Miracle-dz/UniFAR-FTUs huggingface dataset:
Supervised Learning Classification Models for Prediction of Plant Virus Encoded RNA Silencing Suppressors

Viral encoded RNA silencing suppressor proteins interfere with the host RNA silencing machinery, facilitating viral infection by evading host immunity. In plant hosts, the viral proteins have several basic science implications and biotechnology applications. However in silico identification of these proteins is limited by their high sequence diversity. In this study we developed supervised learning based classification models for plant viral RNA silencing suppressor proteins in plant viruses. We developed four classifiers based on supervised learning algorithms: J48, Random Forest, LibSVM and Naïve Bayes algorithms, with enriched model learning by correlation based feature selection. Structural and physicochemical features calculated for experimentally verified primary protein sequences were used to train the classifiers. The training features include amino acid composition; auto correlation coefficients; composition, transition, and distribution of various physicochemical properties; and pseudo amino acid composition. Performance analysis of predictive models based on 10 fold cross-validation and independent data testing revealed that the Random Forest based model was the best and achieved 86.11% overall accuracy and 86.22% balanced accuracy with a remarkably high area under the Receivers Operating Characteristic curve of 0.95 to predict viral RNA silencing suppressor proteins. The prediction models for plant viral RNA silencing suppressors can potentially aid identification of novel viral RNA silencing suppressors, which will provide valuable insights into the mechanism of RNA silencing and could be further explored as potential targets for designing novel antiviral therapeutics. Also, the key subset of identified optimal features may help in determining compositional patterns in the viral proteins which are important determinants for RNA silencing suppressor activities. The best prediction model developed in the study is available as a freely accessible web server pVsupPred at http://bioinfo.icgeb. res.in/pvsup/.
Characterization of electrochemically active bacteria utilizing a high‐throughput voltage‐based screening assay

Metal reduction assays are traditionally used to select and characterize electrochemically active bacteria (EAB) for use in microbial fuel cells (MFCs). However, correlating the ability of a microbe to generate current from an MFC to the reduction of metal oxides has not been definitively established in the literature. As these metal reduction assays may not be generally reliable, here we describe a four‐ to nine‐well prototype high throughput voltage‐based screening assay (VBSA) designed using MFC engineering principles and a universal cathode. Bacterial growth curves for Shewanella oneidensis strains DSP10 and MR‐1 were generated directly from changes in open circuit voltage and current with five percent deviation calculated between each well. These growth curves exhibited a strong correlation with literature doubling times for Shewanella indicating that the VBSA can be used to monitor distinct fundamental properties of EAB life cycles. In addition, eight different organic electron donors (acetate, lactate, citrate, fructose, glucose, sucrose, soluble starch, and agar) were tested with S. oneidensis MR‐1 in anode chambers exposed to air. Under oxygen exposure, we found that current was generated in direct response to additions of acetate, lactate, and glucose. Biotechnol. Bioeng. 2009;102: 436–444. © 2008 Wiley Periodicals, Inc.
IDIOPATHIC EPIRETINAL MEMBRANE

Background: Idiopathic epiretinal membrane (iERM) is a fibrocellular membrane that proliferates on the inner surface of the retina at the macular area. Membrane contraction is an important sight-threatening event and is due to fibrotic remodeling. Methods: Analysis of the current literature regarding the epidemiology, clinical features, and pathogenesis of iERM and fibrotic tissue contraction. Results: Epidemiologic studies report a relationship between iERM prevalence, increasing age, and posterior vitreous detachment. Clinically, iERM progresses through different stages characterized by an increased thickness and wrinkling of the membrane. Pathophysiologically, iERM formation is a fibrotic process in which myofibroblast formation and the deposition of newly formed collagens play key roles. Anomalous posterior vitreous detachment may be a key event initiating the formation of iERM. The age-related accumulation of advanced glycation end products may contribute to anomalous posterior vitreous detachment formation and may also influence the mechanical properties of the iERM. Conclusion: Remodeling of the extracellular matrix at the vitreoretinal interface by aging and fibrotic changes, plays a significant role in the pathogenesis of iERM. A better understanding of molecular mechanisms underlying this process may eventually lead to the development of effective and nonsurgical approaches to treat and prevent vitreoretinal fibrotic diseases.
Full-Time Classes for Gifted Youth

W A T he best educational experi­ ence for highly gifted youth is enrollment in a full-time program in which all or nearly all school time is spent with gifted peers, highly competent teachers who have been trained to work with the gifted, and curriculum designed to be highly concep­ tual and accelerated. While it is clear that youth differ from an early age in their specific areas of strength or talent, it is nevertheless the case that many highly gifted youth are strong in several aca­ demic domains such as language skills, mathematics, and science and excep­ tional in one of the domains. Thus, they can profit from enriched and accelerated instruction in all subject mat ter . However, the special school program must also recognize the domain(s) of highest talent and provide even higher levels of enrichment and acceleration in those areas.
Light ions response of silicon carbide detectors 1

Silicon carbide (SiC) Schottky diodes 21 μm thick with small surfaces and high N-dopant concentration have been used to detect alpha particles and low energy light ions. In particular C and O beams at incident energies between 5 and 18 MeV were used. The diode active-region depletion-thickness, the linearity of the response, energy resolution and signal rise-time were measured for different values of the applied reverse bias. Moreover the radiation damage on SiC diodes irradiated with 53 MeV O beam has been explored. The data show that SiC material is radiation harder than silicon but at least one order of magnitude less hard than epitaxial silicon diodes. An inversion in the signal was found at a fluence of 10 ions/cm.
A sensory grammar for inferring behaviors in sensor networks

The ability of a sensor network to parse out observable activities into a set of distinguishable actions is a powerful feature that can potentially enable many applications of sensor networks to everyday life situations. In this paper we introduce a framework that uses a hierarchy of probabilistic context free grammars (PCFGs) to perform such parsing. The power of the framework comes from the hierarchical organization of grammars that allows the use of simple local sensor measurements for reasoning about more macroscopic behaviors. Our presentation describes how to use a set of phonemes to construct grammars and how to achieve distributed operation using a messaging model. The proposed framework is flexible. It can be mapped to a network hierarchy or can be applied sequentially and across the network to infer behaviors as they unfold in space and time. We demonstrate this functionality by inferring simple motion patterns using a sequence of simple direction vectors obtained from our camera sensor network testbed
Optimal deterministic approximate parallel prefix sums and their applications

We show that extremely accurate approximation to the prefix sums of a sequence of n integers can be computed deterministically in O(log log n) time using O(n/log log n) processors in the COMMON CRCW PRAM model. This complements randomized approximation methods obtained recently by Goodrich, Matias and Vishkin, (1993) and improves previous deterministic results obtained by Hagerup and Raman. Furthermore, our results completely match a lower bound obtained recently by Chaudhuri. Our results have many applications. Using them we improve upon the best known time bounds for deterministic approximate selection and for deterministic padded sorting. <<ETX>>
Brain-Derived Neurotrophic Factor Attracts Geniculate Ganglion Neurites during Embryonic Targeting

Geniculate axons are initially guided to discrete epithelial placodes in the lingual and palatal epithelium that subsequently differentiate into taste buds. In vivo approaches show that brain-derived neurotrophic factor (BDNF) mRNA is concentrated in these placodes, that BDNF is necessary for targeting taste afferents to these placodes, and that BDNF misexpression disrupts guidance. We used an in vitro approach to determine whether BDNF may act directly on geniculate axons as a trophic factor and as an attractant, and whether there is a critical period for responsiveness to BDNF. We show that BDNF promotes neurite outgrowth from geniculate ganglion explants dissected from embryonic day (E) 15, E18, infant, and adult rats cultured in collagen gels, and that there is a concentration optimum for neurite extension. Gradients of BDNF derived from slow-release beads caused the greatest bias in neurite outgrowth at E15, when axons approach the immature gustatory papillae. Further, neurites advanced faster toward the BDNF bead than away from it, even if the average amount of neurotrophic factor encountered was the same. We also found that neurites that contact BDNF beads did not advance beyond them. At E18, when axons would be penetrating pregustatory epithelium in vivo, BDNF continued to exert a tropic effect on geniculate neurites. However, at postnatal and adult stages, the influence of BDNF was predominantly trophic. Our data support a role for BDNF acting as an attractant for geniculate axons during a critical period that encompasses initial targeting but not at later stages.
Evaluation of systolic murmurs using transthoracic echocardiography by anaesthetic trainees

Focused transthoracic echocardiography by anaesthetists in the peri‐operative period has recently been described; the data suggest that the specific skills required can be obtained by non cardiology physicians with limited training. Aortic stenosis is known to increase significantly the peri‐operative risk in non‐cardiac surgery. This study aimed to assess the ability of echocardiography naive trainee anaesthetists to recognise and assess the severity of aortic stenosis after a set amount of training. Five trainees underwent 2 h of didactic and hands‐on teaching in evaluation of the aortic valve, after which they scanned 20 patients each. Their results were compared with those obtained by an experienced cardiac anaesthetist with echocardiography training and qualifications. There was 100% concordance between trainees and the consultant for assessment of clinically significant aortic stenosis, with no cases of misdiagnosis. There was also 90–100% agreement (kappa statistic 0.8–1) between the consultant and each trainee’s assessment of clinically significant aortic stenosis based on a peak aortic velocity > 3 m.sec−1. Anaesthesia trainees can be successfully and rapidly trained to recognise and estimate the severity of aortic stenosis.
Biphasic influence of Miz1 on neural crest development by regulating cell survival and apical adhesion complex formation in the developing neural tube

Miz1 regulates cell survival and integrity of the apical adhesive complexes in the entire neuroepithelium, which specifically affects neural crest development. Knockdown of Miz1 decreases the size of the neural crest domain at the neural plate border and the dorsal neural tube, ultimately leading to a reduced number of migrating neural crest cells.
Adaptive backstepping control of gear transmission systems with elastic deadzone

This paper deals with the tracking control problem of uncertain transmission systems in the presence of elastic deadzone. Due to the derivative term in the elastic deadzone model, it is not straightforward to apply the backstepping control for the elastic system which is not in strict feedback form. To overcome this limitation, the system is first transformed into two cascaded subsystems and an adaptive backstepping controller is proposed based on the transformed cascaded system. The stability analysis is carried out within the framework of Lyapunov functions and shows that all the states of the closed-loop system are bounded and the tracking error is uniformly ultimately bounded. Finally, simulations are presented to demonstrate the performance of the controlled system.
Automatic generation and publication of Web services for the access and integration of distributed data sources

In this paper, we describe the design and implementation of a multiplatform integrated graphical tool for the automatic creation, management, and publication of Web services for the access and publication (in the Web) of query operations (SQL sentences, stored procedures and views) executed over local or distributed relational data sources stored in heterogeneous platforms. The result sets generated by the execution of the operations associated to each Web service are codified in XML. The tool described: i) simplify the query process to distributed DBMS data sources; ii) simplify the information interchange between heterogeneous and homogeneous systems; iii) automates the creation of Web services through a graphical interface without have knowledge of a programming language. The tool was implemented in Java using free software APIs and has been proved with several DBMS. We show the results of some tests realized to our tool and the comparisons with similar approaches. This work is a first step towards a technological solution of the data integration problem.
Automatic generation of sets of keywords for theme characterization and detection

The paper describes a system that automatically detects themes in a textual corpus and characterizes them by sets of keywords, that is, words whose co-occurrence in a paragraph indicates that this paragraph tackles a certain theme. (Pichon and Sebillot, 2000) presents a first version of it where those sets are obtained with the help of the CHAVL hierarchical clustering algorithm, grouping words that have a similar repartition over paragraphs. The weaknesses of the system (quality of the classes highly dependent on manual parameter settings, relevant classes in the classification tree hardly pointed out automatically) are largely reduced here by using a combined classification of the paragraphs based on their lexical cohesion. This new classification first allows to densify the processed data, thus helping CHAVL produce more satisfying classes; it also gives a means to establish an original statistical quality measure that can be exploited both to point out the relevant classes in the tree and to reorganize some of the mergings proposed by CHAVL.
How Medicine Informs Informatics: Information is Asymmetry, Not Entropy§

A concept of information as asymmetry in multiple dimensions is based on the demonstration that causal ac- tion, not hypothetical chance events, is a parsimonious explanation of novelty. The study of heartbeat variation revealed creative features in causal processes, namely greater novelty than random variation, decrease in entropy, temporal change in pattern, and progressive increase in variance. These properties characterize a new type of process, Bios. Bios has been demonstrated at all levels of organization from Number Theory and Quantum Physics to Population Dynamics and Eco- nomics. Mathematical experiments show that Bios is generated causally by generic processes present at multiple levels of organization: (1) unidirectional action, (2) bipolar opposition (e.g. electromagnetic energy, sex, mutual feedback) and (3) conservation. These studies underlie the formulation of information as 1, 2, 3, …, N dimensional order (i.e. asymmetry and transitivity). Thus information channels flux into flow, cycle, structure, and more complex organization in nature. Human reasoning and computer logic may be guided by this logic of nature.
Constraintless Approach of Power and Cost Aware Routing in Mobile Adhoc Networks

Wireless mobile ad-hoc networks require certain mechanisms of tracking and managing power consumption as they are using non-renewable energy sources i.e. the battery sources. A number of cost aware and power aware algorithms have been proposed so far to cope up with the problem of proper utilization of battery lifetime. This paper deals with creating a constraint less power and cost aware routing algorithm for MANETs. The thresholds and cutoffs involved in the previous algorithms are not kept into the consideration . This paper employs the cost aware mechanism when multiple numbers of nodes are capable of receiving and transmitting the packets. This is done to obtain an optimal path for communication. The model proposed by the paper deals with determining the sufficiency of power available in each node to receive and transmit the packet and comparing the available nodes‟ distances to reduce the cost of the total transmission. The power-cost algorithm tends to identify the nodes with certain energy, such that they can receive and transmit a packet of certain size which would be acknowledged by the listening packet, which creates the flexibility of optimal usability of the power of available nodes.
Performance of a Radio Transmission System with Spectrum Pooling and Unequal User Priorities

We examine a radio transmission system based on spectrum pooling, whereby the spectrum owned by the primary user is divided into subchannels, and some users are allowed privileged access to the most reliable unused subchannels. By assuming that a powerful error-control code is used, performance is evaluated by computing the information outage probability. It is shown that choosing the best channels improves considerably the performance of the privileged users, while the remaining (unprivileged) users are penalized only marginally.
Tracking earthworm communities from soil DNA

Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time consuming and often difficult to apply. We showed that combining DNA metabarcoding and next‐generation sequencing facilitates the identification of earthworm species from soil samples. The first step of our experiments was to create a reference database of mitochondrial DNA (mtDNA) 16S gene for 14 earthworm species found in the French Alps. Using this database, we designed two new primer pairs targeting very short and informative DNA sequences (about 30 and 70 bp) that allow unambiguous species identification. Finally, we analysed extracellular DNA taken from soil samples in two localities (two plots per locality and eight samples per plot). The two short metabarcode regions led to the identification of a total of eight earthworm species. The earthworm communities identified by the DNA‐based approach appeared to be well differentiated between the two localities and are consistent with results derived from inventories collected using the handsorting method. The possibility of assessing earthworm communities from hundreds or even thousands of localities through the use of extracellular soil DNA will undoubtedly stimulate further ecological research on these organisms. Using the same DNA extracts, our study also illustrates the potential of environmental DNA as a tool to assess the diversity of other soil‐dwelling animal taxa.
How Does Feedback Impact Training in Audio-Visual Speech Perception?

Integration of visual and auditory speech cues is a process used by listeners in compromised listening situations, as well as in normal environments, as exemplified by the McGurk effect (McGurk and McDonald, 1976). Audio-visual integration of speech appears to be a skill independent of the ability to process auditory or visual speech cues alone. Grant and Seitz (1998) argued for independence of this process based on their findings that integration abilities could not be predicted from auditory-only or visual-only performance. Gariety (2009) and James (2009) further supported this argument by training listeners in the auditory-only modality with degraded speech syllables, then testing those listeners in the auditory-only, visual-only, and audio-visual conditions. Their results showed an increase in auditory-only performance, but no improvement in integration. Recently, DiStefano (2010) conducted a training study in which listeners were trained in the audio-visual modality with degraded speech syllables. Results showed that the performance increased only for the audio-visual conditions, and did not increase in the auditory-only or visual-only conditions. Interestingly, performance improved only for stimulus pairs that were “congruent” (i.e. the auditory and visual inputs were the same syllable) and did not increase for “discrepant” stimuli (i.e. the auditory and visual inputs were different syllables). effective responses. The present study investigated whether McGurk-type integration can be trained. Five normal hearing listeners each received 10 hours of training similar to that in DiStefano’s study, but feedback provided during training was designed to specifically elicit McGurk-type integration responses. It was hypothesized that McGurk-type fusion and combination responses would increase after training sessions were completed, as well as all integration performance. It was also expected that auditory-only and visual-only performance would not show improvement from integration training. The results from this study may provide further insight into the process of audio-visual speech integration and improve methods used in aural rehabilitation.
A new method of designing high efficiency and wideband power amplifier

This paper presents a new method to design high efficiency and wideband power amplifier (PA). Based on the output parasitics network of MOSFET, this method shifts the optimum load impedances from the intrinsic plane to the package plane, which are obtained by the continuous PA theory and then rectified elaborately by multi-harmonic bilateral-pull technology, in order to make the second harmonic load impedances in high efficient region as well as the fundamental load impedances with high power added efficiency (PAE) and output power. A simulated example based on the GaN HEMT device CGH40010F is designed to verify the proposed method.
An Approximate Dual Subgradient Algorithm for Multi-Agent Non-Convex Optimization

We consider a multi-agent optimization problem where agents subject to local, intermittent interactions aim to minimize a sum of local objective functions subject to a global inequality constraint and a global state constraint set. In contrast to previous work, we do not require that the objective, constraint functions, and state constraint sets are convex. In order to deal with time-varying network topologies satisfying a standard connectivity assumption, we resort to consensus algorithm techniques and the Lagrangian duality method. We slightly relax the requirement of exact consensus, and propose a distributed approximate dual subgradient algorithm to enable agents to asymptotically converge to a pair of primal-dual solutions to an approximate problem. To guarantee convergence, we assume that the Slater's condition is satisfied and the optimal solution set of the dual limit is singleton. We implement our algorithm over a source localization problem and compare the performance with existing algorithms.