Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-based analysis of tiling-arrays for ChIP-chip

We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data. MAT is developed in open-source Python and is available at http://chip.dfci. harvard.edu/∼wli/MAT. The general framework presented here can be extended to other oligonucleotide microarrays and tiling array platforms.
Planar Optical Waveguides for Application in Optoelectronic Gas Sensors

In the paper, the results of technological investigations on planar optical waveguides based on high band gap oxide semiconductors were presented. Investigations concerned the technologies of depositing very thin layers of: zinc oxide ZnO, titanium dioxide TiO2 and tin dioxide SnO2 on substrates of quartz glass plates. There were investigated both morphological structures of the produced layers and their optical properties. The paper also presents investigations on the technology of input-output light systems in the Bragg grating structures.
A basic formula for online policy gradient algorithms

This note presents a (new) basic formula for sample-path-based estimates for performance gradients for Markov systems (called policy gradients in reinforcement learning literature). With this basic formula, many policy-gradient algorithms, including those that have previously appeared in the literature, can be easily developed. The formula follows naturally from a sensitivity equation in perturbation analysis. New research direction is discussed.
An Approximation Algorithm for the Traveling Salesman Problem with Backhauls

The Traveling Salesman Problem with Backhauls (TSPB) is defined on a graph G = (V, E). The vertex set is partitioned into V = ({v1}, L, B), where v1 is a depot, L is a set of linehaul customers, and B is a set of backhaul customers. A cost matrix satisfying the triangle inequality is defined on the edge set E. The TSPB consists of determining a least-cost Hamiltonian cycle on G such that all vertices of L are visited contiguously after v1, followed by all vertices of B. Following a result by Christofides for the Traveling Salesman Problem, we propose an approximation algorithm with worst-case performance ratio of 3/2 for the TSPB.
Comparing the Social Skills of Students Addicted to Computer Games with Normal Students

Background This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. Methods The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). Findings The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. Conclusion As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills. ).
Interference alignment for achieving both full DoF and full diversity in the broadcast channel with delayed CSIT

Maddah-Ali and Tse have recently shown that delayed transmitter channel state information (CSIT) can still be useful in increasing the degrees-of-freedom (DoF) over the MIMO broadcast channel. This was achieved by constructing a scheme that, in the presence of two transmit antennas, of two single-antenna receivers, and of CSIT that is delayed by one coherence time, manages to provide each user with 2/3 DoF, improving upon the 1/2 DoF corresponding to no CSIT. This same scheme though, as well as all subsequent schemes pertinent schemes, achieve DoF gains by suppressing the inherent diversity of the broadcast parallel channel. The current work proposes a novel broadcast scheme which, over the above described setting of the delayed CSIT broadcast channel, employs a form of interference alignment to achieve both full DoF as well as full diversity.
Neck Rotation and Neck Mimic Docking in the Noncatalytic Kar3-associated Protein Vik1*

Background: Kar3Vik1 is a heterodimeric kinesin with one catalytic subunit (Kar3) and one noncatalytic subunit (Vik1). Results: Vik1 experiences conformational changes in regions analogous to the force-producing elements in catalytic kinesins. Conclusion: A molecular mechanism by which Kar3 could trigger Vik1's release from microtubules was revealed. Significance: These findings will serve as the prototype for understanding the motile mechanism of kinesin-14 motors in general. It is widely accepted that movement of kinesin motor proteins is accomplished by coupling ATP binding, hydrolysis, and product release to conformational changes in the microtubule-binding and force-generating elements of their motor domain. Therefore, understanding how the Saccharomyces cerevisiae proteins Cik1 and Vik1 are able to function as direct participants in movement of Kar3Cik1 and Kar3Vik1 kinesin complexes presents an interesting challenge given that their motor homology domain (MHD) cannot bind ATP. Our crystal structures of the Vik1 ortholog from Candida glabrata may provide insight into this mechanism by showing that its neck and neck mimic-like element can adopt several different conformations reminiscent of those observed in catalytic kinesins. We found that when the neck is α-helical and interacting with the MHD core, the C terminus of CgVik1 docks onto the central β-sheet similarly to the ATP-bound form of Ncd. Alternatively, when neck-core interactions are broken, the C terminus is disordered. Mutations designed to impair neck rotation, or some of the neck-MHD interactions, decreased microtubule gliding velocity and steady state ATPase rate of CgKar3Vik1 complexes significantly. These results strongly suggest that neck rotation and neck mimic docking in Vik1 and Cik1 may be a structural mechanism for communication with Kar3.
Genetic and Non-Genetic Influences during Pregnancy on Infant Global and Site Specific DNA Methylation: Role for Folate Gene Variants and Vitamin B12

Inter-individual variation in patterns of DNA methylation at birth can be explained by the influence of environmental, genetic and stochastic factors. This study investigates the genetic and non-genetic determinants of variation in DNA methylation in human infants. Given its central role in provision of methyl groups for DNA methylation, this study focuses on aspects of folate metabolism. Global (LUMA) and gene specific (IGF2, ZNT5, IGFBP3) DNA methylation were quantified in 430 infants by Pyrosequencing®. Seven polymorphisms in 6 genes (MTHFR, MTRR, FOLH1, CβS, RFC1, SHMT) involved in folate absorption and metabolism were analysed in DNA from both infants and mothers. Red blood cell folate and serum vitamin B12 concentrations were measured as indices of vitamin status. Relationships between DNA methylation patterns and several covariates viz. sex, gestation length, maternal and infant red cell folate, maternal and infant serum vitamin B12, maternal age, smoking and genotype were tested. Length of gestation correlated positively with IGF2 methylation (rho = 0.11, p = 0.032) and inversely with ZNT5 methylation (rho = −0.13, p = 0.017). Methylation of the IGFBP3 locus correlated inversely with infant vitamin B12 concentration (rho = −0.16, p = 0.007), whilst global DNA methylation correlated inversely with maternal vitamin B12 concentrations (rho = 0.18, p = 0.044). Analysis of common genetic variants in folate pathway genes highlighted several associations including infant MTRR 66G>A genotype with DNA methylation (χ2 = 8.82, p = 0.003) and maternal MTHFR 677C>T genotype with IGF2 methylation (χ2 = 2.77, p = 0.006). These data support the hypothesis that both environmental and genetic factors involved in one-carbon metabolism influence DNA methylation in infants. Specifically, the findings highlight the importance of vitamin B12 status, infant MTRR genotype and maternal MTHFR genotype, all of which may influence the supply of methyl groups for DNA methylation. In addition, gestational length appears to be an important determinant of infant DNA methylation patterns.
Defining the transcriptome of nine vertebrate genomes using RNAseq

To the biomedical research community at large, understanding the content of the genome, particularly the genes, is critically important. The coding and non-coding transcriptomes of both human and mouse have been exquisitely refined through the use of massive amounts of species-specific cDNA sequence data, manual curation and recently mRNA sequencing. However, all other vertebrate genome annotations are largely based on homology to human and mouse genes, due to the lack of cDNA sequence available from other vertebrate species. With the advent of the lower-cost RNAseq technology, the time is right to invest in RNA sequencing from other vertebrate species to improve genome annotations and understand both the coding and non-coding transcriptomes. The Broad Institute currently has laboratory and computational methods in use and under further development to generate high quality RNAseq data for genome annotation. We propose to use <0.02% of NHGRI's annual sequencing capacity at the Broad to improve nine important genome stickleback). At this time, a small investment in RNA sequencing would provide a huge improvement in vertebrate genome annotation, enabling better research across a multitude of biomedical disciplines.
Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test

The study of mRNA methylation is an emerging research field greatly fueled by recent advancement in high throughput sequencing technology. We propose here a binomial likelihood ratio test ("bltest") aiming at detecting differentially methylated mRNA with MeRIP-Seq data, "bltest" models the read counts of each RNA methylation site in IP and input samples with a binomial distribution. If the successful rates of binomial distributions under two experimental conditions are significantly different, the corresponding RNA is identified to be differentially methylated. The proposed "bltest" does not require an independent procedure to unify different library sizes of the MeRIP-Seq samples, thus retaining maximal information from the data. Our simulation results clearly showed that "bltest" consistently outperforms classic "Fisher's exact test" at all settings. The proposed method was also applied to the real data, and the findings are consistent with previous studies.
Supervised Learning of a Probabilistic Lexicon of Verb Semantic Classes

The work presented in this paper explores a supervised method for learning a probabilistic model of a lexicon of VerbNet classes. We intend for the probabilistic model to provide a probability distribution of verb-class associations, over known and unknown verbs, including polysemous words. In our approach, training instances are obtained from an existing lexicon and/or from an annotated corpus, while the features, which represent syntactic frames, semantic similarity, and selectional preferences, are extracted from unannotated corpora. Our model is evaluated in type-level verb classification tasks: we measure the prediction accuracy of VerbNet classes for unknown verbs, and also measure the dissimilarity between the learned and observed probability distributions. We empirically compare several settings for model learning, while we vary the use of features, source corpora for feature extraction, and disam-biguated corpora. In the task of verb classification into all VerbNet classes, our best model achieved a 10.69% error reduction in the classification accuracy, over the previously proposed model.
Transient Analysis of VLSI Tree Interconnects based on Matrix Pade Type Approximation

This paper presents a novel, simple and accurate delay estimation model for single interconnect and tree interconnects, which is based on new matrix Pade-type approximant (MPTA). The proposed model provides a simpler rational function approximation for estimating delay and overshoot in lossy VLSI interconnects. Computational complexity is reduced by considering rational function denominator as scalar polynomial and avoiding matrix inversion. With the reduced order lossy interconnect transfer function, finite ramp responses are obtained and line delay and signal overshoot are estimated. The estimated delay and overshoot values are compared with the existing Pade model and HSPICE W-element model. Single interconnect 50% delay results are in good agreement with those of HSPICE within 0.5% error while the overshoot error is within 1% for a 1 mm long interconnects. For global lines of length more than 1 mm in SOC (system on chip) applications, the proposed model is found to be nearly two times more accurate than existing Pade model. Tree interconnects 50% delay values are also well agreeing with HSPICE and better than existing U-transform model. Furthermore the proposed model is computationally more efficient than HSPICE, Pade model and U-transform model. Key-Words: Delay, matrix rational model, ramp input, RLC interconnects, transient analysis, transfer function, Distributed tree interconnect, new MPTA approximant, U-transform.
Ageing rate of paper insulation used in power transformers Part 1: Oil/paper system with low oxygen concentration

A substantial quantity of testing has been performed on the degradation of paper insulation over the decades. The aim being to better educate the electrical industry on how to best operate expensive assets, such as transformers. The longevity of paper insulation is frequently tested using accelerated ageing experiments, where the effects of temperature and the chemical environment on paper lifespan can be studied. Such research has resulted in paper life expectancy curves being published by the IEEE and the IEC. The investigations tend to use sealed vessels. However, the disadvantage of using this method is that the water content of the paper changes during the ageing process which then changes the ageing rate. In these ageing experiments the water and oxygen content was controlled using a special test rig to compare the ageing rate to previous work and to determine the ageing effect of paper by combining temperature, water content of paper and oxygen content of the oil. We found that the rate of paper ageing can be more accurately determined by controlling the water and oxygen during the experiment which then produced noticeable changes in predicting life expectancy.
Effect of pregraduate preceptorship experience on development of adaptive competencies of baccalaureate nursing students.

Kolb's (1984) theory of experiential learning was used as a framework to study 50 baccalaureate nursing students' perceptions of the contributions of a senior preceptorship experience to the development of adaptive competencies. Nursing learning environments were thought to contribute most to divergent and convergent competencies, reflecting the importance of both people-oriented and scientific skills in nursing. The preceptorship had a significant impact on most learning competencies. Significant increases occurred in competencies considered not important for nursing by students prior to the experience, e.g., assimilative competencies such as testing theories and ideas, and accommodative competencies such as leading and influencing others. These results support the notion of further research of nursing learning environments from the experiential learning perspective.
A speedup SVM decision method for online EEG processing in motor imagery BCI

In BCI research community, support vector machine (SVM) is an effective method for motor imagery (MI)-based electroencephalographic (EEG) classification. However, the computation of decision function during SVM classification stage for a new EEG trial is time-consuming due to the large number of support vectors (SV). This paper proposes a new method to reduce the number of support vectors so that speed up SVM decision. The method first obtains all the support vectors by classical SVM. Then, γ-index measuring the average distance between each support vector and its nearest neighbors is evaluated. Thirdly, the support vector with smallest γ-index is selected. And then iteratively re-weight γ-index and select only a few support vectors to represent all the support vectors. Our experiments show only 10%-30% of the support vectors can be used to speed up the decision while loss in generalization performance remains acceptable.
Low-Cost Air Quality System for Urban Area Monitoring

With the worldwide urban population following a continuous growth, more individuals expose themselves to a less healthy environment by inhaling polluted urban air. The current pollution measurement techniques make use of automated monitoring stations that are usually installed in certain key points around the city but can only provide coarse-grained air quality reports as well as not being able to indicate the sources of the air polluting agents. As traffic related air pollution cannot be traced to a single location, there is the need for a new approach which has the capacity of measuring fine-grained air quality that can reflect any detailed variations that may be caused by traffic jams. In this paper, we intend to offer a solution by implementing a low-cost air quality system using mobile sensing for monitoring the variance of gaseous pollutants in metropolitan areas.
Labeling recursive workflow executions on-the-fly

This paper presents a compact labeling scheme for answering reachability queries over workflow executions. In contrast to previous work, our scheme allows nodes (processes and data) in the execution graph to be labeled on-the-fly, i.e., in a dynamic fashion. In this way, reachability queries can be answered as soon as the relevant data is produced. We first show that, in general, for workflows that contain recursion, dynamic labeling of executions requires long (linear-size) labels. Fortunately, most real-life scientific workflows are linear recursive, and for this natural class we show that dynamic, yet compact (logarithmic-size) labeling is possible. Moreover, our scheme labels the executions in linear time, and answers any reachability query in constant time. We also show that linear recursive workflows are, in some sense, the largest class of workflows that allow compact, dynamic labeling schemes. Interestingly, the empirical evaluation, performed over both real and synthetic workflows, shows that our proposed dynamic scheme outperforms the state-of-the-art static scheme for large executions, and creates labels that are shorter by a factor of almost 3.
Efficient indexing structures for mining frequent patterns

In this paper, we propose a variant of the signature file, called bit-sliced bloom-filtered signature file (BBS), as the basis for implementing filter-and-refine strategies for mining frequent patterns. In the filtering step, the candidate patterns are obtained by scanning BBS instead of the database. The resultant candidate set contains a superset of the frequent patterns. In the refinement phase, each algorithm refines the candidate set to prune away the false drops. Based on this indexing structure, we study two filtering (single and dual filter) and two refinement (sequential scan and probe) mechanisms, thus giving rise to four different strategies. We conducted an extensive performance study to study the effectiveness of BBS, and compared the four proposed processing schemes with the traditional a priori algorithm and the recently proposed FP-tree scheme. Our results show that BBS, as a whole, outperforms the a priori strategy. Moreover, one of the schemes that is based on dual filter and probe refinement performs the best in all cases.
Nectar and Flower Traits of Different Onion Male Sterile Lines Related to Pollination Efficiency and Seed Yield of F1 Hybrids

ABSTRACT Honey bees are the main pollinators of onion crops for seed production, but owing to low attractiveness of flowers, pollination is often inadequate. Pollination problems result in low seed yields. This problem is accentuated when male sterile lines (MSL) are used to produce hybrid onion seeds. In this study, the effect of floral attributes and nectar composition on the preference of honey bees of four MSLs and one onion open pollinated cultivar were assessed. The chemical composition of nectar was described through the analysis of sugars, trace elements, volatile organic compounds, and phenol compounds. The samples studied showed qualitative and quantitative differences in the analyzed traits of flowers and nectar among the different lines. Furthermore, field observations showed a great difference on the number of bee visits and seed yield among the onion lines analyzed. For the first time, this study demonstrates that there are marked differences in the chemical composition of nectar and floral morphology between open pollinated and MSLs and also within MSLs. In addition, these differences were correlated with the number of visits and seed yield. Therefore, it would be possible to select indirectly the most promising productive MSL using simple determinations of chemical compounds or floral morphological characters.
Effectiveness of Group Cognitive Behavior Therapies for Panic Disorder: Systematic Review and Meta-analysis

Although cognitive behavior therapies are vastly studied treatments for panic disorder, reviews on the subject usually don’t discriminate between individual and group settings. This article aims to evaluate, through meta-analytical techniques, the effectiveness of group cognitive behavior therapy for panic disorder. A literature search on LILACS, PsycINFO, ISI Web of Knowledge and Pubmed was conducted. Intra-group Hedges (g) effect size calculations were made for symptoms of panic and anxiety, agoraphobia, and depression. A random effects model was used to estimate the summary effect sizes and the publication bias was calculated. The search identified 22 articles from 14 different studies. Summary effect sizes were large for symptoms of panic and anxiety (g=1,39), moderate for symptoms of depression (g=0,79) and large for agoraphobic symptoms (g=0,92). These results suggest that these therapies in group are effective for panic disorder and constitute an interesting alternative of treatment.