Miracle-dz/UniFAR-FTUs huggingface dataset:
MAGPHYS Multi-wavelength Analysis of Galaxy Physical Properties maintained

MAGPHYS – Multi-wavelength Analysis of Galaxy Physical Properties – is a self-contained, user-friendly model package to interpret observed spectral energy distributions of galaxies in terms of galaxy-wide physical parameters pertaining to the stars and the interstellar medium, following the approach described in da Cunha, Charlot & Elbaz (2008). The present document provides a brief tutorial on MAGPHYS.
UvA-DARE ( Digital Academic Repository ) Epstein-Barr virus specific cytotoxic T cell responses in HIV-1 infection : ifferent kinetics in patients progressing to opportunistic infection or non-Hodgkin ' s lymphoma

Although the high incidence of EBV-associated diffuse large cell lymphomas (DLCL) in HIV-1 infection is believed to be related to loss of immune control due to HIV-induced immune deficiency, it has been claimed that cytotoxic T lymphocyte (CTL) responses to EBV are longer lasting in HIV-1–infected persons than CTL directed against HIV-1 itself. We approached this apparent paradox by performing the first longitudinal study into the kinetics of EBV and HIV-specific CTL responses in HIV-infected patients progressing either to AIDS with non-Hodgkin’s lymphoma (NHL) or AIDS with opportunistic infection (OI). Multiple samples were tested from HIV-1 seroconversion to AIDS-diagnosis. Four out of six patients that were either long-term asymptomatic or progressing to OI showed declining HIV-1 CTL precursor (CTLp) frequencies whereas EBV-CTLp remained stable, suggestive for HIV-1–specific immune exhaustion. In two patients rapidly progressing to AIDS-OI, a parallel decline of HIV-1– and EBV-CTL responses was seen, indicative for total collapse of cellular immunity. In all these six patients EBV-load remained low. However, in four out of five patients that progressed to DLCL, EBV-load was high and increasing several months preceding the NHL. In all five patients, EBVCTLp decreased before the emergence of the NHL. Thus, our data show that in HIV-1 infection loss of HIV1–specific T cell immunity is not necessarily paralleled by loss of EBV-specific T cell responses. The occurrence of AIDS-related DLCL is preceded by decreasing EBV-CTLp and increasing EBV load. Failing EBV-control might therefore be an important step in the pathogenesis of AIDSrelated DLCL. ( J. Clin. Invest. 1997. 99:1525–1533.)
The case of Bagnoli in Naples , Italy

L’attuale clima di instabilità politica ed economica rallenta e complessifica le trasformazioni urbane e la loro gestione politica. Al contempo però, l’“austerity urbanism” spinge le città a sperimentare alternative inedite di policy-making, che a loro volta possono prevedere l’inclusione di attori nuovi nel policy network rilevante. L’articolo esplora i possibili risvolti di pluralizzazione e democratizzazione della gestione del cambiamento urbano analizzando le diverse configurazioni di attori coinvolti nella trasformazione dell’ex zona industriale di Bagnoli, a Napoli tra il 2002 e il 2016. Nel 2015 il governo nazionale ha avocato le competenze di pianificazione e di esecuzione del progetto per Bagnoli. In risposta a tale intervento, diversi movimenti sociali hanno intensificato le loro iniziative per contrastare le modalità e il progetto proposto dal governo nazionale, ritenuti rispettivamente non democratico e “neoliberale”. La compatibilità delle rispettive posizioni e alcune considerazioni pragmatiche, hanno portato ad una peculiare costellazione che ha visto importanti rappresentanti dell’esecutivo cittadino allinearsi con le posizioni dei movimenti sociali e contro il governo nazionale. Tale configurazione, si ritiene, ha reso possibile l’ingresso di attori normalmente esclusi dal circuito di policymaking e costituisce pertanto un’innovazione del paradigma di pianificazione urbana. The current political instability and economic uncertainty slow down and complicate urban transformations and their correspondent decisional processes. At the same time, however, “austerity urbanism” pushes cities to explore alternative policy-making approaches that might include new actors in the policy network. We investigate this democratic potentiality by analyzing different configurations of actors (2002-2016) that have been participating in the over two decades-long, and still incomplete, transformation of a former industrial area in Bagnoli, in western Naples (Italy). In 2015, the central Government took over the city’s planning competences over the area. In response, several social movements have intensified their action against what they regard as an unchecked, “neo-liberal” transformation of the area. The compatibility of the respective views, as well as pragmatic considerations, led to an alignment between movements and the city and to their joint opposition to the Government. This configuration, we argue, makes room for usually excluded actors and is thus an innovative way of urban policy making. Parole Chiave: Rigenerazione urbana, Governance, Movimenti sociali
PHYLOGENETIC RELATIONSHIPS WITHIN OROBANCHE

Holoparasitic genera within the family Orobanchaceae are characterized by greatly reduced vegetative organs; therefore, molecular analysis has proved to be a useful tool in solving taxonomic problems in this family. For this purpose, we studied all species of the genera Orobanche and Phelipanche occurring in Central Europe, specifically in Poland, the Czech Republic, Slovakia, and Austria, supplemented by samples mainly from Spain, France, Germany, and Ukraine. They were investigated using nuclear sequences (ITS region) and a plastid trnLtrnF region. The aim of this study was to examine phylogenetic relationships within Orobanche and Phelipanche from Central Europe; we focused on problematic species and aggregates, recent taxonomic changes in these (rank and secondary ranks), and host ranges. The most interesting results concern the exlusion of O. mayeri from O. alsatica aggr. Additionally, following the rules of traditional taxonomy, the correct names and types of some secondary ranks are given and, as a result of this, a new combination below the Phelipanche genus is made (P. sect. Trionychon). The host ranges of the investigated species in Central Europe include 102 species from 12 families, most often from Asteraceae. For this purpose, ca. 400 localities were examined in the field. Moreover, data acquired from the literature and European and Asian herbaria were used.
PROBIOTICS: IN SICKNESS AND IN HEALTH

Most medications and supplements including probiotics have both desired clinical outcomes and undesired side effects, which play a role when considering them as a modality for treatment. This review is an update about the advantages and disadvantages associated with the use of probiotics as part of a therapeutic armamentarium in health and in disease. Advantages of probiotics run across multiple organ systems and a wide age spectrum. They promote cardiovascular health, accelerate recovery from diarrhea, decrease risk of necrotizing enterocolitis, limit inflammation in IBD, and promote wound healing. Additionally, probiotics serve in combating chronic diseases for patients with type 2 diabetes and HIV/AIDS. Moreover, probiotics play a significant role in the treatment and/or prevention of cancers, especially those of the colon and bladder. On the other hand, probiotics pose serious threats to immunocompromised, genetically predisposed individuals, children and infants. Using probiotics can lead to bacteremia, fungemia or septicemia. Also, probiotics can cause pneumonia, abdominal abscesses, increase platelet aggregation and trigger antibiotic resistance among others. In conclusion, in vitro and in vivo data from our laboratory and others support the selective evidence based use of probiotics. Actually, a huge number of organisms inhabit the human gut and consequently cause a complex network of the interactions of those organisms with each other and with the host cells, which stresses on the necessity of extra care in the use of probiotics as therapy.
PatchNet : Context-Restricted Architectures to Provide Visual Features for Image Classification

Understanding how a complex machine learning model makes a classification decision is essential for its acceptance in sensitive areas such as health care. Towards this end, we present PatchNet, a method that provides the features indicative of each class in an image using a tradeoff between restricting global image context and classification error. We mathematically analyze this tradeoff, demonstrate Patchnet’s ability to construct sharp visual heatmap representations of the learned features, and quantitatively compare these features with features selected by domain experts by applying PatchNet to the classification of benign/malignant skin lesions from the ISBI-ISIC 2017 melanoma classification challenge.
Preliminary Evidence for the Effi cacy of EMDR in Treating Generalized Anxiety Disorder

Journal of EMDR Practice and Research, Volume 2, Number 1, 2008 © 2008 Springer Publishing Company DOI: 10.1891/1933-3196.2. 1.26 E ye movement desensitization and reprocessing (EMDR) therapy was initially developed by Francine Shapiro (1989, 1995) as a treatment for posttraumatic stress disorder (PTSD). EMDR is a complex and structured psychotherapy methodology that includes aspects of diverse theoretical orientations (e.g., psychodynamic, cognitive-behavioral, humanistic, psychophysiologic). Its distinctive feature is instructing the client to focus on disturbing material while simultaneously attending to an alternate stimulus, namely, eye movements or other forms of bilateral stimulation (Shapiro, 1995, 2002a, 2002b, 2002c; Shapiro & Maxfi eld, 2002). The eight-phase treatment protocol of EMDR is guided by Shapiro’s adaptive information processing (AIP) model (Shapiro, 1995, 2002a), which posits that human beings possess a physiological/neurological system in charge of assimilating and integrating the many aspects of an experience (somatic, cognitive, and emotional). However, under highly stressful situations, such as traumatic events, this information processing system is thought to become unbalanced, thus impeding the integration of the experience into autobiographical memory. When this occurs, the initial perceptions are understood to be stored in their initial form along with any distortions provoked by the high arousal (Shapiro, 2002a; van der Kolk, 2002). Shapiro (2002c) proposed that these nonintegrated experiences are at the root of various psychological disorders, such as PTSD, as well as forming the basis for certain personality structures. EMDR treatment is thought to reactivate the natural information processing system and to facilitate adaptive resolution of the previously distorted material (Bergmann, 1998, 2000; Shapiro, 2002a; Stickgold, 2002; van der Kolk, 2002). Standardized protocols are formulated to address the past experiential contributors to the presenting dysfunction, the current triggers that presently reactivate the material related to the past event, and related future situations (Maxfi eld, 2002; Shapiro, 1995, 2002c, 2004). The effi cacy of EMDR in treating PTSD has been clearly demonstrated in 16 randomized controlled trials. Results generally indicate that (a) EMDR is more effective that no treatment (e.g., Wilson, Becker, & Preliminary Evidence for the Effi cacy of EMDR in Treating Generalized Anxiety Disorder
AT AZORIA , 2003 – 2004 , PART 2 The Final Neolithic , Late Prepal atial , and Ear ly Iron Age Occupation

This article constitutes the second of two reports on fieldwork conducted at Azoria in eastern Crete during the 2003 and 2004 excavation seasons. Evidence of Final Neolithic and Early Iron Age occupation and traces of Late Prepalatial activity were found underlying the Archaic civic buildings on the South Acropolis, particularly along the southwest terrace. The recovery of substantial Final Neolithic architectural and habitation remains contributes to our understanding of the 4th millennium in eastern Crete. Stratigraphic excavations have also clarified the spatial extent of the settlement from Late Minoan IIIC to the Late Geometric period, and brought to light evidence for the transition from the Early Iron Age to the Archaic period, and the transformation of the site in the 7th century b.c.
7-8-2011 Histone Modifications Influence Mediator Interactions with Chromatin

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. INTRODUCTION Transcription in purified and extract based systems, in vivo studies, and cell-based assays have identified the eukaryotic Mediator complex as a target for a wide variety of activators. Analysis of purified Mediator has demonstrated that the core of the Saccharomyces cerevisiae complex is composed of 21 polypeptides (1–3). Biochemical (4) and structural studies (5) allowed the assignment of subunits to structurally distinct modules of the Mediator complex referred to as Tail, Middle and Head. In addition, a separate subset of proteins termed the Cdk8 module is variably associated with the core Mediator subunits (6,7). Definitive genomic and proteomic analyses revealed orthologs for nearly all yeast Mediator subunits in higher eukaryotes (8–10). Parallel biochemical and genetic experiments showed that certain subunits are critical for the activation of specific sets of genes (1,11). Transcriptional profiling in vivo demonstrated that other Mediator subunits are essential for transcription of virtually all genes in S. cerevisiae (12), suggesting the complex was also a general transcription factor (GTF). A number of genetic screens and experiments in S. cerevisiae have also established an important role for Mediator in transcriptional repression (13–19). The mechanism used by Mediator to facilitate repression is not understood, but could be related to its recently discovered localization at silenced or repressed chromatin. Transcriptional activators recruit Mediator and govern the occupancy of the complex at the promoters of certain highly induced genes (20). There are, however, patterns of Mediator occupancy that do not appear to be regulated by *To whom correspondence should be addressed. Tel: +1 603 65
Assassination Campaigns ” : Corruption Scandals and News Media

This article offers a different view of media scandals than the one that is prevalent in the West. In many countries (and partially also in the West), corruption scandals respond mainly to a logic of instrumentalization: They come to light and occupy the front pages of newspapers and privileged slots on television news because they are occasions and tools to attack political and business competitors following the logic of what John Thompson calls the “politics of trust. ” With findings from a series of studies on media corruption, the article explores how instrumentalization drives the coverage of corruption cases in new and transitional democracies.
Three dimensional digital holographic profiling of microfibers

A method to measure the size, orientation, and location of opaque micro-fibers using digital holography is presented. The method involves the recording of a digital hologram followed by reconstruction at different depths. A novel combination of automated image analysis and statistical techniques, applied on the intensity of reconstructed digital holograms is used to accurately determine the characteristics of the microfibers. The performance of the proposed method is verified with a single fiber of known length and orientation. The potential of the method for measurement of fiber length is further demonstrated through its application to a suspension of fibers in a liquid medium. © 2009 Optical Society of America OCIS codes: (090.1995) Digital holography; (100.5010) Pattern recognition; (100.6890) Three-dimensional image processing; (110.6880) Three-dimensional image acquisition; (180.6900) Three-dimensional microscopy; (350.4990) Particles References and links 1. U. Schnars and W. Jueptner, “Digital Holography: Digital Hologram Recording, Numerical Reconstruction, and Related Techniques,” (Springer, Berlin, 2005). 2. Y. Frauel, T. J. Naughton, O. Matoba, E. Tajahuerce, and B. Javidi, “Three-dimensional imaging and processing using computational holographic imaging,” Proc. IEEE 94, 636-653 (2006). 3. J. Garcia-Sucerquia, W. Xu, S. K. Jericho, P. Klages, M. H. Jericho, and H. J. Kreuzer, ”Digital in-line holographic microscopy,” Appl. Opt. 45, 836-850 (2006). 4. O. C. Chee, V. R. Singh, E. Sim, and A. K. Asundi, “Development of a simple user-friendly commercial digital holographic microscope,” Proc. SPIE 6912, 69120V (2008). 5. E. Darakis, T. Khanam, A. Rajendran, V. Kariwala, A. K. Asundi, and T. J. Naughton, “Processing of digital holograms for size measurements of microparticles,” Proc. SPIE 7155, 715524 (2008). 6. T. Khanam, E. Darakis, A. Rajendran, V. Kariwala, A. K. Asundi, and T. J. Naughton, “On-line digital holographic measurement of size and shape of microparticles for crystallization processes,” Proc. SPIE 7155, 71551K (2008). #104298 $15.00 USD Received 20 Nov 2008; revised 10 Feb 2009; accepted 10 Feb 2009; published 12 Feb 2009 (C) 2009 OSA 16 February 2009 / Vol. 17, No. 4 / OPTICS EXPRESS 2938 7. M. Malek, S. Coëtmellec, D. Allano, and D. Lebrun, “Formulation of in-line holography process by a linear shift invariant system: Application to the measurement of fiber diameter,” Opt. Commun. 223, 263-271 (2003). 8. D. Lebrun, A. Benkouider, S. Coëtmellec, and M. Malek, “Particle field digital holographic reconstruction in arbitrary tilted planes,” Opt. Express 11, 224-229 (2003). 9. L. Denis, T. Fournel, C. Fournier, and D. Jeulin, “Reconstruction of the rose of directions from a digital microhologram of fibres,” J. Microsc. 225, 283-292 (2007). 10. S. Wold, K. Esbensen, and P. Geladi, “Principal component analysis,” Chemom. Intell. Lab. Syst. 2, 37-52 (1987).
Phenotypic diversity and carcass quality of creole goats with genetic potential for resistance to infection caused by worm

Abstract: The objective of this work was to phenotypically characterize creole goats of the Moxotó, Azul, Canindé, Repartida, Marota, and Graúna breeds, comparing them with the Boer, Anglo Nubian, and Alpine exotic breeds, to identify the genetic groups of greater potential for carcass quality and resistance to infection caused by worm. Data on morphometric measurements were obtained for the count of worm eggs in grams of feces (WEGF), Famacha score, carcass measurements, and body weight from 308 animals, in a farm in the state of Piauí, Brazil. Repartida goats showed the highest average for wither height (61.55 cm) and rump height (62.16 cm), and Moxotó goats had the greatest ear length (13.45 cm). The Moxotó breed showed the highest means for carcass and body weight. The lowest average for body weight was observed in Azul goats (24.35 kg), and the lowest WEGF was detected in Repartida goats (200 eggs per gram of feces). The average Famacha score was 2.77. Average linkage was the method that best summarized the information on the morphometric and carcass data. The use of morphometric and carcass measurements provides satisfactory results in the phenotypic characterization of the animals. The Brazilian creole goats, which are considered resistant to worm infection and show high-quality carcass traits, may be indicated for conservation and genetic breeding programs.
Ectomycorrhizal diversity and community structure in stands of Quercus oleoides in the seasonally dry tropical forests of Costa Rica

Most conservation efforts in seasonally dry tropical forests have overlooked less obvious targets for conservation, such asmycorrhizal fungi, that are critical to plant growth and ecosystem structure.We documented the diversity of ectomycorrhizal (EMF) and arbuscularmycorrhizal (AMF) fungal communities inQuercus oleoides (Fagaceae) inGuanacaste province, Costa Rica. Soil cores and sporocarpswere collected from regeneratingQ. oleoides plots differing in stand age (early vs late regeneration) during thewet season. Sequencing of the nuclear ribosomal ITS region in EMF root tips and sporocarps identified 37 taxa in the Basidiomycota; EMFAscomycotawere uncommon. The EMF community was dominated by one species (Thelephora sp. 1; 70%of soil cores), more than half of all EMF species were found only once in an individual soil core, and there were few conspecific taxa.Most EMF taxawere also restricted to either Early or Late plots. Levels of EMF species richness and diversity, andAMF root colonizationwere similar between plots. Our results highlight the need for comprehensive spatiotemporal samplings of EMF communities inQ. oleoides to identify and prioritize rare EMF for conservation, and document their genetic and functional diversity.