Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparative Study on the Antioxidant Activity of Commonly Used South Asian Herbs

The antioxidant activities of curry leaves, fenugreek seeds, Indian malabar leaves, red silk cotton tree leaves, cowitch leaves, holyfruit tree leaves, and black mustard seeds were compared. Their effects on reactive oxygen species (ROS) and superoxide dismutase (SOD) activity were investigated. The Oxygen Radical Absorbance Capacity (ORAC) assay determined the antioxidant potential of the extracts, while the ROS scavenging ability was explored in hyperglycemia-induced human umbilical vein endothelial cells (HUVECs). The SOD assay determined if the extracts stimulated the enzyme activity in the HUVECs. Curry leaf and fenugreek extracts had high ORAC values and superior free radical scavenging abilities compared with the rest of the extracts. The curry leaf extract had also increased the SOD activity. Fenugreek extract had not increased the SOD activity of the HUVECs. Thus, the two herbs displayed two distinct pathways of action for scavenging of ROS.
Design of Fuzzy Controller Used in Lower Limbs Rehabilitative Robot Drive System Based on Genetic Algorithm

This paper presents a fuzzy controller design for a drive system of lower limbs rehabilitative robot. In this system, turning the design of the fuzzy controller into an optimization of the parameters, using genetic algorithm to make an optimizing design of the fuzzy controller could get rid of the reliance on the experience knowledge and the cut and try method in the design of the fuzzy controller years before. By the theory of analyzing and the simulation experiments, we can conclude that, in the robots' drive system, using fuzzy controller to instead of PID controller could get better control effect, also improve the dynamic performance, especially on rapidity and robustness.
Validity of time-predictable seismicity model for Nepal and its adjoining regions

Earthquake generation model for the Nepal Himalaya and its adjoining regions was studied using seismicity data from 1963 to 2004 reported in the catalogs of National Geophysical Data Centre, Colorado and U. S. Geological Survey. The earthquakes having a surface wave magnitude M s ≥5.1 were considered to establish the statistical relation. Four seismogenic sources based on clusters of earthquakes have been identified in the region. It is observed that the time interval between two consecutive main shocks depends on the preceding main shock magnitude (M p ) and not on the forthcoming main shock magnitude (M f ). The result supports the applicability of time-predictable model for Nepal and its adjoining regions. A linear relation is established connecting the logarithm of the inter-event times between two successive main shocks (T) and magnitude of preceding main shock in the form log T =CM p +a where parameter a is a function of the minimum magnitude of the earthquake considered and the tectonic loading, and c is a positive constant. The physical meaning of the model is that larger the magnitude of the preceding main shock the longer will be the time interval for the forthcoming earthquake. The values of constants c and a for Nepal Himalaya and its adjoining regions are computed to be 0.25 and -0.65 respectively. This result can be utilised to compute the time of occurrence of the impending strong earthquake within the delineated seismogenic sources and may be used for assessing the long-term seismic hazard in the region.
Ecogenomics and Taxonomy of Cyanobacteria Phylum

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.
Natural immunity and HIV disease progression.

OBJECTIVE To investigate the clinical implications of impaired levels of the natural immunity mediated by natural killer (NK) cells and lymphokine activated killer (LAK) cells during infection with HIV-1. DESIGN Data used were from 172 individuals with an estimated measure of NK cell activity and 146 with an estimated measure of LAK cell activity. Patients had active HIV infection at the time of enrolment in the study and have been followed-up prospectively for a median of 3.0 years. METHODS The lytic activity of NK cells and LAK cells, the CD4 T lymphocyte count, and the concentration of CD16/CD56 NK cells were measured at enrolment. HIV RNA in plasma was measured retrospectively. Survival analysis was performed considering three main endpoints: CD4 cell counts below 100 x 10(6) cells/l, clinical AIDS, and death. RESULTS In unadjusted analysis and after adjustment for age, CD4 T lymphocyte count and plasma HIV RNA at enrolment, low LAK cell activity was significantly associated with higher risk of progression to a CD4 T lymphocyte count < 100 x 10(6) cells/l (crude P = 0.001; adjusted P = 0.04) and to death (crude P = 0.0002; adjusted P = 0.02). Patients with low NK cell responsiveness to interferon-alpha tended to be at higher risk of death (crude P = 0.04; adjusted P = 0.13) whereas unstimulated NK cell activity and the concentration of NK cells were of no prognostic value for patients in this cohort. CONCLUSIONS The present study suggests that low LAK cell activity and low NK cell responsiveness to interferon-alpha may be important in the pathogenesis of HIV infection.
Process Mining to Support Students' Collaborative Writing

Writing, particularly collaborative writing is a commonly needed skill. Investigating how ideas and concepts are developed during the process of writing can be used to improve not only the quality of the written documents but more importantly the writing skills of those involved. In this paper, process mining is used to analyze the process that groups of writers follow, and how the process correlates to the quality and semantic features of the final product. Particularly, we developed heuristics to extract the semantic nature of text changes during writing. These semantic changes were then used to identify writing activities in writing processes. We conducted a pilot study using documents collected from groups of undergraduate students writing collaboratively in order to evaluate the proposed heuristics and illustrate the applicability of process mining techniques in analyzing the process of writing.
Tension transients initiated by photogeneration of MgADP in skinned skeletal muscle fibers

Addition of MgADP to skinned skeletal muscle fibers causes a rise in Ca(2+)-activated isometric tension. Mechanisms underlying this tension increase have been investigated by rapid photogeneration of ADP within skinned single fibers of rabbit psoas muscle. Photolysis of caged ADP (P2-1(2-nitrophenyl)ethyladenosine 5'-diphosphate) resulted in an exponential increase in isometric tension with an apparent rate constant, kADP, of 9.6 +/- 0.3 s-1 (mean +/- SE, n = 28) and an amplitude, PADP, of 4.9 +/- 0.3% Po under standard conditions (0.5 mM photoreleased MgADP, 4 mM MgATP, pH 7.0, pCa 4.5, 0.18 M ionic strength, 15 degrees C). PADP depended upon the concentration of photoreleased MgADP as well as the concentration of MgATP. A plot of 1/PADP vs. 1/[MgADP] at three MgATP concentrations was consistent with competition between MgADP and MgATP for the same site on the crossbridge. The rate of the transient, kADP, also depended upon the concentration of MgADP and MgATP. At both 4 and 1 mM MgATP, kADP was not significantly different after photorelease of 0.1-0.5 mM MgADP, but was reduced by 28-40% when 3.5 mM MgADP was added before photorelease of 0.5 mM MgADP. kADP was accelerated by about twofold when MgATP was varied from 0.5 to 8 mM MgATP. These effects of MgATP and MgADP were not readily accounted for by population of high force-producing states resulting from reversal of the ADP dissociation process. Rather, the results suggest that competition between MgADP and MgATP for crossbridges at the end of the cycle slows detachment leading to accumulation of force-generating crossbridges. Elevation of steady- state Pi concentration from 0.5 to 30 mM caused acceleration of kADP from 10.2 +/- 0.5 to 27.8 +/- 1.8 s-1, indicating that the tension rise involved crossbridge flux through the Pi dissociation step of the cycle.
How Much Does a VM Cost? Energy-Proportional Accounting in VM-Based Environments

The costs of current data centers are mostly driven by their energy consumption (specifically by the air conditioning, computing and networking infrastructure). Yet, current pricing models are usually static and rarely consider the facilities' energy consumption per user. The challenge is to provide a fair and predictable model to attribute the overall energy costs per virtual machine (VM). Current pay-as-you-go models of Cloud providers allow users to easily know how much their computing will cost. However, this model is not fully transparent as to where the costs come from (e.g., energy). In this paper we introduce EPAVE, a model for Energy-Proportional Accounting in VM-based Environments. EPAVE allows transparent, reproducible and predictive cost calculation for users and for Cloud providers. We show these characteristics of EPAVE by a number of use cases in heterogeneous data centers and discuss the applicability of EPAVE.
Fast and Compact Hamming Distance Index

Searching for similar objects in a collection is a core task of many applications in databases, pattern recognition, and information retrieval. As there exist similarity-preserving hash functions like SimHash, indexing these objects reduces to the solution of the Approximate Dictionary Queries problem. In this problem we have to index a collection of fixed-sized keys to efficiently retrieve all the keys which are at a Hamming distance at most k from a query key. In this paper we propose new solutions for the approximate dictionary queries problem. These solutions combine the use of succinct data structures with an efficient representation of the keys to significantly reduce the space usage of the state-of-the-art solutions without introducing any time penalty. Finally, by exploiting triangle inequality, we can also significantly speed up the query time of the existing solutions.
Automated Guiding Task of a Flexible Micropart Using a Two-Sensing-Finger Microgripper

This paper studies automated tasks based on hybrid force/position control of a flexible object at the microscale. A guiding task of a flexible micropart is the case of the study and is achieved by a two-sensing-finger microgripper. An experimental model of the behavior of the microgripper is given and the interaction forces are studied. Based on grasp stability, a guiding strategy taking into account the pull off forces is proposed. A specific control strategy using an external hybrid force/position control and taking into account microscale specificities is proposed. The experimental results of automated guiding task are presented.
Semantic Annotation for Microblog Topics Using Wikipedia Temporal Information

Trending topics in microblogs such as Twitter are valuable resources to understand social aspects of real-world events. To enable deep analyses of such trends, semantic annotation is an effective approach; yet the problem of annotating microblog trending topics is largely unexplored by the research community. In this work, we tackle the problem of mapping trending Twitter topics to entities from Wikipedia. We propose a novel model that complements traditional text-based approaches by rewarding entities that exhibit a high temporal correlation with topics during their burst time period. By exploiting temporal information from the Wikipedia edit history and page view logs, we have improved the annotation performance by 17-28%, as compared to the competitive baselines.
Intelligent Network Control Using Object-Oriented Term-Rewriting

In this paper, we describe the theoretical framework that allows us to use of the expert system shell CLIPS to define the network model in the Distribution Management System (DMS) for the Indonesian State Power system (PLN). The rules defining the behavior of the system are developed using the framework of Object-Oriented Term-Rewriting (OOTR) in order to guarantee the asynchronous character of the program’s execution. Furthermore, we can provide syntactic tests that allow us to guarantee non-interaction between rules in our systems so that we can combine both the rules for power propagation in the network, and the rules for the intelligent control of the network in a safe and uniform fashion.
Species Tree Inference by Minimizing Deep Coalescences

In a 1997 seminal paper, W. Maddison proposed minimizing deep coalescences, or MDC, as an optimization criterion for inferring the species tree from a set of incongruent gene trees, assuming the incongruence is exclusively due to lineage sorting. In a subsequent paper, Maddison and Knowles provided and implemented a search heuristic for optimizing the MDC criterion, given a set of gene trees. However, the heuristic is not guaranteed to compute optimal solutions, and its hill-climbing search makes it slow in practice. In this paper, we provide two exact solutions to the problem of inferring the species tree from a set of gene trees under the MDC criterion. In other words, our solutions are guaranteed to find the tree that minimizes the total number of deep coalescences from a set of gene trees. One solution is based on a novel integer linear programming (ILP) formulation, and another is based on a simple dynamic programming (DP) approach. Powerful ILP solvers, such as CPLEX, make the first solution appealing, particularly for very large-scale instances of the problem, whereas the DP-based solution eliminates dependence on proprietary tools, and its simplicity makes it easy to integrate with other genomic events that may cause gene tree incongruence. Using the exact solutions, we analyze a data set of 106 loci from eight yeast species, a data set of 268 loci from eight Apicomplexan species, and several simulated data sets. We show that the MDC criterion provides very accurate estimates of the species tree topologies, and that our solutions are very fast, thus allowing for the accurate analysis of genome-scale data sets. Further, the efficiency of the solutions allow for quick exploration of sub-optimal solutions, which is important for a parsimony-based criterion such as MDC, as we show. We show that searching for the species tree in the compatibility graph of the clusters induced by the gene trees may be sufficient in practice, a finding that helps ameliorate the computational requirements of optimization solutions. Further, we study the statistical consistency and convergence rate of the MDC criterion, as well as its optimality in inferring the species tree. Finally, we show how our solutions can be used to identify potential horizontal gene transfer events that may have caused some of the incongruence in the data, thus augmenting Maddison's original framework. We have implemented our solutions in the PhyloNet software package, which is freely available at: http://bioinfo.cs. rice.edu/phylonet.
Estimating chlorophyll content at leaf scale in viroid-inoculated oil palm seedlings (Elaeis guineensis Jacq.) using reflectance spectra (400 nm–1050 nm)

ABSTRACT Orange Spotting (OS) is an emerging disease in oil palm (Elaeis guineensis Jacq) that has been associated with Coconut cadang-cadang viroid (CCCVd; Cocadviroid, Pospiviroidae). This study was aimed at selecting efficient wavebands in the Visible/near infrared (VNIR) spectrum (400–1050 nm) for estimation of chlorophyll content in CCCVd-inoculated oil palm seedlings. The VNIR spectrum is most sensitive to chlorophyll stress and able to differentiate between healthy and diseased plants. Therefore, a greenhouse experiment was conducted to remotely sense the chlorophyll content using a hyperspectral hand-held spectroradiometer (Analytical Spectral Device (ASD) FieldSpec–II) and a portable chlorophyll meter (Minolta Soil-Plant Analysis Development (SPAD)−502). FieldSpec–II provides reflectance spectra with narrow and contiguous wavebands while SPAD-502 churns out SPAD readings corresponding to chlorophyll content. Interval Partial Least Squares (iPLS) model was used to assess the relationship between independent variable (spectra) and dependent variable (SPAD readings). Five different spectral datasets (i.e. raw spectra, first-order derivatives, Savitzky-Golay smoothing, Multiplicative Scatter Correction (MSC), and standard normal transformation) were investigated. Results showed that the MSC dataset yielded the most accurate estimation with a root mean square error of prediction of 3.70% and a correlation coefficient for prediction of 0.72. A total of thirty wavebands within a range between 601 nm and 630 nm was selected. This work showed that VNIR spectra has the potential to diagnose OS disease in oil palm using the iPLS regression method. This is completely a new application of hyperspectral remote sensing for the oil palm industry, particularly in the domain of plant protection.
Pharmacokinetics and Safety of Single and Multiple Doses of ACHN-490 Injection Administered Intravenously in Healthy Subjects

ABSTRACT ACHN-490 is an aminoglycoside with activity against multidrug-resistant pathogens, including those resistant to currently used aminoglycosides. Two randomized, double-blind, placebo-controlled clinical studies investigated the pharmacokinetics (PK), safety, and tolerability of ACHN-490 injection in healthy subjects. Study 1 used a parallel-group design with escalating single (SD) and multiple doses (MD). Study 2 explored a longer duration of the highest dose tolerated in the first study. Subjects were randomly assigned to receive either ACHN-490 injection or a placebo administered by a 10-min intravenous infusion. Study 1 enrolled 39 subjects (30 active and 9 placebo) and consisted of a single dose of 1 mg/kg body weight followed by ascending SD and MD cohorts of 4, 7, 11, and 15 mg/kg for 10, 10, 5, and 3 days, respectively. Study 2 enrolled 8 subjects (6 active and 2 placebo) who received 15 mg/kg for 5 days. Safety was assessed from adverse event (AE) reporting, standard clinical laboratory procedures, and testing for renal, cochlear, and vestibular function. ACHN-490 exhibited linear and dose-proportional PK, with agreement between the studies for PK parameters assessed. The 15-mg/kg dose did not accumulate with repeated dosing over 5 days. Mean steady-state (±standard deviation) area under the concentration-time curve from 0 to 24 h (AUC0-24), maximum concentration of drug in serum (Cmax), half-life (t1/2), clearance, and volume of distribution at steady state (Vss) for the 15-mg/kg, day 5 dose were 239 ± 45 h·mg/liter, 113 ± 17 mg/liter, 3 ± 0.3 h, 1.1 ± 0.1 ml/min/kg, and 0.24 ± 0.04 liters/kg, respectively. AEs were mild to moderate and rapidly resolved. No evidence of nephrotoxicity or ototoxicity was observed.
Effect of Cholesterol Deposition on Bacterial Adhesion to Contact Lenses

Purpose. To examine the effect of cholesterol on the adhesion of bacteria to silicone hydrogel contact lenses. Methods. Contact lenses, collected from subjects wearing Acuvue Oasys or PureVision lenses, were extracted in chloroform:methanol (1:1, v/v) and amount of cholesterol was estimated by thin-layer chromatography. Unworn lenses were soaked in cholesterol, and the numbers of Pseudomonas aeruginosa strains or Staphylococcus aureus strains that adhered to the lenses were measured. Cholesterol was tested for effects on bacterial growth by incubating bacteria in medium containing cholesterol. Results. From ex vivo PureVision lenses, 3.4 ± 0.3 &mgr;g/lens cholesterol was recovered, and from Acuvue Oasys lenses, 2.4 ± 0.2 to 1.0 ± 0.1 &mgr;g/lens cholesterol was extracted. Cholesterol did not alter the total or viable adhesion of any strain of P. aeruginosa or S. aureus (p > 0.05). However, worn PureVision lenses reduced the numbers of viable cells of P. aeruginosa (5.8 ± 0.4 log units) compared with unworn lenses (6.4 ± 0.2 log units, p = 0.001). Similarly, there were fewer numbers of S. aureus 031 adherent to worn PureVision (3.05 ± 0.8 log units) compared with unworn PureVision (4.6 ± 0.3 log units, p = 0.0001). Worn Acuvue Oasys lenses did not affect bacterial adhesion. Cholesterol showed no effect on the growth of any test strain. Conclusions. Although cholesterol has been shown to adsorb to contact lenses during wear, this lipid does not appear to modulate bacterial adhesion to a lens surface.
Simplicity-expressiveness tradeoffs in mechanism design

A fundamental result in mechanism design theory, the so-called revelation principle, asserts that for many questions concerning the existence of mechanisms with a given outcome one can restrict attention to truthful direct-revelation mechanisms. In practice, however, many mechanisms use a restricted message space. This motivates the study of the tradeoffs involved in choosing simplified mechanisms, which can sometimes bring benefits in precluding bad or promoting good equilibria, and other times impose costs on welfare and revenue. We study the simplicity-expressiveness tradeoff in two representative settings, sponsored search auctions and combinatorial auctions, each being a canonical example for complete information and incomplete information analysis, respectively. We observe that the amount of information available to the agents plays an important role for the tradeoff between simplicity and expressiveness.
Characteristics of injuries caused by paragliding accidents: A cross-sectional study.

BACKGROUND This study was undertaken to analyze the characteristics and risk factors relating to fatalities and injuries caused by paragliding. METHODS The judicial examination reports and hospital documents of 82 patients traumatized in 64 accidents during 242 355 paragliding jumps between August 2004 and September 2011 were analyzed. RESULTS In these accidents, 18 of the 82 patients lost their lives. In the patients with a confirmed cause of accident, most of them were involved with multiple fractures and internal organ injuries (n=8, 44.4%). CONCLUSION We investigated the incidence of paragliding injuries, the types of the injuries, and the severity of affected anatomical regions. The findings are significant for the prevention of paragliding injuries and future research.