cells, which is related to early inflammatory response, is still a problem in cell therapy. Our previous study proved that nordihydroguaiaretic acid (NDGA) inhibits inflammation after SCI. In this study, we tested a strategy of combining the early administration of NDGA and the transplantation of AEC-seeded CEAMC to treat SCI. The results showed that simply increasing the number of surviving AECs had no significant benefits in SCI therapy, but NDGA administration ameliorated transplanted AEC survival demonstrating the potential value of NDGA in the cellular transplantation treatment of SCI.
From Backup to Hot Standby: High Availability for HDFS

Cluster-based distributed file systems generally have a single master to service clients and manage the namespace. Although simple and efficient, that design compromises availability, because the failure of the master takes the entire system down. Before version 2.0. 0-alpha, the Hadoop Distributed File System (HDFS) -- an open-source storage, widely used by applications that operate over large datasets, such as MapReduce, and for which an uptime of 24x7 is becoming essential -- was an example of such systems. Given that scenario, this paper proposes a hot standby for the master of HDFS achieved by (i) extending the master's state replication performed by its check pointer helper, the Backup Node, and by (ii) introducing an automatic fail over mechanism. The step (i) took advantage of the message duplication technique developed by other high availability solution for HDFS named Avatar Nodes. The step (ii) employed another Hadoop software: ZooKeeper, a distributed coordination service. That approach resulted in small code changes, 1373 lines, not requiring external components to the Hadoop project. Thus, easing the maintenance and deployment of the file system. Compared to HDFS 0.21, tests showed that both in loads dominated by metadata operations or I/O operations, the reduction of data throughput is no more than 15% on average, and the time to switch the hot standby to active is less than 100 ms. Those results demonstrate the applicability of our solution to real systems. We also present related work on high availability for other file systems and HDFS, including the official solution, recently included in HDFS 2.0. 0-alpha.