Miracle-dz/UniFAR-FTUs huggingface dataset:
A Single-Copy IS5-Like Transposon in the Genome of a Bdelloid Rotifer

Abstract In the course of sequencing telomeric chromosomal regions of the bdelloid rotifer Adineta vaga, we encountered an unusual DNA transposon. Unlike other bdelloid and, more generally, eukaryotic transposable elements (TEs), it exhibits similarity to prokaryotic insertion sequences (ISs). Phylogenetic analysis indicates that this transposon, named IS5_Av, is related to the ISL2 group of the IS5 family of bacterial IS elements. Despite the apparent intactness of the single open reading frame coding for a DDE transposase and the perfect identity of its 213-bp terminal inverted repeats (TIRs), the element is present in only one copy per diploid genome. It does not exhibit any detectable levels of transcription, so that its transposase gene appears to be silent in the bdelloid host. Although horizontal transfers of TEs between kingdoms are not known to happen in nature, it appears likely that IS5_Av underwent integration into the A. vaga genome relatively recently, but was not successful in adapting to the new host and failed to increase in copy number. Alternatively, it might be the only known member of a novel eukaryotic DNA TE superfamily which is so rare that its other members, if any, have not yet been identified in eukaryotic genomes sequenced to date.
A Simplified Finite-State Predictive Direct Torque Control for Induction Motor Drive

Finite-state predictive torque control (FS-PTC) is computationally expensive, since it uses all voltage vectors (VVs) available from a power converter for prediction and actuation. The computational burden is rapidly increased with the number of VVs and objectives to be controlled. Moreover, designing a cost function with more than two control objectives is a complex task. This paper proposes a simplified algorithm based on a new direct torque control (DTC) switching table to reduce the number of VVs to be predicted and objectives to be controlled. The new switching table also assists to reduce average switching frequency and its variation range. As a result, the cost function is simplified by not requiring to include the frequency term. Experimental results show that the average execution time and the average switching frequency for the proposed algorithm are greatly reduced without affecting the torque and flux performances achieved in the conventional FS-PTC.
Near-infrared quantum dot light emitting diodes employing electron transport nanocrystals in a layered architecture

PbSe quantum dot light emitting diodes (QD-LEDs) of a multi-layer architecture are reported in the present work to exhibit high external quantum efficiencies. In these devices, a ligand replacement technique was employed to activate PbSe QDs, and ZnO nanoparticles were used for the electron transport layer. The emission wavelength of this solution processed device is QD size tunable over a broad spectral range, and an LED efficiency of 0.73% was measured at 1412 nm. Higher efficiencies at longer wavelengths are also inferred from spectral characterization.
LineMe: A platform for constructing evolving social networks

Although online social network platforms such as Facebook and WeChat have collected huge amount of online ties, many of the ties do not correspond to real-world (offline) friendships and the amount of online communication between a pair of people does not necessarily quantify the strength of the tie in real-world. Traditionally, real-world strong and weak ties were collected via questionnaires which were not scalable. Can we collect massive offline social ties via online platforms? In this work, we design LineMe, an online website and toolkit which allows users to map their offline friend ties within a group. LineMe is scalable and flexible to handle large-scale and controllable experiments on social networks. We perform an empirical experiment to collect evolving network data in a class of graduates for 4 weeks. LineMe is open to everyone and is now available at http://lime.seeleit. com.
Using Minimal Recursion Semantics for Entailment Recognition

This paper describes work on using Minimal Recursion Semantics (MRS) representations for the task of recognising textual entailment. I use entailment data from a SemEval-2010 shared task to develop and evaluate an entailment recognition heuristic. I compare my results to the shared task winner, and discuss differences in approaches. Finally, I run my system with multiple MRS representations per sentence, and show that this improves the recognition results for positive entailment sentence pairs.
Detecting stable scales in images via non-smooth K-functional

In image decompositions, one is interested in decomposing f into u+v where u and v have different features. In a variational approach, such a decomposition is achieved by solving the following variational problem inf (u,v)∈X1×X2 {tF1(u) + F2(v) : f = u+ v} , where F1 and F2 are positive functionals defined on some function spaces X1 and X2 respectively. Often the scale parameter t is fixed a prior. In this paper, we address the problem of selecting the scale parameter t in a multiscale fashion, and introduce the notion of interpolating scales that are stable with respect to the functional or energy being minimized. The motivation is coming from Peetre’s K-functional in interpolation theory.
Individual SNP Allele Reconstruction from Informative Markers Selected by a Non-Linear Gauss-Type Algorithm

Objectives: In view of the linkage disequilibrium structure of the genome, the selection of maximally informative SNP markers is a fundamental issue in the design of association studies. Currently used selection methods rely on pairwise marker correlation or informativity measures for subsets of markers. Nevertheless, the selected markers do not provide a completely satisfactory description of the individual remaining markers. The number of tag markers can be further reduced by using haplotypic information, but then the results of association analysis are difficult to interpret. Methods and Results: We propose a non-linear Gauss-type algorithm selecting a subset of markers which is optimal with respect to the informativity measures and allows an explicit reconstruction of all other known markers, thus permitting direct inference of allelic association. The selection is based on the haplotype distribution in the population, but can be adapted to work with unphased genotypes directly. Conclusions: The proposed algorithm provides a rational methodology of informative marker selection, allowing for control and optimisation of information content and full marker reconstruction. Moreover, the reconstruction step can also be applied to tag markers selected using a different method at the stage of study design, identifying those markers which cannot be uniquely recovered from the chosen tags.
Towards gait-pattern adaptation algorithms for exoskeletons based on the ZMP criterion

This paper presents a gait-pattern adaptation algorithm for exoskeletons based on the Zero Moment Point criterion. The proposed exoskeleton is developed for lower limbs and based on a commercially available orthosis. The step length and duration are considered as the adaptation parameters, they are computed through minimization based on direct dynamics and considering the orthosis-patient interaction forces. Also, a robust controller based on the ℋ∞ method is designed to attenuate the effects of external disturbances and parametric uncertainties in the trajectory tracking errors. The dynamic model of the actual exoskeleton, with interaction forces included, is used to generate simulation results.
Potassium current activated by depolarization of dissociated neurons from adult guinea pig hippocampus

Currents were generated by depolarizing pulses in voltage-clamped, dissociated neurons from the CA1 region of adult guinea pig hippocampus in solutions containing 1 microm tetrodotoxin. When the extracellular potassium concentration was 100 mM, the currents reversed at -8.1 +/- 1.6 mV (n = 5), close to the calculated potassium equilibrium potential of -7 mV. The currents were depressed by 30 mM tetraethylammonium in the extracellular solution but were unaffected by 4-aminopyridine at concentrations of 0.5 or 1 mM. It was concluded that the currents were depolarization-activated potassium currents. Instantaneous current- voltage curves were nonlinear but could be fitted by a Goldman-Hodgkin- Katz equation with PNa/PK = 0.04. Conductance-voltage curves could be described by a Boltzmann-type equation: the average maximum conductance was 65.2 +/- 15.7 nS (n = 9) and the potential at which gK was half- maximal was -4.8 +/- 3.9 mV (mean +/- 1 SEM, n = 10). The relationship between the null potential and the extracellular potassium concentration was nonlinear and could be fitted by a Goldman-Hodgkin- Katz equation with PNa/PK = 0.04. The rising phase of potassium currents and the decay of tail currents could be fitted with exponentials with single time constants that varied with membrane potential. Potassium currents inactivated to a steady level with a time constant of approximately 450 ms that did not vary with potential. The currents were depressed by substituting cobalt or cadmium for extracellular calcium but similar effects were not obtained by substituting magnesium for calcium.
Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster

Sexual selection drives faster evolution in males. The X chromosome is potentially an important target for sexual selection, because hemizygosity in males permits accumulation of alleles, causing tradeoffs in fitness between sexes. Hemizygosity of the X could cause fundamentally different modes of inheritance between the sexes, with more additive variation in males and more nonadditive variation in females. Indeed, we find that genetic variation for the transcriptome is primarily additive in males but nonadditive in females. As expected, these differences are more pronounced on the X chromosome than the autosomes, but autosomal loci are also affected, possibly because of X-linked transcription factors. These differences may be of evolutionary significance because additive variation responds quickly to selection, whereas nonadditive genetic variation does not. Thus, hemizygosity of the X may underlie much of the faster male evolution of the transcriptome and potentially other phenotypes. Consistent with this prediction, genes that are additive in males and nonadditive in females are overrepresented among genes responding to selection for increased mating speed.
InP DHBT 68 GHz frequency divider

We report a 68 GHz 2:1 frequency divider with measured input sensitivity less than 6 dBm from 53-68 GHz. To our knowledge, this is the fastest digital frequency divider reported to date in any semiconductor technology. The divider is implemented in differential current mode logic (CML) using undercut collector InP Double Heterojunction Bipolar Transistor (DHBT) technology, with measured f/sub T/ of 150 GHz and f/sub max/ of 163 GHz at J/sub x/=1.2/spl times/10/sup 5/ A/cm/sup 2/. It draws 25.1 mA from a single -3 V supply, dissipating 75 mW. Test results were obtained for wafer probe using micro-coax probes.
Consequences of Ultra-Violet Irradiation on the Mechanical Properties of Spider Silk

The outstanding combination of high tensile strength and extensibility of spider silk is believed to contribute to the material’s toughness. Thus, there is great interest in engineering silk for biomedical products such as suture or implants. Additionally, over the years, many studies have also sought to enhance the mechanical properties of spider silk for wider applicability, e.g., by irradiating the material using ultra-violet radiation. However, the limitations surrounding the use of ultra-violet radiation for enhancing the mechanical properties of spider silk are not well-understood. Here, we have analyzed the mechanical properties of spider silk at short ultra-violet irradiation duration. Specimens of spider silk were subjected to ultra-violet irradiation (254-nm wavelength, i.e. UVC) for 10, 20, and 30 min, respectively, followed by tensile test to rupture to determine the strength (maximum stress), extensibility (rupture strain), and toughness (strain energy density to rupture). Controls, i.e., specimens that did not received UVC, were also subjected to tensile test to rupture to determine the respective mechanical properties. One-way analysis of variance reveals that these properties decrease significantly (p < 0.05) with increasing irradiation duration. Among the three mechanical parameters, the strength of the spider silk degrades most rapidly; the extensibility of the spider silk degrades the slowest. Overall, these changes correspond to the observed surface modifications as well as the bond rupture between the peptide chains of the treated silk. Altogether, this simple but comprehensive study provides some key insights into the dependence of the mechanical properties on ultra-violet irradiation duration.
MEACA: efficient gene-set interpretation of expression data using mixed models

Competitive gene-set analysis, also called enrichment analysis, is a widely used tool for functional interpretation of high-throughput biological data such as gene expression data. It aims at testing a known category (e.g. a pathway) of genes for enriched differential expression (DE) signals compared to genes not in the category. Most enrichment testing methods ignore the widespread correlations among genes, which has been shown to result in excessive false positives. We show, both theoretically and empirically, that existing methods to account for correlations, such as GSEA and CAMERA, can result in severely mis-calibrated type 1 error and/or considerable power loss due to the failure to properly accommodate the DE heterogeneity across genes. We propose MEACA, a new gene-set testing framework based on a mixed effects model. Our method flexibly incorporates the unknown distribution of DE effects, effectively adjusts for completely unknown, unstructured correlations among genes, and does not rely on time-consuming permutations. Compared to existing methods, MEACA enjoys robust type 1 error control in widely ranging scenarios and substantially improves power. Applications of MEACA to a Huntington’s disease study and a lymphoblastoid cell line data set demonstrate its ability to recover biologically meaningful relationships. MEACA is available as an R package.
The impact of selected environmental factors on the educational level of black adult family members

SNOWDEN-REECE, YVONNE M.A., UNIVERSITY OF SOUTH FLORIDA, 1976 THE IMPACT OF SELECTED ENVIRONMENTAL FACTORS ON THE EDUCATIONAL LEVEL OF ADULT BLACK FAMILY MEMBERS. Dissertation Advisor: Dissertation dated: Dr. Rudolph v. Green July, 1987 The purpose of this study is to determine how selected environmental factors of the family of origin correlate with the educational levels of adult family members. The sample consisted of 71 Black adult family members who were administered the Moos' Environment Scale and the investigator's interview form for measuring educational level. The four null hypotheses presented were found not to be statistically significant at the . 05 level. There were no statistically significant correlations between the family of origin environment levels of cohesion, independence, achievement orientation, and intellectual-cultural orientation. The findings of this study have the potential of sensitizing investigators to the impact of selected environmental factors on the educational level of adult family members. The findings derived from this study seem to warrant that there is no statistically significant relationship between (a) family of origin environment level of cohesion and adult family members' educational level; (b) family of origin environment level of independence and adult family members' educational level; (c) family of origin environment level of achievement orientation and adult family members' educational level; and (d) family of origin environment level of intellectual-cultural orientation and adult family members' educational level. Impact of Environmental Factors
Growth and division of Streptococcus pneumoniae: localization of the high molecular weight penicillin‐binding proteins during the cell cycle

The bacterial peptidoglycan, the main component of the cell wall, is synthesized by the penicillin‐binding proteins (PBPs). We used immunofluorescence microscopy to determine the cellular localization of all the high molecular weight PBPs of the human pathogen Streptococcus pneumoniae, for a wild type and for several PBP‐deficient strains. Progression through the cell cycle was investigated by the simultaneous labelling of DNA and the FtsZ protein. Our main findings are: (i) the temporal dissociation of cell wall synthesis, inferred by the localization of PBP2x and PBP1a, from the constriction of the FtsZ‐ring; (ii) the localization of PBP2b and PBP2a at duplicated equatorial sites indicating the existence of peripheral peptidoglycan synthesis, which implies a similarity between the mechanism of cell division in bacilli and streptococci; (iii) the abnormal localization of some class A PBPs in PBP‐defective mutants which may explain the apparent redundancy of these proteins in S. pneumoniae.
Real-time characteristics of Switched Ethernet for "1553B"-Embedded Applications: Simulation and Analysis

In our previous work, Full Duplex Switched Ethernet was put forward as an attractive candidate to replace the MIL-STD 1553B data bus, in next generation "1S53B"-embedded applications. An analytic study was conducted, using the Network Calculus formalism, to evaluate the deterministic guarantees offered by our proposal. Obtained results showed the effectiveness of traffic shaping techniques, combined with priority handling mechanisms on Full Duplex Switched Ethernet in order to satisfy 1553B-like real-time constraints. In this paper, we extend this work by the use of simulation. This gives the possibility to capture additional characteristics of the proposed architecture with respect to the analytical study, which was basically used to evaluate worst cases and deterministic guarantees. Hence, to assess the real-time characteristics of our proposed interconnection technology, the results yielded by simulation are discussed and average latencies distributions are considered.
Molecular Characterization of a Novel Putative Partitivirus Infecting Cytospora sacchari, a Plant Pathogenic Fungus

Three double-stranded RNAs (dsRNAs), approximately 1.85, 1.65 and 1.27 kb in size, were detected in an isolate of Cytospora sacchari from Iran. Partial nucleotide sequence revealed a 1,284 bp segment containing one ORF that potentially encodes a 405 aa protein. This protein contains conserved motifs related to RNA dependent RNA polymerases (RdRp) that showed similarity to RdRps of partitiviruses. The results indicate that these dsRNAs represent a novel Partitivirus that we tentatively designate Cytospora sacchari partitivirus (CsPV). Treatment of the fungal strain by cyclohexamide and also hyphal tip culture had no effect on removing the putative virus. Phylogenetic analysis of putative RdRp of CsPV and other partitiviruses places CsPV as a member of the genus Partitivirus in the family Partitiviridae, and clustering with Aspergillus ochraceous virus 1.
A taxonomy of model‐based testing approaches

Model‐based testing (MBT) relies on models of a system under test and/or its environment to derive test cases for the system. This paper discusses the process of MBT and defines a taxonomy that covers the key aspects of MBT approaches. It is intended to help with understanding the characteristics, similarities and differences of those approaches, and with classifying the approach used in a particular MBT tool. To illustrate the taxonomy, a description of how three different examples of MBT tools fit into the taxonomy is provided. Copyright © 2011 John Wiley & Sons, Ltd.
Assessment of tubular reabsorption of sodium, glucose, phosphate and amino acids based on spot urine samples

Reference values for tubular transport of sodium, phosphate, glucose and amino acids are generally based on inulin or creatinine short‐term clearances, which are difficult to obtain in children. Hence, quantitative assessment of tubular transport capacities is rarely performed. For a simplified procedure, reference values for fractional sodium excretion, phosphate reabsorption related to glomerular filtration rate, percent glucose and percent amino acid reabsorption were established in 62 children from spot urine and simultaneously obtained blood samples. Sodium excretion, and glucose and amino acid reabsorption were significantly lower in infants than children, whereas phosphate reabsorption decreased during the first year of life. Results using the proposed protocol and those obtained from timed urine specimens correlated well; the phenomenon of renal adaptation during childhood could equally well be demonstrated. Renal tubular dysfunction can be diagnosed without timed urine specimens.
Genomic analysis of Pediococcus starter cultures used to control Listeria monocytogenes in turkey summer sausage

The pulsed-field technique of clamped homogeneous electric field electrophoresis was employed to characterize and size genomic DNA of three pediocin-producing (Ped+) and two non-pediocin-producing (Ped-) strains of Pediococcus acidilactici. Comparison of genomic fingerprints obtained by digestion with the low-frequency-cleavage endonuclease AscI revealed identical restriction profiles for four of the five strains analyzed. Summation of results for 10 individually sized AscI fragments estimated the genome length to be 1,861 kb for the four strains (H, PAC1.0, PO2, and JBL1350) with identical fingerprints. Genomic analysis of the pediocin-sensitive, plasmid-free strain P. acidilactici LB42 with the unique fingerprint revealed nine AscI fragments and a genome length of about 2,133 kb. Ped- (JBL1350) and Ped+ (JBL1095) starter cultures (one each) were used to separately prepare turkey summer sausage coinoculated with a four-strain Listeria monocytogenes mixture (ca. 10(5) CFU/g). The starter cultures produced equivalent amounts of acid during fermentation, but counts of L. monocytogenes were reduced to a greater extent in the presence of the Ped+ starter culture (3.4 log10 unit decrease) than in the presence of the Ped- starter culture (0.9 log10 unit decrease). Although no listeriae were recovered from sausages following the cook/shower, appreciable pediocin activity was recovered from sausages prepared with the Ped+ strain for at least 60 days during storage at 4 degrees C. The results of this study revealed genomic similarities among pediococcal starter cultures and established that pediocins produced during fermentation provide an additional measure of safety against listerial proliferation in turkey summer sausage.