Miracle-dz/UniFAR-FTUs huggingface dataset:
Exogenous Melatonin Suppresses Dark-Induced Leaf Senescence by Activating the Superoxide Dismutase-Catalase Antioxidant Pathway and Down-Regulating Chlorophyll Degradation in Excised Leaves of Perennial Ryegrass (Lolium perenne L.)

Leaf senescence is a typical symptom in plants exposed to dark and may be regulated by plant growth regulators. The objective of this study was to determine whether exogenous application of melatonin (N-acetyl-5-methoxytryptamine) suppresses dark-induced leaf senescence and the effects of melatonin on reactive oxygen species (ROS) scavenging system and chlorophyll degradation pathway in perennial grass species. Mature perennial ryegrass (Lolium perenne L. cv. ‘Pinnacle’) leaves were excised and incubated in 3 mM 2-(N-morpholino) ethanesulfonic buffer (pH 5.8) supplemented with melatonin or water (control) and exposed to dark treatment for 8 days. Leaves treated with melatonin maintained significantly higher endogenous melatonin level, chlorophyll content, photochemical efficiency, and cell membrane stability expressed by lower electrolyte leakage and malondialdehyde (MDA) content compared to the control. Exogenous melatonin treatment also reduced the transcript level of chlorophyll degradation-associated genes and senescence marker genes (LpSAG12.1, Lph36, and Lpl69) during the dark treatment. The endogenous O2- production rate and H2O2 content were significantly lower in these excised leaves treated with melatonin compared to the water control. Exogenous melatonin treatment caused increases in enzymatic activity and transcript levels of superoxide dismutase and catalase but had no significant effects on ascorbate peroxidase, glutathione reductase, dehydroascorbate reductase, and monohydroascorbate reductase. The content of non-enzymatic antioxidants, such as ascorbate and dehydroascorbate, were decreased by melatonin treatment, while the content of glutathione and oxidized glutathione was not affected by melatonin. These results suggest that the suppression of dark-induced leaf senescence by exogenous melatonin may be associated with its roles in regulating ROS scavenging through activating the superoxide dismutase-catalase enzymatic antioxidant pathway and down-regulating chlorophyll degradation in perennial ryegrass.
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa

SUMMARY The IRMa toolbox provides an interactive application to assist in the validation of Mascot search results. It allows automatic filtering of Mascot identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention. AVAILABILITY http://biodev.extra. cea.fr/docs/irma (java 1.5 or higher needed).
Automation of object extraction from LiDAR in urban areas

Light Detection and Ranging (LiDAR) has become a valuable data source for urban data acquisition. This paper gives an overview about current trends in the automation of object extraction from LiDAR data. These trends are caused by the technical development of LiDAR sensors that enable the acquisition of point clouds at higher resolution as well as the recording of the full waveform of the returned signal, and by the adoption of processing techniques from the Computer Vision and Pattern Recognition communities. Triggered by these developments, new applications are being found for LiDAR data.
Capacity Outage Probability for Multi-Cell Processing Under Rayleigh Fading

In this paper we provide an analytical expression of the capacity outage probability for Coordinated Multiple Point (CoMP) downlink transmission in Rayleigh fading. The theoretical derivation and simulation results match perfectly. Used in dense urban interference limited networks, CoMP is expected to improve cell-edge users' throughput and allow a better coverage and fairness. We demonstrate that our closed-form derivation can be helpful to maximise the capacity with outage and the goodput, by tuning appropriately the transmission data-rate and selecting optimal set of cooperating stations.
Design of Decoder using Modified Hybrid Weighted Symbol Flipping for Nonbinary Ldpc Codes

A hybrid decoding algorithm which proposed for nonbinary and binary low density parity (LDPC) codes, both the algorithm combines the weighted symbol flipping (WSF) algorithm with the fast Fourier transform q-ary sum product algorithm (FFT-QSPA). The flipped position and value are determined by the symbol flipping metric and the received bit values in the first stage WSF algorithm. If the low complexity WSF algorithm is failed, the second stage FFT-QSPA is activated as a switching strategy. They are particularly effective for decoding LDPC codes constructed based on finite geometries and finite fields. Analyzing both the techniques nonbinary LDPC codes gives the better error performance and greatly reduces the computation complexity compared to binary LDPC codes. The proposed hybrid algorithm is used for some applications in communication systems for high speed and low power consumption.
Characterisation of THz Schottky diodes for MetOp-SG instruments

Schottky diode technology is used for frequency conversion and generation in three of the mm-wave and THz instruments on-board the European Space Agency’s MetOp-SG satellites. The instruments are MWS (MicroWave Sounder), MWI (Microwave Imager) and ICI (Ice Cloud Imager). In order to ensure the storage and operational life time in addition to performance requirements, reliability assessment for the diodes is performed well before the fabrication of the instruments flight models. This paper presents the thermal characterisation of Schottky diodes used in the instruments as a part of reliability assessment process. Different multiplier and mixer prototype modules have been developed and thermally tested. In addition, thermal simulations are also carried out for comparison with the measurement results. Furthermore, thermal measurements on several identical multiplier blocks are also made that provides information on reproducibility of the assembly of discrete RF devices from the thermal perspective. Finally, some RF measurements are also carried out for comparison to the thermal impedance measurement results made on the same block and the same diodes.
Geobacter sp. SD-1 with enhanced electrochemical activity in high-salt concentration solutions.

An isolate, designated strain SD-1, was obtained from a biofilm dominated by Geobacter sulfurreducens in a microbial fuel cell. The electrochemical activity of strain SD-1 was compared with type strains, G. sulfurreducens PCA and Geobacter metallireducens GS-15, and a mixed culture in microbial electrolysis cells. SD-1 produced a maximum current density of 290 ± 29 A m−3 in a high-concentration phosphate buffer solution (PBS-H, 200 mM). This current density was significantly higher than that produced by the mixed culture (189 ± 44 A m−3) or the type strains (< 70 A m−3). In a highly saline water (SW; 50 mM PBS and 650 mM NaCl), current by SD-1 (158 ± 4 A m−3) was reduced by 28% compared with 50 mM PBS (220 ± 4 A m−3), but it was still higher than that of the mixed culture (147 ± 19 A m−3), and strains PCA and GS-15 did not produce any current. Electrochemical tests showed that the improved performance of SD-1 was due to its lower charge transfer resistance and more negative potentials produced at higher current densities. These results show that the electrochemical activity of SD-1 was significantly different than other Geobacter strains and mixed cultures in terms of its salt tolerance.
Male Contraception, IV: Hypotonic-Like Effect from Echeveria gibbiflora on Human Sperm

At present there is no accepted method for the regulation of male fertility. The most appropriate form of contraception would undoubtedly be to develop from traditional plant-derived folk drugs a contraceptive male method. Hypoosmotic shock is used for validate plasma membrane function and its fertilizing capacity of human sperm. Such effect is induced in human sperm in the presence of a purified fraction from Echeveria gibbiflora (PFEG) aqueous crude extract. The hypotonic-like effect included a distension of the plasma membrane over the acrosome region and in some occasions around the sperm middle piece. An enhanced activity of the immobilizing and agglutination effects was induced instantaneously after the addition of PEFG versus aqueous crude extract activity (OBACE). Using electron microscopy it was possible to observe a deposit of a ''sticky'' dense material intercalated along the plasma membrane. The membrane was sealed making it impossible to measure the viability or metabolic activity of the treated sperm by the fluorescence (FDA-IP) technique. It was also possible to corroborate the dispersion of the acrosomal content and the disappearance of the acrosomal and nuclear membrane. Results that makes PFEG hypotonic-like effect a serious candidate to conduct a study to determine the predicting capacity of this compound in human infertility and suggest that the plant may yield a compound suitable for use as male contraceptive agent.
Semi-supervised Verb Class Discovery Using Noisy Features

We cluster verbs into lexical semantic classes, using a general set of noisy features that capture syntactic and semantic properties of the verbs. The feature set was previously shown to work well in a supervised learning setting, using known English verb classes. In moving to a scenario of verb class discovery, using clustering, we face the problem of having a large number of irrelevant features for a particular clustering task. We investigate various approaches to feature selection, using both unsupervised and semi-supervised methods, comparing the results to subsets of features manually chosen according to linguistic properties. We find that the unsupervised method we tried cannot be consistently applied to our data. However, the semi-supervised approach (using a seed set of sample verbs) overall outperforms not only the full set of features, but the hand-selected features as well.
Joint evolution of multiple social traits: a kin selection analysis

General models of the evolution of cooperation, altruism and other social behaviours have focused almost entirely on single traits, whereas it is clear that social traits commonly interact. We develop a general kin-selection framework for the evolution of social behaviours in multiple dimensions. We show that whenever there are interactions among social traits new behaviours can emerge that are not predicted by one-dimensional analyses. For example, a prohibitively costly cooperative trait can ultimately be favoured owing to initial evolution in other (cheaper) social traits that in turn change the cost–benefit ratio of the original trait. To understand these behaviours, we use a two-dimensional stability criterion that can be viewed as an extension of Hamilton's rule. Our principal example is the social dilemma posed by, first, the construction and, second, the exploitation of a shared public good. We find that, contrary to the separate one-dimensional analyses, evolutionary feedback between the two traits can cause an increase in the equilibrium level of selfish exploitation with increasing relatedness, while both social (production plus exploitation) and asocial (neither) strategies can be locally stable. Our results demonstrate the importance of emergent stability properties of multidimensional social dilemmas, as one-dimensional stability in all component dimensions can conceal multidimensional instability.
What is the role of albumin in proteinuric glomerulopathies?

Albumin is a 69 kDa plasma protein (molecular radius 36 A) with a variety of functions, including maintenance of plasma oncotic pressure, buffering of plasma acid–base changes and functioning as a transport protein for hormones, fatty acids, phospholipids, ions and heavy metals [1]. Albumin was early identified as critical in regulating endothelial permeability, especially in studies on single perfused microvessels [2]. Later, plasma acidic glycoproteins, especially orosomucoid, were found to be (additional) crucial factors in maintaining normal microvascular permeability, particularly to negatively charged macromolecules (e.g. albumin) [3]. The critical role of albumin and orosomucoid in maintaining vascular permeability has also been demonstrated for glomerular capillaries [4,5]. Paradoxically, in Nagase analbuminaemic rats (NARs), a mutant of the Sprague–Dawley strain devoid of circulating albumin, the clearance of proteins (albumin and IgG) to the interstitium was, however, only moderately increased [6]. Furthermore, in a recent study, the glomerular permeability to macromolecules was only slightly altered in this rat strain [7]. Albumin and its ligands have also been implicated in the progression of proteinuric renal disease, by direct or indirect tubulotoxic effects [8]. This tubulotoxicity, during continuous protein overload, apparently results not only in injury to the tubular cells, but also in overall tubulointerstitial damage [8–10]. Although proteinuria is an established risk factor for the progression of glomerular disorders, the concept that albumin may be tubulotoxic is partly controversial. Also, the concept of albumin regulating microvascular (glomerular) permeability has been questioned [11]. Moreover, the classic concept of the glomerular barrier functioning as a highly sizeand charge-selective filter has been put into serious doubt recently [12].
A Hybrid Convolution Tree Kernel for Semantic Role Labeling

A hybrid convolution tree kernel is proposed in this paper to effectively model syntactic structures for semantic role labeling (SRL). The hybrid kernel consists of two individual convolution kernels: a Path kernel, which captures predicate-argument link features, and a Constituent Structure kernel, which captures the syntactic structure features of arguments. Evaluation on the datasets of CoNLL-2005 SRL shared task shows that the novel hybrid convolution tree kernel out-performs the previous tree kernels. We also combine our new hybrid tree kernel based method with the standard rich flat feature based method. The experimental results show that the combinational method can get better performance than each of them individually.
Free energy and phase transition of the matrix model on a plane wave

It has recently been observed that the weakly coupled plane-wave matrix model has a density of states which grows exponentially at high energy. This implies that the model has a phase transition. The transition appears to be of first order. However, its exact nature is sensitive to interactions. In this paper, we analyze the effect of interactions by computing the relevant parts of the effective potential for the Polyakov loop operator in the finite temperature plane-wave matrix model to three-loop order. We show that the phase transition is indeed of first order. We also compute the correction to the Hagedorn temperature to order two loops.
Topiramate placebo-controlled dose-ranging trial in refractory partial epilepsy using 600-, 800-, and 1,000-mg daily dosages

We conducted a multicenter, double-blind, randomized, parallel, placebo-controlled trial in 190 patients to evaluate the safety and efficacy of three dosages of topiramate (600, 800, and 1,000 mg/day) as adjunctive therapy for patients with refractory partial epilepsy. During an 18-week double-blind treatment period, median percent reductions from baseline in average monthly seizure rates were 1% for placebo, 41% for topiramate 600 mg/day and topiramate 800 mg/day, and 38% for topiramate 1,000 mg/day. There was a 50% or greater reduction from baseline in seizure frequency in 9% of patients in the placebo group and in 44% for topiramate 600 mg/day, 40% for topiramate 800 mg/day, and 38% for topiramate 1,000 mg/day. No placebo patients were improved by 75 to 100% in seizure frequency, whereas 20% of the topiramate patients were improved to this degree. All intent-to-treat drug-placebo comparisons including seizure reduction, percent responders, and investigator and patient global evaluations significantly (p <or=to 0.02) favored topiramate. Treatment-emergent adverse events consisted mainly of neurologic symptoms commonly observed during antiepileptic drug (AED) therapy. Sixteen percent of patients on topiramate discontinued therapy due to adverse events. Results of this study indicate that topiramate is a highly efficacious and generally well tolerated new AED. When large groups of patients are compared, incremental efficacy in the add-on setting is not observed at topiramate dosages above 600 mg/day; however, higher doses may prove beneficial to individual patients who tolerate them. NEUROLOGY 1996;46: 1678-1683
Endocytosis and Nuclear Trafficking of Adeno-Associated Virus Type 2 Are Controlled by Rac1 and Phosphatidylinositol-3 Kinase Activation

ABSTRACT Adeno-associated virus (AAV) is a single-stranded DNA parvovirus that causes no currently known pathology in humans. Despite the fact that this virus is of increasing interest to molecular medicine as a vector for gene delivery, relatively little is known about the cellular mechanisms controlling infection. In this study, we have examined endocytic and intracellular trafficking of AAV-2 using fluorescent (Cy3)-conjugated viral particles and molecular techniques. Our results demonstrate that internalization of heparan sulfate proteoglycan-bound AAV-2 requires αVβ5 integrin and activation of the small GTP-binding protein Rac1. Following endocytosis, activation of a phosphatidylinositol-3 (PI3) kinase pathway was necessary to initiate intracellular movement of AAV-2 to the nucleus via both microfilaments and microtubules. Inhibition of Rac1 using a dominant N17Rac1 mutant led to a decrease in AAV-2-mediated PI3 kinase activation, indicating that Rac1 may act proximal to PI3 kinase during AAV-2 infection. In summary, our results indicate that αVβ5 integrin-mediated endocytosis of AAV-2 occurs through a Rac1 and PI3 kinase activation cascade, which directs viral movement along the cytoskeletal network to the nucleus.
Improving brain–machine interface performance by decoding intended future movements

Objective. A brain–machine interface (BMI) records neural signals in real time from a subject's brain, interprets them as motor commands, and reroutes them to a device such as a robotic arm, so as to restore lost motor function. Our objective here is to improve BMI performance by minimizing the deleterious effects of delay in the BMI control loop. We mitigate the effects of delay by decoding the subject's intended movements a short time lead in the future. Approach. We use the decoded, intended future movements of the subject as the control signal that drives the movement of our BMI. This should allow the user's intended trajectory to be implemented more quickly by the BMI, reducing the amount of delay in the system. In our experiment, a monkey (Macaca mulatta) uses a future prediction BMI to control a simulated arm to hit targets on a screen. Main Results. Results from experiments with BMIs possessing different system delays (100, 200 and 300 ms) show that the monkey can make significantly straighter, faster and smoother movements when the decoder predicts the user's future intent. We also characterize how BMI performance changes as a function of delay, and explore offline how the accuracy of future prediction decoders varies at different time leads. Significance. This study is the first to characterize the effects of control delays in a BMI and to show that decoding the user's future intent can compensate for the negative effect of control delay on BMI performance.
Wikipedia-Based Semantic Interpreter Using Approximate Top-k Processing and Its Application

Proper representation of the meaning of texts is crucial for enhancing many data mining and information retrieval tasks, including clustering, computing semantic relatedness between texts, and searching. Representing of texts in the concept-space derived from Wikipedia has received growing attention recently. This concept-based representation is capable of extracting semantic relatedness between texts that cannot be deduced with the bag of words model. A key obstacle, however, for using Wikipedia as a semantic interpreter is that the sheer size of the concepts derived from Wikipedia makes it hard to efficiently map texts into concept-space. In this paper, we develop an efficient and effective algorithm which is able to represent the meaning of a text by using the concepts that best match it. In particular, our approach first computes the approximate top-k Wikipedia concepts that are most relevant to the given text. We then leverage these concepts for representing the meaning of the given text. The experimental results show that the proposed technique provides significant gains in execution time without causing significant reduction in precision. We then explore the effectiveness of the proposed algorithm on a real world problem. In particular, we show that this novel scheme could be leveraged to boost the effectiveness in finding topic boundaries in a news video.
YSK2 Type Dehydrin (SbDhn1) from Sorghum bicolor Showed Improved Protection under High Temperature and Osmotic Stress Condition

YSK2 type dehydrin from Sorghum bicolor (SbDhn1) showed a high level of transcript accumulation when subjected to high temperature and osmotic stress. The high transcript level occurring in such stress situation might lead to a protective effect; though the exact mechanism by which this is achieved remains poorly understood. Nevertheless, our results provide compelling evidence to prove that transgenic tobacco lines overexpressing SbDhn1 gene showed improve stress tolerance as assessed by reduced membrane damage and low MDA content. Furthermore, we demonstrate here SbDhn1 expressing lines were only able to recover after stress treatment. In this study, we have provided direct evidence for the protection rendered by SbDHN1 protein to a temperature-sensitive enzyme under both high temperature and osmotic stress. We extended this analysis to the whole plant proteome where the addition of SbDHN1 protein helped in retaining the solubility of the protein was demonstrated. Interestingly, in vitro experiments carried out with lactate dehydrogenase (LDH), showed aggregate formation upon subjecting it to high temperature. However, in presence of SbDHN1 protein very few aggregates were observed. Aggregation assay showed a high level of aggregates in wild-type or empty vector transformed plants as compared to SbDhn1 transgenic lines. Confocal microscopy images in leaf peel sections of wild-type plants showed high amounts of aggregates as compared with transgenic lines. This study provides evidence for the protection rendered by SbDHN1 protein under high temperature by inhibiting the aggregate formation and provide the rational for the mechanism how these proteins ameliorate the adverse stress conditions.