Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Antiplasmodial Activity of Phospholipases A2 and a Phospholipase Homologue Isolated from the Venom of the Snake Bothrops asper

The antimicrobial and antiparasite activity of phospholipase A2 (PLA2) from snakes and bees has been extensively explored. We studied the antiplasmodial effect of the whole venom of the snake Bothrops asper and of two fractions purified by ion-exchange chromatography: one containing catalytically-active phospholipases A2 (PLA2) (fraction V) and another containing a PLA2 homologue devoid of enzymatic activity (fraction VI). The antiplasmodial effect was assessed on in vitro cultures of Plasmodium falciparum. The whole venom of B. asper, as well as its fractions V and VI, were active against the parasite at 0.13 ± 0.01 µg/mL, 1.42 ± 0.56 µg/mL and 22.89 ± 1.22 µg/mL, respectively. Differences in the cytotoxic activity on peripheral blood mononuclear cells between the whole venom and fractions V and VI were observed, fraction V showing higher toxicity than total venom and fraction VI. Regarding toxicity in mice, the whole venom showed the highest lethal effect in comparison to fractions V and VI. These results suggest that B. asper PLA2 and its homologue have antiplasmodial potential.
Selection for Robustness in Mutagenized RNA Viruses

Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we experimentally validate this hypothesis, dubbed the “survival of the flattest,” using two populations of the vesicular stomatitis RNA virus. Characterization of fitness distributions and genetic variability indicated that one population showed a higher replication rate, whereas the other was more robust to mutation. The faster replicator outgrew its robust counterpart in standard competition assays, but the outcome was reversed in the presence of chemical mutagens. These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis.
Using depth and appearance features for informed robot grasping of highly wrinkled clothes

Detecting grasping points is a key problem in cloth manipulation. Most current approaches follow a multiple re-grasp strategy for this purpose, in which clothes are sequentially grasped from different points until one of them yields to a desired configuration. In this paper, by contrast, we circumvent the need for multiple re-graspings by building a robust detector that identifies the grasping points, generally in one single step, even when clothes are highly wrinkled. In order to handle the large variability a deformed cloth may have, we build a Bag of Features based detector that combines appearance and 3D geometry features. An image is scanned using a sliding window with a linear classifier, and the candidate windows are refined using a non-linear SVM and a “grasp goodness” criterion to select the best grasping point. We demonstrate our approach detecting collars in deformed polo shirts, using a Kinect camera. Experimental results show a good performance of the proposed method not only in identifying the same trained textile object part under severe deformations and occlusions, but also the corresponding part in other clothes, exhibiting a degree of generalization.
AbCD: arbitrary coverage design for sequencing-based genetic studies

Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbitrary coverage (0.5-30×) and sample size (20-10 000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans). In addition, we also present two software tools: ShotGun and DesignPlanner, which were used to generate the estimates behind AbCD. ShotGun is a flexible short-read simulator for arbitrary user-specified read length and average depth, allowing cycle-specific sequencing error rates and realistic read depth distributions. DesignPlanner is a full pipeline that uses ShotGun to generate sequence data and performs initial SNP discovery, uses our previously presented linkage disequilibrium-aware method to call genotypes, and, finally, provides minor allele frequency-specific effective sample sizes. ShotGun plus DesignPlanner can accommodate effective sample size estimate for any combination of high-depth and low-depth data (for example, whole-genome low-depth plus exonic high-depth) or combination of sequence and genotype data [for example, whole-exome sequencing plus genotyping from existing Genomewide Association Study (GWAS)].
Construction of a nrdA::luxCDABE Fusion and Its Use in Escherichia coli as a DNA Damage Biosensor

The promoter of nrdA gene which is related with DNA synthesis was used to construct a DNA damage sensitive biosensor. A recombinant bioluminescent E. coli strain, BBTNrdA, harboring a plasmid with the nrdA promoter fused to the luxCDABE operon, was successfully constructed. Its response to various chemicals including genotoxic chemicals substantiates it as a DNA damage biosensor. In characterization, three different classes of toxicants were used: DNA damaging chemicals, oxidative stress chemicals, and phenolics. BBTNrdA only responded strongly to DNA damaging chemicals, such as nalidixic acid (NDA), mitomycin C (MMC), 1-methyl-1-nitroso-N-methylguanidine (MNNG), and 4-nitroquinoline N-oxide (4-NQO). In contrast, there were no responses from the oxidative stress chemicals and phenolics, except from hydrogen peroxide (H2O2) which is known to cause DNA damage indirectly. Therefore, the results of the study demonstrate that BBTNrdA can be used as a DNA damage biosensor.
Saffron : An Efficient Crop Production System in Energy Use in Iran

Efficient use of energy helps to achieve increased production and productivity, and contributes to the economy, profitability and competitiveness of agricultural sustainability of rural communities. Evaluation of saffron production system in view of energy balance was conducted in Khorasan Razavi province, Iran. Data and information was collected by using a face to face questionnaire from saffron fields in 2013. Results revealed that the total energy used in various production processes for producing saffron was 21580 MJ ha. Amongst the production practices in saffron production, consumed corm for cultivation (seed) was the most energy consuming input (59.66%), followed by nitrogen fertilizer (13.79%) and manure (13.35%). Outputs in saffron are consist stigma, leaf and corm. Stigma, leaf and corm yields were 3.86, 1230 and 1630 kg ha, respectively for average of five years period. The total energy input consumed could be classified in saffron fields as direct (17.14%), indirect (82.86%), renewable (79.95%), and nonrenewable (20.05%), energies. The share of renewable energy input used in total energy input was around 4 times more than non-renewable energy in saffron fields. Overall, in view of sustainability saffron production was a sustainable system.
Focus in Donegal Irish (gaelic) and Donegal English bilinguals

This paper examines the effects of focus on the global and local f0 variations in the contours of Donegal Irish and Donegal English, produced by bilingual speakers. The analysis was conducted on a controlled data set, where contrastive focus was elicited on each of the 3 potentially accented syllables along with broad focus. Results suggest that focus in non-final IP position in both of these Northern varieties is realised by expanding the f0 range associated with the focal accent and subsequent obligatory deaccentuation of the postfocal material, as well as range reduction or deaccentuation of prefocal accents. IP-final focus largely resembles broad focus.
A Novel Distributed Single Sign-On Scheme with Dynamically Changed Threshold Value

A Single Sign-On (SSO) system allow single authentication for multiple services. It is a potential solution to the implications of security, credentials management, et al. Recently, several works have used the threshold-based secret sharing scheme to create a distributed SSO service. All these works setup the threshold parameters first in the system initiation. But in some real-world applications, the threshold value should be dynamically changed in the authentication phase. In this paper, we present a novel threshold-based distributed Single Sign-On scheme with a dynamically changed threshold value(DctSSO). In DctSSO, two different degree secret polynomials are constructed. Each authentication server has two kinds of secret keys: keys for initiation shares and keys for authentication shares. Through the simply XOR operation, authentication shares keys can be delivered securely. DctSSO is not only as good as Threspassport on the aspects of security, portability, intrusion and fault tolerance, scalability, reliability, and availability, but also it offers two significant advantages over ThresPassport : it has the dynamically, securely and availably changed threshold value in the authentication phase, and it can prevent conspiracy-impersonation attacks.
ISM@FIRE-2014: Named Entity Recognition for Indian Languages

This paper describes the approaches we have adopted to identify the classes of named entities and annotate them with proper tags. Named Entity Recognition (NER) is a subtask of information extraction that seeks to locate and classify the entity names (proper nouns) in a text. NER systems are useful in many Natural Language Processing (NLP) applications such as question answering, machine translation, information extraction and so on. IN this task, Conditional Random Field (CRF) is used for the classification where tokens are classified hierarchically. We discuss two approaches: one for the official submission and the other its extended version. The performance of our systems were moderate.
Bayesian imitation learning in game characters

Imitation learning is a powerful mechanism applied by primates and humans. It allows for a straightforward acquisition of behaviours that, through observation, are known to solve everyday tasks. Recently, a Bayesian formulation has been proposed that provides a mathematical model of imitation learning. In this paper, we apply this framework to the problem of programming believable computer games characters. We will present experiments in imitation learning from the network traffic of multi-player online games. Our results underline that this indeed produces agents that behave more human-like than characters controlled by common game AI techniques.
Demonstration of a Tunable Microwave-Photonic Notch Filter Using Low-Loss Silicon Ring Resonators

We present a fully tunable multistage narrowband optical pole-zero notch filter that is fabricated in a silicon complementary metal oxide semiconductor (CMOS) foundry. The filter allows for the reconfigurable and independent tuning of the center frequency, null depth, and bandwidth for one or more notches simultaneously. It is constructed using a Mach-Zehnder interferometer (MZI) with cascaded tunable all-pass filter (APF) ring resonators in its arms. Measured filter nulling response exhibits ultranarrow notch 3 dB BW of 0.6350 GHz, and nulling depth of 33 dB. This filter is compact and integrated in an area of 1.75 mm2. Using this device, a novel method to cancel undesired bands of 3 dB bandwidth of < 910 MHz in microwave-photonic systems is demonstrated. The ultranarrow filter response properties have been realized based on our developed low-propagation loss silicon channel waveguide and tunable ring-resonator designs. Experimentally, they yielded a loss of 0.25 dB/cm and 0.18 dB/round trip, respectively.
Functional–Anatomic Study of Episodic Retrieval II. Selective Averaging of Event-Related fMRI Trials to Test the Retrieval Success Hypothesis

In a companion paper (R. L. Buckner et al., 1998, NeuroImage 7, 151-162) we used fMRI to identify brain areas activated by episodic memory retrieval. Prefrontal areas were shown to differentiate component processes related to retrieval success and retrieval effort in block-designed paradigms. Importantly, a right anterior prefrontal area was most active during task blocks involving greatest retrieval success, consistent with an earlier PET study by M. D. Rugg et al. (1996, Brain 119, 2073-2083). However, manipulation of these variables within the context of blocked trials confounds differences related to varying levels of retrieval success with potential shifts in subjects' strategies due to changes in the probability of target events across blocks. To test more rigorously the hypothesis that certain areas are directly related to retrieval success, we adopted recently developed procedures for event-related fMRI. Fourteen subjects studied words under deep encoding and were then tested in a mixed trial paradigm where old and new words were randomly presented. This recognition testing procedure activated similar areas to the blocked trial paradigm, with all areas showing similar levels of activation across old and new items. Of critical importance, significant activation was detected in right anterior prefrontal cortex for new items when subjects correctly indicated they were new (correct rejections). These findings go against the retrieval success hypothesis as formally proposed and provide an important constraint for interpretation of this region's role in episodic retrieval. Furthermore, anterior prefrontal activation was found to occur late, relative to other brain areas, suggesting that it may be involved in retrieval verification or monitoring processes or perhaps even in anticipation of subsequent trial events (although an alternative possibility, that the late onset is mediated by a late vascular response, cannot be ruled out). These findings and their relation to the results obtained in the companion blocked-trial paradigm are discussed.
Seapolynol Extracted from Ecklonia cava Inhibits Adipocyte Differentiation in Vitro and Decreases Fat Accumulation in Vivo

Seapolynol (SN) is a polyphenol mixture derived from Ecklonia cava. We evaluated the effects of SN on lipid accumulation in adipocytes, zebrafish, and mice. SN effectively inhibited lipid accumulation in three experimental models by suppressing adipogenic factors. Triglyceride synthetic enzymes such as diacylglycerol acyltransferase 1 (DGAT1) and GPAT3 were also downregulated by SN. This SN-induced inhibition of adipogenic factors was shown to be due to the regulatory effect of SN on early adipogenic factors; SN downregulated the expression of Krueppel-like factor 4 (KLF4), KLF5, CCAAT-enhancer-binding protein β (C/EBPβ), C/EBPδ, and Protein C-ets-2 (ETS2), while KLF2, an anti-early adipogenic factor, was upregulated by SN. SN-mediated inhibition in early adipogenesis was closely correlated with the inhibition of mitotic clonal expansion via cell cycle arrest. SN inhibited cell cycle progression by suppressing cell cycle regulators, such as cyclin A, cyclinD, and pRb but increased p27, a cell cycle inhibitor. In a mouse study, SN effectively reduced body weight and plasma lipid increases induced by a high-fat diet; triglycerides, total cholesterol, and low-density lipoprotein (LDL) levels were markedly reduced by SN. Moreover, SN remarkably improved high-fat-diet-induced hepatic lipid accumulation. Furthermore, SN activated AMP-activated protein kinase-α (AMPKα), an energy sensor, to suppress acetyl-coA carboxylase (ACC), inhibiting lipid synthesis. Our study suggests that SN may be an edible agent that can play a positive role in prevention of metabolic disorders.
De novo inference of protein function from coarse‐grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high‐throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse‐grained (CG) molecular dynamics trajectories were used to compute normalized root‐mean‐square‐fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three‐dimensional autocorrelation vectors. Our in‐house custom‐built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics‐signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof‐of‐principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom‐made CG FF, useful to all. Proteins 2014; 82:2443–2454. © 2014 Wiley Periodicals, Inc.
Journal of Graph Algorithms and Applications Hardness Results and an Exact Exponential Algorithm for the Spanning Tree Congestion Problem

Spanning tree congestion is a relatively new graph parameter, which has been studied intensively. This paper studies the complexity of the problem to determine the spanning tree congestion for non-sparse graph classes, while it was investigated for some sparse graph classes before. We prove that the problem is NP-hard even for chain graphs and split graphs. To cope with the hardness of the problem, we present a fast (exponential-time) exact algorithm that runs in O * (2 n) time, where n denotes the number of vertices. Additionally, we present simple combinatorial lem-mas, which yield a constant-factor approximation algorithm for cographs, and a linear-time algorithm for chordal cographs. Extended abstract of this paper appeared in the proceedings of TAMC 2011 [22].
Field-oriented asynchronous pulsewidth modulation for high performance AC machine drives operating at low switching frequency

A novel pulsewidth-modulation technique is reported that is based on the prediction of the trajectory patterns which the stator current vector describes in a field-oriented coordinate system. The method limits only the error of the torque-producing current component while exerting no constraint on the harmonics of the field-producing current. High dynamic performance and minimum switching frequency is achieved with the help of precalculated memory data, permitting implementation in low-cost hardware. <<ETX>>
Kinetics of transient hiatus hernia during transient lower esophageal sphincter relaxations and swallows in healthy subjects

Background Proximal displacement of the gastro‐esophageal junction (GEJ) is present in hiatus hernia but also occurs transiently during transient lower esophageal sphincter relaxations (TLESRs) and swallows. Using a novel magnetic‐based technique we have performed detailed examination of the GEJ movement during TLESRs and swallows in healthy subjects.
Analysis of heavy metals concentration in wastewater along highways in Croatia

In this paper we have analysed concetrations of heavy metals (lead, copper, nickel, zink, mercury, cadmium, and chromium) in wastewater along highways in Croatia. We have used standard statistical methods: analysis of variance, Kruskal-Wallis test and principal analysis. Analysis of variance and Kruskal-Wallis test were used to detect factors that influence the concentration of lead, copper, nickel, and zink in wastewater. We have investigated the influence of the highway section, the side of a highway, and the influence of the season of the year. Principal components were used to identify groups of elements with similar characteristics in wastewater.
Behavioral Neuroscience

Until several years ago, the predominant view in the literature was that the same classes of vertebrate central nervous system (CNS) neurons can generate multiple, distinct kinds of movements , through either a reconfiguration of a single, shared circuit or through an increase in the number of neurons recruited within each identifiable class of neurons (Jankowska et al. For example, it was proposed in pioneering studies in the cat that a single spinal cord central pattern generator (CPG) produces both scratching and walking motor patterns (Berkinblit et al., 1978). In addition, many brainstem neurons were shown to contribute to multiple forms of breathing and oromotor movements early data from the hatchling Xenopus tadpole suggested that the same classes of spinal cord interneurons produce swimming and a
A Spatially Varying Scaling Method for InSAR Tropospheric Corrections Using a High‐Resolution Weather Model

Variation in tropospheric delay is a major limiting factor on the accuracy of interferometric synthetic aperture radar (InSAR) measurements. This is particularly the case when deformation and topography are correlated. To address limitations of previous InSAR tropospheric correction methods, here we present a new approach that combines the use of both external weather model data and the interferometric phase. We assume that vertical refractivity profiles calculated from a high‐resolution weather model data can generally describe the form of the relationship between tropospheric delay and height but that the magnitude can be incorrect. We estimate a magnitude correction by scaling the original delays to best match the interferometric phase. We validated our new method using simulated data and demonstrate that both coseismic and interseismic signals can be separated from strong tropospheric delays. We also applied our algorithm to the central portion of the Altyn Tagh Fault in northern Tibet, where deformation correlates strongly with topographic relief of 6,000 m, and show that the derived velocity field is more internally consistent and agrees better with independent Global Positioning System measurements.