Miracle-dz/UniFAR-FTUs huggingface dataset:
Winds of Planet Hosting Stars

The field of exoplanetary science is one of the most rapidly growing areas of astrophysical research. As more planets are discovered around other stars, new techniques have been developed that have allowed astronomers to begin to characterise them. Two of the most important factors in understanding the evolution of these planets, and potentially determining whether they are habitable, are the behaviour of the winds of the host star and the way in which they interact with the planet. The purpose of this project is to reconstruct the magnetic fields of planet hosting stars from spectropolarimetric observations, and to use these magnetic field maps to inform simulations of the stellar winds in those systems using the Block Adaptive Tree Solar-wind Roe Upwind Scheme (BATS-R-US) code. The BATS-R- US code was originally written to investigate the behaviour of the Solar wind, and so has been altered to be used in the context of other stellar systems. These simulations will give information about the velocity, pressure and density of the wind outward from the host star. They will also allow us to determine what influence the winds will have on the space weather environment of the planet. This paper presents the preliminary results of these simulations for the star ��τ Bootis, using a newly reconstructed magnetic field map based on previously published observations. These simulations show interesting structures in the wind velocity around the star, consistent with the complex topology of its magnetic field.
NUT SELECTION BY CAPTIVE BLUE JAYS: IMPORTANCE OF AVAILABILITY AND IMPLICATIONS FOR SEED DISPERSAL

Abstract We assessed dietary preference of 14 captive Blue Jays (Cyanocitta cristata) for different food types under different conditions of availability. In four separate feeding trials, we provisioned jays with the following: Trial 1, two nuts each of white oak (Quercus alba), pin oak (Q. palustris), black oak (Q. velutina), northern red oak (Q. rubra), and shagbark hickory (Carya ovata); Trial 2, two small and two large red oak acorns; Trial 3, two germinating and two nongerminating white oak acorns; and Trial 4, one large red oak acorn, one large white oak acorn, and one shagbark hickory nut. We used discrete choice models to describe selection under conditions of changing choice sets. Blue Jays displayed a clear preference for pin oak and strong avoidance of red oak acorns when alternative foods were available. White oak and black oak acorns were selected intermediately. Shagbark hickory nuts were never used. Correlation coefficients suggested that preference was inversely related to seed size and the proportion of seed consisting of hard seed coat. In the absence of alternative food items, small red oak acorns were readily taken, whereas large red oak acorns were mostly avoided but still used by some birds. These results highlight the importance of considering food availability when making conclusions about preference, and lend support to the hypothesis that Blue Jays can be important dispersers of even less-preferred oak species. We discuss the potential as well as the limitations for Blue Jays to act as seed dispersers, with respect to postglacial range expansion of fagaceous tree species, and in the context of present-day dispersal in regions where forests are highly fragmented.
Molecular Dynamics Simulation of Octadecaborane Implantation into Silicon

We have carried out molecular dynamics simulations of monatomic B and octadecaborane cluster implantations into Si in order to make a comparative study and determine the advantages and drawbacks of each approach when used to fabricate shallow junctions. We have simulated a total of 1000 cascades of monatomic boron and an equivalent of 56 cascades of octadecaborane in order to have good statistics. We have obtained and analyzed the doping profiles and the amount and morphology of the damage produced within the target. Our simulation results indicate that the use of octadecaborane clusters for the implantation process shows several advantages with respect to monatomic B beams, mainly related to the reduction of channeling and the lower amount of residual damage at the end of range.
The fluorescent properties of maturing arterial elastin.

Two fluorescent peaks resembling dityrosine have been found in arterial elastin. The high intensity of fluorescence in neonatal elastin residues suggests an early cross-linking role. Increases of wavelength with age follow differing patterns for the two peaks. Pulmonary artery elastin fluorescence changes more slowly with age than aortic elastin, except in children with pulmonary hypertension.
Deficiency in recapitulation of stage‐specific embryonic gene transcription in two‐cell stage cloned mouse embryos

One possible explanation to account for the ability to clone animals by somatic cell nuclear transfer is that the donor genome is reprogrammed by the oocyte to recapitulate a normal embryonic pattern of gene expression. Mouse embryos display transient transcriptional induction of a group of genes (TIGs) at the mid two‐cell stage, the first major transcriptional output of the embryonic genome, uniquely suited for evaluating whether the oocyte directs correct and efficient recapitulation of an embryo stage‐specific gene expression program before any in vitro selection occurs. We analyzed the expression of eight TIGs in two‐cell stage clones prepared with cumulus cell nuclei. One failed to be transcribed, and seven others were transcribed, but supported significantly reduced mRNA expression. The reduction ranged from 1.6‐ to 17‐fold at the mid two‐cell stage, and 1.5‐ to 13‐fold for the late two‐cell stage. Five genes were not expressed in the donor cells, and these displayed the most pronounced deficiencies in expression. Two genes were expressed in cumulus cell donors, and supported progressive accumulation of their mRNAs in clones during this period, albeit at reduced rates. One other gene expressed in cumulus cells was not activated in clones. Although a significant proportion of these genes is reactivated in two‐cell stage clones, this recapitulation is grossly imperfect, occurs at a substantially reduced level, and even fails entirely to occur for some genes. Thus, the oocyte is incapable of efficiently directing the recapitulation of early embryonic stage‐specific gene expression. Mol. Reprod. Dev. 74: 1548–1556, 2007. © 2007 Wiley‐Liss, Inc.
Vehicle detection based on the use of shadow region and edge

Automotive and advanced driver assistance systems have attracted a great deal of attention lately. In these systems, effective and reliable vehicle detection is important because such systems can reduce the number of accidents and save human’ lives. This paper describes an approach to detecting a forward vehicle using a camera mounted on the moving vehicle. In this paper, we describe two methods to detect a vehicle on the road. First, by using the vehicle’s shadow, we can obtain the general location of the vehicular candidate. Second, we can identify the strong vertical edges at the left and right position of a vehicle. By combining the shadows and the edge, we can detect the vehicle’s location. But other regions may also be detected, such as car windows, reflections, and illumination by the sun. In order to remove these other factors, defined as noises, we need to use a filter. After using the filter, we can calculate the exact location of the vehicle. Additionally, by using connected component labeling, we can obtain coordinates and establish the vehicle’s location. Connected component labeling find all connected components in an image and assigns a unique label to all points in the same component. These methods are very useful for vehicle detection and the development of the driving assistance systems, and they can protect drivers’ safety from having an accident.
Discovery and revision of Arabidopsis genes by proteogenomics

Gene annotation underpins genome science. Most often protein coding sequence is inferred from the genome based on transcript evidence and computational predictions. While generally correct, gene models suffer from errors in reading frame, exon border definition, and exon identification. To ascertain the error rate of Arabidopsis thaliana gene models, we isolated proteins from a sample of Arabidopsis tissues and determined the amino acid sequences of 144,079 distinct peptides by tandem mass spectrometry. The peptides corresponded to 1 or more of 3 different translations of the genome: a 6-frame translation, an exon splice-graph, and the currently annotated proteome. The majority of the peptides (126,055) resided in existing gene models (12,769 confirmed proteins), comprising 40% of annotated genes. Surprisingly, 18,024 novel peptides were found that do not correspond to annotated genes. Using the gene finding program AUGUSTUS and 5,426 novel peptides that occurred in clusters, we discovered 778 new protein-coding genes and refined the annotation of an additional 695 gene models. The remaining 13,449 novel peptides provide high quality annotation (>99% correct) for thousands of additional genes. Our observation that 18,024 of 144,079 peptides did not match current gene models suggests that 13% of the Arabidopsis proteome was incomplete due to approximately equal numbers of missing and incorrect gene models.
Phosphatidylserine Transport to the Mitochondria Is Regulated by Ubiquitination*

Mitochondrial membrane biogenesis requires the interorganelle transport of phospholipids. Phosphatidylserine (PtdSer) synthesized in the endoplasmic reticulum and related membranes (mitochondria-associated membrane (MAM)) is transported to the mitochondria by unknown gene products and decarboxylated to form phosphatidylethanolamine at the inner membrane by PtdSer decarboxylase 1 (Psd1p). We have designed a screen for strains defective inPtdSer transport (pstAmutants) between the endoplasmic reticulum and Psd1p that relies on isolating ethanolamine auxotrophs in suitable (psd2Δ) genetic backgrounds. Following chemical mutagenesis, we isolated an ethanolamine auxotroph that we designatepstA1-1. Using in vivo and in vitro phospholipid synthesis/transport measurements, we demonstrate that the pstA1-1 mutant is defective in PtdSer transport between the MAM and mitochondria. The gene that complements the growth defect and PtdSer transport defect of the pstA1-1 mutant is MET30, which encodes a substrate recognition subunit of the SCF (suppressor of kinetochore protein 1, cullin,F-box) ubiquitin ligase complex. Reconstitution of different permutations of MAM and mitochondria from wild type andpstA1-1 strains demonstrates that theMET30 gene product affects both organelles. These data provide compelling evidence that interorganelle PtdSer traffic is regulated by ubiquitination.
Computer-aided cartographical system for map digitizing

The authors present a PC-based cartographical system to digitize maps. A memory restriction made us develop special technologies and techniques to digitize large-sized map-drawings. The combination of manual digitizing and labeling with automatic vectorization and recognition, and interactive editing allowed us to get satisfactory time characteristics for digitizing complex maps. To process automatically scanned maps in a restrictive computer memory, an effective pipeline oriented scheme and new techniques have been developed. A new process called object labeling has been introduced to speed up the interpretation process. An output database structure has been suggested to store all needed information about the map. <<ETX>>
Water molecules in the binding cavity of intestinal fatty acid binding protein: dynamic characterization by water 17O and 2H magnetic relaxation dispersion.

The hydration of intestinal fatty acid binding protein (IFABP) in apo-form and complexed with palmitate, oleate, and 1-anilino-8-naphthalene sulfonate (ANS) has been studied by water 17O and 2H magnetic relaxation dispersion (MRD) measurements. These ligands bind in a large internal cavity, displacing most of the crystallographically identified cavity water molecules. Unlike most other proteins, IFABP gives rise to MRD profiles with two dispersion steps. The low-frequency dispersion yields a correlation time of 7 ns at 300 K, matching the known tumbling time of IFABP. The dispersion amplitude requires only three (apo) or four (holo) long-lived and ordered water molecules (residence time 0.01-4 microseconds at 300 K). Comparison of MRD profiles from the different complexes indicates that the displaced cavity water molecules are short-lived. The few long-lived (>10 ns) water molecules required by the MRD data are tentatively assigned to crystallographic hydration sites on the basis of accessibility, positional order, and H-bonding. The amplitude of the high-frequency dispersion corresponds to 10-20 moderately ordered water molecules, with a correlation time of ca. 1 ns that may reflect a transient opening of the cavity required for exchange with external water.
Severity of Concurrent Visual and Hearing Impairment and Mortality

Purpose: Visual impairment and, to a lesser extent, hearing impairment are independent predictors of reduced survival in selected studies of community-residing adults. To date, the association of severity of concurrent impairment and mortality has not been examined. Method: The National Health Interview Survey is a continuous, multistage, area probability survey of the U.S. civilian noninstitutionalized population. Mortality linkage with the National Death Index of 116,796 adult participants from 1986 to 1994 with complete impairment data was performed through 1997. Results: Findings indicate that moderate to severe concurrent hearing and visual impairment in women is associated with significantly increased risk of mortality. More modest mortality associations are evident for men and for adults with less severe impairments, irrespective of gender. Discussion: Prevention of severe visual and hearing impairment should be a national public health priority, especially given the aging of the U.S. population.
Forbidden ordinal patterns of periictal intracranial EEG indicate deterministic dynamics in human epileptic seizures

Purpose: Epileptic seizures typically reveal a high degree of stereotypy, that is, for an individual patient they are characterized by an ordered and predictable sequence of symptoms and signs with typically little variability. Stereotypy implies that ictal neuronal dynamics might have deterministic characteristics, presumably most pronounced in the ictogenic parts of the brain, which may provide diagnostically and therapeutically important information. Therefore the goal of our study was to search for indications of determinism in periictal intracranial electroencephalography (EEG) studies recorded from patients with pharmacoresistent epilepsy.
Estrogen‐dependent alterations in differentiation state of myeloid cells caused by a v‐myb/estrogen receptor fusion protein.

The oncogene v‐myb and its cellular progenitor c‐myb encode nuclear, DNA binding phosphoproteins that are thought to regulate the expression of myb‐responsive genes during myeloid differentiation. To identify such myb‐regulated genes, and to explore the mechanisms by which v‐myb affects their expression, we have established a conditional expression system for v‐myb. We have converted the v‐myb protein to an estrogen‐inducible transactivator by fusing the protein to the hormone binding domain of the human estrogen receptor. Expression of the chimeric protein in a chicken macrophage cell‐line causes estrogen‐dependent, reversible changes in the differentiation state as well as alterations in the gene expression program of the cells. We have used this estrogen‐dependent v‐myb expression system to identify a novel v‐myb regulated gene.
Inosine improves gut permeability and vascular reactivity in endotoxic shock

ObjectiveTo investigate the effects of inosine administration on vascular reactivity, gut permeability, neutrophil accumulation and lipid peroxidation in tissues in murine endotoxin shock. DesignRandomized, prospective laboratory study. SettingResearch laboratory. SubjectsBALB/c mice 6–8 wks age. InterventionsBALB/c mice were randomly assigned to one of five groups: a) vehicle controls, which received saline intraperitoneally; b) inosine controls, which received inosine alone (100 mg/kg, ip); c) lipopolysaccharide (LPS)-treated animals, which received LPS (40 and 100 mg/kg, ip, depending on the experimental protocol); d) inosine pretreatment group, which received inosine (100 mg/kg, ip) 30 mins before LPS; and finally, e) inosine posttreatment group, which received inosine (100 mg/kg, ip) 60 mins after LPS. Measurements and Main Results The passage of fluorescein isothiocyanate-conjugated dextran (4 kDa, FD4) was analyzed in everted gut ileal sacs incubated ex vivo as an index of gut permeability. LPS induced a significant intestinal hyperpermeability, and inosine exerted protective effects both in pre- and posttreatment regimens. Myeloperoxidase and malondialdehyde were also measured to study neutrophil accumulation and lipid peroxidation in selected tissues. Inosine, both in pre- and posttreatment regimens ameliorated the increases in myeloperoxidase and malondialdehyde in the lung and gut. LPS-treated animals showed decreased contractile and relaxant responses, and inosine pretreatment (but not posttreatment) partially improved these responses. ConclusionsTaken together, inosine has organ protective effects during shock. A significant portion of its protective action is maintained even in the posttreatment scenario.
New approaches for text readability

This thesis describes new approaches to text readability that can help in making written communications more readily understood. The research aims to undergo a deeper exploration of readability and the properties of text that make it easier to understand. The work will attempt to gain an improved understanding of the relationship between text and the reader and propose new methods for assessing readability that will move away from existing surface measures of readability. These existing readability formulas, in spite of their popularity, raise various concerns in failing to detect a number of common writing problems because their focus is largely on word and sentence length. Many users also attempt to improve their writing on the basis of the results produced by these formulas, but acting on the basis of a single numerical output for an entire text presents difficulties in locating troublesome writing. There is criticism, also, that the existing readability formulas were validated using out-dated school grades. In our research, we are taking an extended view of readability that incorporates features of text cohesion, propositional density, word familiarity and the abilities and knowledge of the reader. We have devised a framework that incorporates these features, and derived a number of new configurable measures of readability that can provide reader-specific scoring. Some of the new measures can be applied at sentence level to direct authors to specific writing problems and provide automated feedback on their resolution. To assess the success of our new approaches, we critique and assess existing methods for evaluating readability measures. We use reader preferences over short text passages, when controlled for other features of readability to evaluating our readability methods. We found close agreement between the new measures and reader preferences, demonstrating that the measures can be configured to provide agreement for different types of reader. In addition, we devised a new method for evaluating readability measures using reading times from eye-tracking data. One of our measures, for word familiarity, shows a strong correlation (0.941) with average reading time in comparison to the next best performing existing readability measure (0.906). This particular measure incorporates sentence length in characters, due to the finding of a significant correlation (0.963) between sentence-level reading time and sentence length in characters. The latter indicates that character counts might reflect sentence-level text difficulty rather more accurately than the existing readability measures but would be insufficient alone to offer targeted feedback, and our combination is advantageous even with the cost of a slightly lowered correlation. Using the word familiarity measure, we have also derived a way to estimate how much reading time can be saved by improving readability. We demonstrate our approach in several software prototypes which can provide additional automated feedback to users on how to improve their readability. One of these prototypes, for Open Office, has generated over 12,000 downloads to date.
Adaptation by Means of Associative Learning

Cognitive control is responsible for adapting information processing in order to carry out tasks more efficiently. Contrasting global versus local control accounts, it has recently been proposed that control operates in an associative fashion, that is, by binding stimulus–response associations after detection of conflict (Verguts & Notebaert, 2009). Here, this prediction is explicitly tested for the first time. In a task-switching study where both tasks use the same relevant information, we previously reported conflict adaptation over tasks (Notebaert & Verguts, 2008). In the current experiment, we demonstrate that this is restricted to conditions where both tasks use the same effectors, thereby supporting the associative control account.
Advanced modeling of characteristic mode theory for antenna applications

This paper is to share and review recent development of characteristic mode (CM) theory and its applications, including CM theory based optimization, CM theory for simple antenna design, CM theory for integrated structural antenna design, CM theory for dielectric resonator antenna (DRA) design, and CM theory for layered medium structures.
Molecular Cloning and Functional Characterization of a Novel Human CC Chemokine Receptor (CCR5) for RANTES, MIP-1β, and MIP-1α*

Chemokines affect leukocyte chemotactic and activation activities through specific G protein-coupled receptors. In an effort to map the closely linked CC chemokine receptor genes, we identified a novel chemokine receptor encoded 18 kilobase pairs downstream of the monocyte chemoattractant protein-1 (MCP-1) receptor (CCR2) gene on human chromosome 3p21. The deduced amino acid sequence of this novel receptor, designated CCR5, is most similar to CCR2B, sharing 71% identical residues. Transfected cells expressing the receptor bind RANTES (regulated on activation normal T cell expressed), MIP-1β, and MIP-1α with high affinity and generate inositol phosphates in response to these chemokines. This same combination of chemokines has recently been shown to potently inhibit human immunodeficiency virus replication in human peripheral blood leukocytes (Cocchi, F., DeVico, A. L., Garzino-Demo, A., Arya, S. K., Gallo, R. C., and Lusso, P. (1995) Science 270, 1811-1815). CCR5 is expressed in lymphoid organs such as thymus and spleen, as well as in peripheral blood leukocytes, including macrophages and T cells, and is the first example of a human chemokine receptor that signals in response to MIP-1β.