Miracle-dz/UniFAR-FTUs huggingface dataset:
Negative and Positive Outflow-Feedback in Nearby (U)LIRGs

The starburst-AGN coexistence in local (U)LIRGs makes these galaxies excellent laboratories for the study of stellar and AGN outflows and feedback. Outflows regulate star formation and AGN activity, redistributing gas, dust and metals over large scales in the interstellar and intergalactic media (negative feedback) being also considered to be able to undergo vigorous star formation (positive feedback). In this contribution, I will summarize the results from a search for outflows in a sample of nearby 38 local (U)LIRG systems observed with VIMOS/VLT integral field unit. For two galaxies of the sample I will detail the outflow properties and discuss the observational evidence for negative and positive outflow-feedback. The assessment of both negative and positive feedback effects represent a novel approach towards a comprehensive understanding of the impact of outflow feedback in the galaxy evolution.
Variation in the CYP2D6 genotype is not associated with carvedilol dose changes in patients with heart failure

Carvedilol is the standard of care for heart failure (HF) patients. Carvedilol is partially metabolized by the highly polymorphic enzyme, CYP2D6. To reach an effective dose while avoiding adverse drug reactions (ADRs), testing of CYP2D6 genotype prior to carvedilol initiation may be considered. The objectives of this study were to determine CYP2D6 metabolic genotypes in an Israeli cohort of HF patients and to investigate the relationship between genotype, carvedilol dose and number of ADRs to determine the importance of CYP2D6 genotyping prior to treatment initiation.
Fast Discrete Curvelet Transforms

This paper describes two digital implementations of a new mathematical transform, namely, the second generation curvelet transform in two and three dimensions. The first digital transformation is based on unequally spaced fast Fourier transforms, while the second is based on the wrapping of specially selected Fourier samples. The two implementations essentially differ by the choice of spatial grid used to translate curvelets at each scale and angle. Both digital transformations return a table of digital curvelet coefficients indexed by a scale parameter, an orientation parameter, and a spatial location parameter. And both implementations are fast in the sense that they run in O(n^2 log n) flops for n by n Cartesian arrays; in addition, they are also invertible, with rapid inversion algorithms of about the same complexity. Our digital transformations improve upon earlier implementations—based upon the first generation of curvelets—in the sense that they are conceptually simpler, faster, and far less redundant. The software CurveLab, which implements both transforms presented in this paper, is available at http://www.curvelet. org.
Isolation and Genomic Characterization of the T4-Like Bacteriophage PM2 Infecting Pectobacterium carotovorum subsp. carotovorum

In order to control Pectobacterium carotovorum subsp. carotovorum, a novel virulent bacteriophage PM2 was isolated. Bacteriophage PM2 can infect 48% of P. carotovorum subsp. carotovorum and 78% of P. carotovorum subsp. brasilliensis but none of atrosepticum, betavasculorum, odoriferum and wasabiae isolates had been infected with PM2. PM2 phage belongs to the family Myoviridae, and contains a large head and contractile tail. It has a 170,286 base pair genome that encodes 291 open reading frames (ORFs) and 12 tRNAs. Most ORFs in bacteriophage PM2 share a high level of homology with T4-like phages including IME08, RB69, and JS98. Phylogenetic analysis based on the amino acid sequence of terminase large subunits confirmed that PM2 is classified as a T4-like phage. It contains no integrase- or no repressor-coding genes related to the lysogenic cycle, and lifestyle prediction using PHACT software suggested that PM2 is a virulent bacteriophage.
The Evolution of Gene Expression QTL in Saccharomyces cerevisiae

Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.
Overlapping Antisense Transcription in the Human Genome

Accumulating evidence indicates an important role for non-coding RNA molecules in eukaryotic cell regulation. A small number of coding and non-coding overlapping antisense transcripts (OATs) in eukaryotes have been reported, some of which regulate expression of the corresponding sense transcript. The prevalence of this phenomenon is unknown, but there may be an enrichment of such transcripts at imprinted gene loci. Taking a bioinformatics approach, we systematically searched a human mRNA database (RefSeq) for complementary regions that might facilitate pairing with other transcripts. We report 56 pairs of overlapping transcripts, in which each member of the pair is transcribed from the same locus. This allows us to make an estimate of 1000 for the minimum number of such transcript pairs in the entire human genome. This is a surprisingly large number of overlapping gene pairs and, clearly, some of the overlaps may not be functionally significant. Nonetheless, this may indicate an important general role for overlapping antisense control in gene regulation. EST databases were also investigated in order to address the prevalence of cases of imprinted genes with associated non-coding overlapping, antisense transcripts. However, EST databases were found to be completely inappropriate for this purpose.
Reaction of guanyl radicals in plasmid DNA with biological reductants: chemical repair of DNA damage produced by the direct effect of ionizing radiation

Purpose : It has been previously argued that the use of the one-electron oxidants (SCN) 2 •- and Br 2 •- with plasmid DNA leads to the formation of DNA guanyl radicals. These guanyl radical species are intermediates in the DNA damage produced by processes such as photo-ionization and ionizing irradiation. The present paper evaluates the use of thallium(II) ions (Tl II OH +) as the one-electron oxidant, and also determines rate constants for the reduction (repair) of guanyl radicals in plasmid DNA by a variety of reducing agents including the biologically important compounds ascorbate and glutathione. Materials and methods : Aqueous solutions of plasmid DNA containing 10 -3 mol dm -3 thiocyanate or thallous ions and a reducing agent (azide, nitrite, ferrocyanide, hexachloroiridate(III), iodide, ascorbate, glutathione, glutathione disulphide, methionine, tyrosine, 5-hydroxyindole-3-acetic acid, 10 -7 -10 -4 mol dm -3) were irradiated with 137 Cs γ-rays (662 keV). After irradiation, the plasmid was incubated with the E. coli base excision repair endonuclease formamidopyrimidine-DNA N -glycosylase (FPG). Strand break yields after incubation were quantified by means of agarose gel electrophoresis. Results : High yields of FPG-sensitive sites produced by the oxidants (SCN)2 •- and Tl II OH + were strongly attenuated by the presence of the reducing agents. Conclusions : From the results, it is possible to arrive at estimates of the rate constants for the reduction of the DNA guanyl radical by the reducing agents. Values lie in the range 10 4 -10 7 dm 3 mol -1 s -1. Using the values for ascorbate and glutathione, it is possible to estimate an upper limit on the order of milliseconds for the lifetime of DNA guanyl radicals under cellular conditions. The implication is that there may well be a significant chemical repair of DNA base damage by the direct effect of ionizing radiation.
Imaging techniques in treatment algorithms of pulmonary embolism

Pulmonary embolism (PE) is more often diagnosed post mortem by pathologists than in vivo by clinicians. The identification of practical diagnostic algorithms could reduce the rate of diagnoses first made at autopsy. The literature was reviewed for evidence-based approaches to PE diagnosis. Since the PE mortality rate greatly exceeds that of deep vein thrombosis (DVT), more emphasis was given to reports specifically dealing with PE diagnosis by objective pulmonary vascular imaging techniques than to those aimed at DVT detection. Several studies have shown that standardized clinical estimates can be effectively used to give a pretest probability to calculate, after appropriate objective testing, the post-test probability of PE. A prospective trial has shown that perfusion scanning, rather than ventilation/perfusion scanning, should be the imaging technique of first choice for the management of patients suspected of having PE. The clinical usefulness of spiral computed tomography has not as yet been firmly established. However, ongoing technological developments would probably render the technique accurate enough to replace conventional angiography. The authors propose a noninvasive diagnostic algorithm with high predictive accuracy (positive predictive value 96%; negative predictive value 98%) starting with a standardized assessment of clinical likelihood, followed by a perfusion scan and, eventually, spiral computed tomography in only a minority of patients (<20%) with discordant clinical and scintigraphic findings.
Pregabalin or morphine and gabapentin for neuropathic pain

Common causes of neuropathic pain are diabetes and herpes zoster, with 15% of patients with long-standing diabetes and 11% of herpes patients suffering from this pain. Gabapentin and pregabalin modulate the α2δ calcium-channel subunits, possibly decreasing the neurotransmitter release associated with the central sensitisation that occurs in neuropathic pain. Gabapentin has been shown to be effective in neuropathic pain and, recently, so has pregabalin. These agents seem to have similar efficacy when used alone, but this needs to be tested in a head-to-head trial. A clinical trial comparing morphine, gabapentin or their combination at lower doses showed that the combination of morphine and gabapentin reduced the pain score to a greater extent than either agent alone. This combination treatment represents a novel approach to neuropathic pain.
Density-dependent reproductive and vegetative allocation in the aquatic plant Pistia stratiotes (Araceae).

Pistia stratiotes is an aquatic macrophyte that grows in temporary-ponds in the southern Pantanal, Brazil. It reproduces both sexually and asexually and is usually observed forming dense mats on the water surface, a condition favored by the plant's vegetative reproduction coupled with an ability for rapid growth. In this study we examined the effect of densely crowded conditions on the production of reproductive and vegetative structures. In addition, we verified whether there is a trade-off between clonal growth and investment in sexual reproductive structures, and whether there is an allocation pattern with plant size. Individual plant biomass and the number of the rosettes producing sexual reproductive structures and vegetative growth structures both increased with density. Increase in plant size resulted in increased proportional allocation to sexual reproductive structures and vegetative growth structures. Allocation of biomass to reproduction did not occur at the expense of clonal growth. Thus, the density response appears as a increase of rosettes producing sexual reproductive structures and vegetative growth structures. Therefore, long leaves and stolons may be adaptive under densely crowded conditions where competition for light is intense. An important aspect in the study of trade-offs is the size-dependency of the allocation patterns . Usually, larger plants produce more biomass. Therefore, larger plants can allocate more biomass to both vegetative and sexual reproduction than smaller plants and thus show a positive correlation between both traits rather than the expected negative one.
Adaptive security for multilevel ad hoc networks

Secure communication is critical in military environments in which the network infrastructure is vulnerable to various attacks and compromises. A conventional centralized solution breaks down when the security servers are destroyed by the enemies. In this paper we design and evaluate a security framework for multilevel ad hoc wireless networks with unmanned aerial vehicles (UAVs). In battlefields, the framework adapts to the contingent damages on the network infrastructure. Depending on the availability of the network infrastructure, our design is composed of two modes. In infrastructure mode, security services, specifically the authentication services, are implemented on UAVs that feature low overhead and flexible managements. When the UAVs fail or are destroyed, our system seamlessly switches to infrastructureless mode, a backup mechanism that maintains comparable security services among the surviving units. In the infrastructureless mode, the security services are localized to each node's vicinity to comply with the ad hoc communication mechanism in the scenario. We study the instantiation of these two modes and the transitions between them. Our implementation and simulation measurements confirm the effectiveness of our design. Copyright © 2002 John Wiley & Sons, Ltd.
The use of notated and aural exercises as pedagogical procedures intended to develop harmonic accuracy among beginning jazz improvisers

This study compared the effects from the use of aural and notated exercises as pedagogical procedures for teaching harmonic accuracy to beginning jazz improvisation students. The methods of pedagogy were identified from published pedagogic and historical sources, the results of oral and written traditions of jazz pedagogy. The performance objective was produced from a review of the related literature as a recognized and measurable characteristic of jazz improvisation. The purpose of this study was to compare measurements of harmonic accuracy, following the use of notated and aural exercises as experimental procedures of jazz improvisation pedagogy. A lesson plan, materials, curriculum and outline were developed followed by student recruitment and participation. A total of 20 student volunteers participated in the methods of pedagogy (aural or notation). Data collection consisted of a musical background questionnaire and pre and posttest performance recordings. Student recordings were evaluated by six judges using the “experimental performance evaluation measure. ” Statistical analyses were conducted, including comparisons of pre to posttest effects between, and among the methods of pedagogy. Although all student participants performed mostly from notated music prior to this study, students who received the aural method of pedagogy produced greater improvement for all measurement items. While the aural method produced no differences between grade level, the notation method produced significantly lower scores for 9th graders compared to 12th graders; no other significant grade level differences were noted. Conclusions were that although many sources of pedagogy do not include aural exercises as the predominate activity, beginning improvisers who have more experience reading music than playing by ear, learn better from aural, than notated exercises.
Fibroblast growth factor stimulates the proliferation and differentiation of neural precursor cells in vitro

We have developed an in vitro culture system to study the regulation of proliferation and differentiation of neural precursor cells contained within the neuroepithelium of embruonic day 10 mice. Adnumber of soluble growth factoes have been tested for their ability to regulate these early events and, of these factors, we have found that the fibroblast growth factors [FGFs] can directly stimulate the proliferation and survival of the neuroepithelial cells. At least 50% of the neuroepithekuak cekks divide in the presence of FGF whereas in the absence of FGF all of the cells die within 6 days of cultural. At higher concentrations of FGF, the cells change from being nonadherent round cells in tight clusters into a more flattened cell type which adheres to the substratum. This morphological change is accompanied by the expression of both neurofilament and GFAP, which are definitive markersof the two major cell types in the central nervous system: neurons and glia. In addition a neuroepithelial cell line, which does not rely on FGF for survival or proliferation, expresses both of these markers in response to FGF. These results indicate that FGF is stimulating the differentation of the neuroepithelial cells into mature neurons and glia.
Syndrome of inappropriate secretion of antidiuretic hormone associated with amyotrophic lateral sclerosis in respiratory failure

A 65‐year‐old man who had muscle weakness and dysarthria was admitted for investigation of motor neuron disease. He had lost 12 kg of weight in 6 months. Neurological findings disclosed upper and lower motor neuron disturbances with normal sensory nerve function, and needle electromyography showed a neurogenic pattern. Laboratory findings on admission demonstrated dilutional hyponatraemia due to an excessive secretion of antidiuretic hormone (ADH). Based on these findings, the patient was diagnosed as having the syndrome of inappropriate secretion of antidiuretic hormone (SIADH) associated with amyotrophic lateral sclerosis (ALS). During the night of first hospital day, the patient complained of severe dyspnoea, and mechanical ventilation was commenced. Following the mechanical ventilation, plasma ADH levels and serum sodium concentration were normalized. We propose that respiratory failure secondary to the atrophy of respiratory muscle might be responsible for the development of SIADH.
Fine Mapping, Transcriptome Analysis, and Marker Development for Y2, the Gene That Conditions β-Carotene Accumulation in Carrot (Daucus carota L.)

Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y2. Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot.
Multi-level annotation of natural scenes using dominant image components and semantic concepts

Automatic image annotation is a promising solution to enable semantic image retrieval via keywords. In this paper, we propose a multi-level approach to annotate the semantics of <b><i>natural scenes</i></b> by using both the dominant image components (salient objects) and the relevant semantic concepts. To achieve automatic image annotation at the content level, we use salient objects as the dominant image components for image content representation and feature extraction. To support automatic image annotation at the concept level, a novel image classification technique is developed to map the images into the most relevant semantic image concepts. In addition, Support Vector Machine (SVM) classifiers are used to learn the detection functions for the pre-defined salient objects and finite mixture models are used for semantic concept interpretation and modeling. An <b><i>adaptive EM algorithm</i></b> has been proposed to determine the optimal model structure and model parameters simultaneously. We have also demonstrated that our algorithms are very effective to enable multi-level annotation of <b><i>natural scenes</i></b> in a large-scale image dataset.
Cortical cartography: Mapping functional areas across the human brain with resting state functional connectivity MRI

OF THE DISSERTATION Cortical Cartography: Mapping functional areas across the human brain with resting state functional connectivity MRI by Alexander Li Cohen Doctor of Philosophy in Biology and Biomedical Sciences Neurosciences Washington University in St. Louis, 2011 Professor Steven E. Petersen, Chairperson Human behavior and cognition are largely supported by the cerebral cortex, a structure organized at many physical scales ranging from individual neurons up to distributed systems of multiple interconnected “functional areas”. Each functional area possesses a unique combination of inputs, outputs, and internal structure, and is thought to make a distinct contribution to information processing. Thus, the study of each area’s normal function, developmental trajectory, and modified responses following loss or injury may greatly enhance our understanding of cognition. Indeed, one of the (often unsaid) overarching goals of functional neuroimaging is to use differential activity between conditions to identify specific information processing operations reflected in these functional areas. Unfortunately, delineating a complete collection of functional areas in any mammal, let alone non-invasively in humans, is not straightforward and