Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

MOTIVATION Coexpression networks are data-derived representations of genes behaving in a similar way across tissues and experimental conditions. They have been used for hypothesis generation and guilt-by-association approaches for inferring functions of previously unknown genes. So far, the main platform for expression data has been DNA microarrays; however, the recent development of RNA-seq allows for higher accuracy and coverage of transcript populations. It is therefore important to assess the potential for biological investigation of coexpression networks derived from this novel technique in a condition-independent dataset. RESULTS We collected 65 publicly available Illumina RNA-seq high quality Arabidopsis thaliana samples and generated Pearson correlation coexpression networks. These networks were then compared with those derived from analogous microarray data. We show how Variance-Stabilizing Transformed (VST) RNA-seq data samples are the most similar to microarray ones, with respect to inter-sample variation, correlation coefficient distribution and network topological architecture. Microarray networks show a slightly higher score in biology-derived quality assessments such as overlap with the known protein-protein interaction network and edge ontological agreement. Different coexpression network centralities are investigated; in particular, we show how betweenness centrality is generally a positive marker for essential genes in A.thaliana, regardless of the platform originating the data. In the end, we focus on a specific gene network case, showing that although microarray data seem more suited for gene network reverse engineering, RNA-seq offers the great advantage of extending coexpression analyses to the entire transcriptome.
Diode laser operation under orthogonal feedback: Experiments and theory

We report experimental and numerical investigations concerning semiconductor lasers emission under polarization-rotated feedback. We experimentally observe that for some semiconductor lasers the weak TM mode does lase even in the absence of TM feedback and we monitor how the TE and TM emissions evolve with the increase of the TM feedback strength. The emission frequency of a semiconductor laser subject to polarization-rotated feedback experiences a shift proportional to the optical power fed back into the laser [1]. We aim to investigate what affects the sensibility of the frequency of semiconductor lasers to polarization-rotated feedback. Experimentally, we measured the proportionality coefficient β between frequency shift and feedback power for different lasers and characterized how it varies with some parameters. Theoretically, we made numerical calculations using a rate equation model [2], and our results show a critical dependence of the β coefficient on the gain self- and cross-saturation of both modes and the relations between these saturation coefficients.
Countertransference in child and adolescent psychiatry-a forgotten concept?

OBJECTIVES The purpose of this paper is to review the evolution of the concept of countertransference, its clinical utility and unique features in the child and adolescent psychiatry setting. METHODS This article employs a selective literature review of papers relevant to countertransference in general and in child and adolescent psychiatry. RESULTS Reviewed papers indicate that countertransference is a ubiquitous phenomenon in child and adolescent psychiatric practice and that it can have important clinical implications. CONCLUSIONS Recognition and management of countertransference is a crucial skill in child and adolescent psychiatry. Recommendations are made regarding its incorporation in residency training and psychiatric practice.
Age-Related Enhancement of the Slow Outward Calcium-Activated Potassium Current in Hippocampal CA1 Pyramidal Neurons In Vitro

Aging is associated with learning deficits and a decrease in neuronal excitability, reflected by an enhanced post-burst afterhyperpolarization (AHP), in CA1 hippocampal pyramidal neurons. To identify the current(s) underlying the AHP altered in aging neurons, whole-cell voltage-clamp recording experiments were performed in hippocampal slices from young and aging rabbits. Similar to previous reports, aging neurons were found to rest at more hyperpolarized potentials and have larger AHPs than young neurons. Given that compounds that reduce the slow outward calcium-activated potassium current (sIAHP), a major constituent of the AHP, also facilitate learning in aging animals, the sIAHP was pharmacologically isolated and characterized. Aging neurons were found to have an enhanced sIAHP, the amplitude of which was significantly correlated to the amplitude of the AHP (r = 0.63; p < 0.001). Thus, an enhanced sIAHP contributes to the enhanced AHP in aging. No differences were found in the membrane resistance, capacitance, or kinetic and voltage-dependent properties of the sIAHP. Because enhanced AHP in aging neurons has been hypothesized to be secondary to an enhanced Ca2+ influx via the voltage-gated L-type Ca2+ channels, we further examined the sIAHP in the presence of an L-type Ca2+ channel blocker, nimodipine (10 μm). Nimodipine caused quantitatively greater reductions in the sIAHP in aging neurons than in young neurons; however, the residual sIAHP was still significantly larger in aging neurons than in young neurons. Our data, in conjunction with previous studies showing a correlation between the AHP and learning, suggest that the enhancement of the sIAHP in aging is a mechanism that contributes to age-related learning deficits.
The Pathway-Selective Estrogen Receptor Ligand WAY-169916 Reduces Infarct Size After Myocardial Ischemia and Reperfusion by an Estrogen Receptor Dependent Mechanism

Previous studies have shown that estrogen treatment protects the heart from reperfusion injury. The adverse effects of long-term estrogen treatment limit its clinical use and emphasize the need for the development of specific pharmacological interventions such as pathway-selective estrogen receptor (ER) ligands. Pathway-selective ER ligands are compounds that retain estrogen's anti-inflammatory ability, but they are devoid of conventional estrogenic action. In the present study, the pathway-selective ER ligand WAY-169916 was assessed for its cardioprotective potential in an in vivo model of ischemia-reperfusion injury. Anesthetized, ovariectomized rabbits were administered WAY-169916 (1 mg/kg), 17β-estradiol (E2; 20 μg/rabbit), or vehicle intravenously 30 minutes before a 30-minute occlusion and 4 hours of reperfusion. Acute treatment with either WAY-169916 or E2 resulted in a decrease in infarct size, expressed as a percent of area at risk (WAY-169916, 21.2 ± 3.3; P < 0.001 and E2, 18.8 ± 1.7; P < 0.001) compared with vehicle 59.4 ± 5.4). Pretreatment with estrogen receptor antagonist ICI 182,780 significantly limited the infarct size sparing effect of both WAY-169916 and E2 when expressed as a percent of the risk region (WAY 169916, 47.4 ± 4.4; E2, 53.01 ± 5.0). The results demonstrate that WAY-169916 protects the heart against ischemia-reperfusion injury through an ER-dependent mechanism.
On the communication complexity of randomized broadcasting in random-like graphs

Broadcasting algorithms have a various range of applications in different fields of computer science. In this paper we analyze the number of message transmissions generated by efficient randomized broadcasting algorithms in random-like networks. We mainly consider the classical random graph model, i.e., a graph <i>G<sub>p</sub></i> with <i>n</i> nodes in which any two arbitrary nodes are connected with probability <i>p</i>, independently. For these graphs, we present an efficient broadcasting algorithm based on the random phone call model introduced by Karp et al. [21], and show that the total number of message transmissions generated by this algorithm is bounded by an asymptotically optimal value in almost all connected random graphs. More precisely, we show that if <i>p</i> ≥ log<sup>δ</sup> <i>n</i>/<i>n</i> for some constant δ > 2, then we are able to broadcast any information <i>r</i> in a random graph <i>G<sub>p</sub></i> of size <i>n</i> in <i>O</i>(log <i>n</i>) steps by using at most <i>O</i>(<i>n</i> max{log log <i>n</i>, log <i>n</i>/ log <i>d</i>}) transmissions related to <i>r</i>, where <i>d</i> = <i>pn</i> denotes the expected average degree in <i>G<sub>p</sub></i>. We also show that for these kind of graphs there is a a matching lower bound on the number of transmissions generated by any efficient broadcasting algorithm which works within the limits of the random phone call model. Please note that the main result holds with probability 1-1/<i>n</i><sup>Ω(1)</sup>, even if <i>n</i> and <i>d</i> are unknown to the nodes of the graph.The algorithm we present in this paper is based on a simple communication model [21], is scalable, and robust. It can efficiently handle restricted communication failures and certain changes in the size of the network, and can also be extended to certain types of truncated power law graphs based on the models of [1, 2, 5]. In addition, our methods and results might be useful for further research on this field.
Molecular Epidemiology of the SRL Pathogenicity Island

ABSTRACT The Shigella resistance locus (SRL), which is carried on the SRL pathogenicity island (PAI) in Shigella flexneri 2a YSH6000, mediates resistance to the antibiotics streptomycin, ampicillin, chloramphenicol, and tetracycline. In the present study, we investigated the distribution and structural variation of the SRL and the SRL PAI in 71 Shigella isolates and 28 other enteric pathogens by PCR and Southern analysis. The SRL and SRL-related loci, although absent from the other enteric pathogens evaluated in this study, were found to be present in a number of Shigella isolates. SRL PAI markers were also present in the majority of strains carrying the SRL and SRL-related loci. PCR linkage studies with six of these strains demonstrated that the SRL is carried on elements similar in structure and organization to the YSH6000 SRL PAI, consistent with the hypothesis that the SRL PAI may be involved in the spread of multiple-antibiotic resistance in these strains.
Aged Garlic Extract Improves Adiponectin Levels in Subjects with Metabolic Syndrome: A Double-Blind, Placebo-Controlled, Randomized, Crossover Study

Background. Garlic (Allium sativum) has been shown to have important benefits in individuals at high cardiovascular risk. The aim of the present study was to evaluate the effects of the administration of aged garlic extract (AGE) on the risk factors that constitute the cluster of metabolic syndrome (MS). Methods and Design. Double-blind, crossover, randomized, placebo-controlled clinical trial to assess the effect of 1.2 g/day of AGE (Kyolic), for 24 weeks of treatment (12 weeks of AGE and 12 weeks of placebo), on subjects with MS. Results. The administration of AGE increased the plasma levels of adiponectin (P = 0.027). No serious side effects associated with the intervention were reported. Conclusion. The present results have shown for the first time that the administration of AGE for 12 weeks increased plasma adiponectin levels in patients with MS. This suggests that AGE might be a useful, novel, nonpharmacological therapeutic intervention to increase adiponectin and to prevent cardiovascular (CV) complications in individuals with MS.
Multiple domains of ADAMTS13 are targeted by autoantibodies against ADAMTS13 in patients with acquired idiopathic thrombotic thrombocytopenic purpura

Background Type G immunoglobulins against ADAMTS13 are the primary cause of acquired (idiopathic) thrombotic thrombocytopenic purpura. However, the domains of ADAMTS13 which the type G anti-ADAMT13 immunoglobulins target have not been investigated in a large cohort of patients with thrombotic thrombocytopenic purpura. Design and Methods Sixty-seven patients with acquired idiopathic thrombotic thrombocytopenic purpura were prospectively collected from three major U.S. centers. An enzyme-linked immunosorbent assay determined plasma concentrations of anti-ADAMTS13 type G immunoglobulins, whereas immunoprecipitation plus western blotting determined the binding domains of these type G immunoglobulins. Results Plasma anti-ADAMTS13 type G immunoglobulins from 67 patients all bound full-length ADAMTS13 and a variant truncated after the eighth TSP1 repeat (delCUB). Approximately 97% (65/67) of patients harbored type G immunoglobulins targeted against a variant truncated after the spacer domain (MDTCS). However, only 12% of patients’ samples reacted with a variant lacking the Cys-rich and spacer domains (MDT). In addition, approximately 37%, 31%, and 46% of patients’ type G immunoglobulins interacted with the ADAMTS13 fragment containing TSP1 2-8 repeats (T2-8), CUB domains, and TSP1 5-8 repeats plus CUB domains (T5-8CUB), respectively. The presence of type G immunoglobulins targeted against the T2-8 and/or CUB domains was inversely correlated with the patients’ platelet counts on admission. Conclusions This multicenter study further demonstrated that the multiple domains of ADAMTS13, particularly the Cys-rich and spacer domains, are frequently targeted by anti-ADAMTS13 type G immunoglobulins in patients with acquired (idiopathic) thrombotic thrombocytopenic purpura. Our data shed more light on the pathogenesis of acquired thrombotic thrombocytopenic purpura and provide further rationales for adjunctive immunotherapy.
Analysis and implications of the sequence of ridge jumps that eliminated the Surveyor Transform Fault

By using magnetic anomaly data from a detailed geophysical survey west of the Juan de Fuca rise between longitudes 143°W–134°W and latitudes 42°N–48°N the history of spreading at the Pacific-Farallon spreading center in this region can be reconstructed for the period 35–20 m.y. ago (anomalies 12–5E). During this time period, relative migration of spreading axes separated by transform faults resulted in the elimination of the offset represented by the Surveyor fracture zone. Magnetic anomalies in the southern part of the region require eastward jumps of spreading centers of between 40 and 50 km, and those in the northern part imply westward jumps of up to 70 km. The locations of the spreading center jumps migrate along spreading axes with time, concurrently with northward or southward jumps of transform faults, and leave zones of extensively sheared crust with unidentifiable magnetic anomaly patterns in the crust between old and new spreading centers. Such a process may account for the disturbed zone of magnetic anomalies between the Murray and Molokai fracture zones and could be common to all ridge jumps. If so, it suggests that the new spreading centers do not begin simultaneously over long lengths but instead develop in a manner somewhat similar, but not identical, to a crack propagating through a solid.
Extreme value modelling of daily areal rainfall over Mediterranean catchments in a changing climate

Heavy rainfall events during the fall season are causing extended damages in Mediterranean catchments. A peaks‐over‐threshold model is developed for the extreme daily areal rainfall occurrence and magnitude in fall over six catchments in Southern France. The main driver of the heavy rainfall events observed in this region is the humidity flux (FHUM) from the Mediterranean Sea. Reanalysis data are used to compute the daily FHUM during the period 1958–2008, to be included as a covariate in the model parameters. Results indicate that the introduction of FHUM as a covariate can improve the modelling of extreme areal precipitation. The seasonal average of FHUM can improve the modelling of the seasonal occurrences of heavy rainfall events, whereas daily FHUM values can improve the modelling of the events magnitudes. In addition, an ensemble of simulations produced by five different general circulation models are considered to compute FHUM in future climate with the emission scenario A1B and hence to evaluate the effect of climate change on the heavy rainfall distribution in the selected catchments. This ensemble of climate models allows the evaluation of the uncertainties in climate projections. By comparison to the reference period 1960–1990, all models project an amplification of the mean seasonal FHUM from the Mediterranean Sea for the projection period 2070–2099, on average by +22%. This increase in FHUM leads to an increase in the number of heavy rainfall events, from an average of 2.55 events during the fall season in present climate to 3.57 events projected for the period 2070–2099. However, the projected changes have limited effects on the magnitude of extreme events, with only a 5% increase in the median of the 100‐year quantiles. Copyright © 2011 John Wiley & Sons, Ltd.
Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

ABSTRACT Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of Nanoarchaeota in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed Nanobsidianus stetteri from a more neutral YNP hot spring than to the marine Nanoarchaeum equitans. Single-cell and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP Nanoarchaeota as a Sulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate that Nanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one Nanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP Nanoarchaeota.
Apoptosis in a neonatal rat model of cerebral hypoxia-ischemia.

BACKGROUND AND PURPOSE The mechanisms of excitotoxic cell death in cerebral ischemia are poorly understood. In addition to necrosis, apoptotic cell death may occur. The purpose of this study was to determine whether an established model of cerebral hypoxia-ischemia in the neonatal rat demonstrates any features of apoptosis. METHODS Seven-day-old neonatal rats underwent bilateral, permanent carotid ligation followed by 1 hour of hypoxia, and their brains were examined 1, 3, and 4 days after hypoxia-ischemia. The severity of ischemic damage was assessed in the dentate gyrus and frontotemporal cortex by light microscopy. Immunocytochemistry was performed to detect the cleavage of actin by caspases, a family of enzymes activated in apoptosis. Terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) reactivity was examined in the cortical infarction bed and dentate gyrus. Neonatal rat brain DNA was run on agarose gel electrophoresis to detect DNA fragmentation. Ethidium bromide-staining and electron microscopy were used to determine whether apoptotic bodies, 1 of the hallmarks of apoptosis, were present. RESULTS The frontotemporal cortex displayed evidence of infarction, and in most rats the dentate gyrus showed selective, delayed neuronal death. Immunocytochemistry demonstrated caspase-related cleavage of actin. TUNEL and DNA electrophoresis provided evidence of DNA fragmentation. Ethidium bromide-staining and electron microscopy confirmed the presence of chromatin condensation and apoptotic bodies. CONCLUSIONS Features of apoptosis are present in the described model of cerebral hypoxia-ischemia. Apoptosis may represent a mode of ischemic cell death that could be the target of novel treatments that could potentially expand the therapeutic window for stroke.
Influence of mask induced polarization effects on a pattern printability

Through ArF immersion lithography a road towards increased optical resolution at the 193nm wavelength has been opened. According to recently proposed roadmaps, ArF immersion lithography will be used for 65nm and 45nm technology nodes. Consequently, keeping the same 4x optical demagnification factor, the dimensions on mask scale down to wavelength values when entering these nodes. Moreover CD control becomes tighter and approaches values of 2-3nm. At such conditions, topography on mask, its type and materials cannot be ignored anymore while evaluating image formation either for design analysis or OPC adjustments. The objective of this paper is to analyze the influence of mask topography on imaging. The mask topography influences polarization state and diffraction efficiencies, which are determine further image formation. Therefore these parameters and their dependence on mask type, materials and pitches are of the major concern during the analyses. We analyze the process latitude and CD variations through pitch. The complete rigorous analysis shows improved process windows with the increase of feature aspect ratio and at the same time a large through pitch CD deviation compared to the conventional Kirchhoff diffraction model.
Efectos de la especie invasora Ailanthus altissima (Mill.) Swingle sobre la diversidad vegetal en bosques de ribera del LIC Serra de Mariola y Carrascal de la Font Roja

Este trabajo ha sido financiado por el proyecto “Estrategias de restauracion para combatir la desertificacion en un contexto de cambio climatico. Efectos de los balances hidricos (Estres)” 063/SGTB/2007/7.1 y el proyecto “Restauracion de cubiertas vegetales degradadas en la transicion seco-semiarido (Recuves)”, ambos financiados por el Ministerio de Medio Ambiente.