cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Coastal fisheries and community-based support systems in post disaster contexts
Creators: name: Obregón, Clara
name: Sokach, Ada
name: Neihapi, Pita
name: Arudere, Ajay
name: Joy, Lucy
name: Ephraim, Regina
name: Ham, Jayven
name: Koran, Douglas
name: Malverus, Vasemaca
name: Sami, Abel
name: Gereva, Sompert
name: Steenbergen, Dirk J.
Publisher: name: figshare
Year: 2024
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology

description: Supplementary file1 (DOCX 14 kb)
Bacterial Bioluminescence Regulates Expression of a Host Cryptochrome Gene in the Squid-Vibrio Symbiosis
Creators: name: McFall-Ngai, M. J.
name: Apicella, M. A.
name: Whistler, C. A.
name: Peyer, S. M.
name: Heath-Heckman, E. A. C.
name: Goldman, W. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: ABSTRACTThe symbiosis between the squid Euprymna scolopes and its luminous symbiont, Vibrio fischeri, is characterized by daily transcriptional rhythms in both partners and daily fluctuations in symbiont luminescence. In this study, we sought to determine whether symbionts affect host transcriptional rhythms. We identified two transcripts in host tissues (E. scolopes cry1 [escry1] and escry2) that encode cryptochromes, proteins that influence circadian rhythms in other systems. Both genes cycled daily in the head of the squid, with a pattern similar to that of other animals, in which expression of certain cry genes is entrained by environmental light. In contrast, escry1 expression cycled in the symbiont-colonized light organ with 8-fold upregulation coincident with the rhythms of bacterial luminescence, which are offset from the day/night light regime. Colonization of the juvenile light organ by symbionts was required for induction of escry1 cycling. Further, analysis with a mutant strain defective in light production showed that symbiont luminescence is essential for cycling of escry1; this defect could be complemented by presentation of exogenous blue light. However, blue-light exposure alone did not induce cycling in nonsymbiotic animals, but addition of molecules of the symbiont cell envelope to light-exposed animals did recover significant cycling activity, showing that light acts in synergy with other symbiont features to induce cycling. While symbiont luminescence may be a character specific to rhythms of the squid-vibrio association, resident microbial partners could similarly influence well-documented daily rhythms in other systems, such as the mammalian gut.IMPORTANCEIn mammals, biological rhythms of the intestinal epithelium and the associated mucosal immune system regulate such diverse processes as lipid trafficking and the immune response to pathogens. While these same processes are affected by the diverse resident microbiota, the extent to which these microbial communities control or are controlled by these rhythms has not been addressed. This study provides evidence that the presentation of three bacterial products (lipid A, peptidoglycan monomer, and blue light) is required for cyclic expression of a cryptochrome gene in the symbiotic organ. The finding that bacteria can directly influence the transcription of a gene encoding a protein implicated in the entrainment of circadian rhythms provides the first evidence for the role of bacterial symbionts in influencing, and perhaps driving, peripheral circadian oscillators in the host.
Softwaretechnische Absicherung intelligenter Systeme im Fahrzeug
Creators: name: Rumpe, Bernhard
name: Berger, Christian
name: Krahn, Holger
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: "This article describes software engineering techniques to be used in order to ensure the necessary quality of intelligent and therefore massive software-based systems in vehicles. Quality assurance for intelligent software is achieved through a bundle of modern software engineering methods. Architecture and design patterns for securing the software components are supplemented by test concepts and frameworks for validation and checks of robustness of the implementation. These patterns describe established and therefore consolidated solutions for certain problems as for instance reliability or efficient execution. -- Dieser Artikel skizziert, welche Software-Entwurfstechniken heute zum Einsatz kommen können, um intelligente, Software-lastige Systeme im Fahrzeug abzusichern. Dabei spielt zunächst das Qualitätsmanagement durch Software-technische Maßnahmen eine zentrale Rolle. Architektur- und Entwurfmuster für die Software-technische Absicherung von Komponenten werden ergänzt um Test-Konzepte zur Validierung von Spezifikationen und der Robustheit der Implementierung. Architekturen und Entwurfs-Muster beschreiben erprobte und damit konsolidierte Lösungen für bestimmte Problemklassen wie etwa Zuverlässigkeit oder effiziente Ausführung.
description: 14 pages, 1 figure in German
The Horizon 2020 project rurAllure. Studying pilgrimage as slow tourism, territorial development, social cohesion
Creators: name: López Nores, Martín;Pazos Arias José Juan;Reboreda Morillo, Susana;Penín Romero, Óscar
Publisher: name: La Rivista di Engramma
Year: 2023
Subjects: International Cooperation
Pilgrimage
Slow Tourism
Italian Cultural Heritage

description: This article presents the motivations, key ideas and main outputs of the Horizon 2020 project rurAllure, carried out between January 2021 and December 2023 with the participation of 16 partners from 6 European countries. This endeavour has grown to become a network of more than 100 associated partners interested in promoting rural development and sustainable tourism by harnessing the heritage of the regions traversed by historical pilgrimage routes.
On the lack of correlation between Mg II 2796, 2803 Angstrom and Lyman alpha emission in lensed star-forming galaxies
Creators: name: Rigby, J. R.
name: Bayliss, M. B.
name: Gladders, M. D.
name: Sharon, K.
name: Wuyts, E.
name: Dahle, H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We examine the Mg II 2796, 2803 Angstrom, Lyman alpha, and nebular line emission in five bright star-forming galaxies at 1.66
description: The Astrophysical Journal, in press. 6 pages, 2 figures
Blow-up results for a strongly perturbed semilinear heat equation: Theoretical analysis and numerical method
Creators: name: Nguyen, Van Tien
name: Zaag, Hatem
Publisher: name: arXiv
Year: 2014
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We consider a blow-up solution for a strongly perturbed semilinear heat equation with Sobolev subcritical power nonlinearity. Working in the framework of similarity variables, we find a Lyapunov functional for the problem. Using this Lyapunov functional, we derive the blow-up rate and the blow-up limit of the solution. We also classify all asymptotic behaviors of the solution at the singularity and give precisely blow-up profiles corresponding to these behaviors. Finally, we attain the blow-up profile numerically, thanks to a new mesh-refinement algorithm inspired by the rescaling method of Berger and Kohn in 1988. Note that our method is applicable to more general equations, in particular those with no scaling invariance.
description: 32 pages, 3 figures. arXiv admin note: text overlap with arXiv:1404.4018
Lipid A's Structure Mediates Neisseria gonorrhoeae Fitness during Experimental Infection of Mice and Men
Creators: name: Kandler, J. L.
name: Begum, A. A.
name: Carlson, R. W.
name: Anderson, J. E.
name: Sparling, P. F.
name: Balthazar, J. T.
name: Ganguly, J.
name: Duncan, J. A.
name: Shafer, W. M.
name: Jerse, A. E.
name: Lin, J. T.
name: Hobbs, M. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: ABSTRACT Phosphoethanolamine (PEA) on Neisseria gonorrhoeae lipid A influences gonococcal inflammatory signaling and susceptibility to innate host defenses in in vitro models. Here, we evaluated the role of PEA-decorated gonococcal lipid A in competitive infections in female mice and in male volunteers. We inoculated mice and men with mixtures of wild-type N.gonorrhoeae and an isogenic mutant that lacks the PEA transferase, LptA. LptA production conferred a marked survival advantage for wild-type gonococci in the murine female genital tract and in the human male urethra. Our studies translate results from test tube to animal model and into the human host and demonstrate the utility of the mouse model for studies of virulence factors of the human-specific pathogen N.gonorrhoeae that interact with non-host-restricted elements of innate immunity. These results validate the use of gonococcal LptA as a potential target for development of novel immunoprophylactic strategies or antimicrobial treatments.IMPORTANCE Gonorrhea is one of the most common bacterial sexually transmitted infections, and increasing antibiotic resistance threatens the use of currently available antimicrobial therapies. In this work, encompassing in vitro studies and in vivo studies of animal and human models of experimental genital tract infection, we document the importance of lipid A’s structure, mediated by a single bacterial enzyme, LptA, in enhancing the fitness of Neisseria gonorrhoeae. The results of these studies suggest that novel agents targeting LptA may offer urgently needed prevention or treatment strategies for gonorrhea.IMPORTANCE Gonorrhea is one of the most common bacterial sexually transmitted infections, and increasing antibiotic resistance threatens the use of currently available antimicrobial therapies. In this work, encompassing in vitro studies and in vivo studies of animal and human models of experimental genital tract infection, we document the importance of lipid A’s structure, mediated by a single bacterial enzyme, LptA, in enhancing the fitness of Neisseria gonorrhoeae. The results of these studies suggest that novel agents targeting LptA may offer urgently needed prevention or treatment strategies for gonorrhea.
Comparison of Phylogenetically Distinct Histoplasma Strains Reveals Evolutionarily Divergent Virulence Strategies
Creators: name: Goldman, W. E.
name: Sepulveda, V. E.
name: Williams, C. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: ABSTRACTInfection with the dimorphic fungus Histoplasma capsulatum results from the inhalation of contaminated soil. Disease outcome is variable and depends on the immune status of the host, number of organisms inhaled, and the H.capsulatum strain. H.capsulatum is divided into seven distinct clades based on phylogenetic analyses, and strains from two separate clades have been identified in North America (denoted as NAm strains). We characterized an H.capsulatum isolate (WU24) from the NAm 1 lineage in relation to two other well-characterized Histoplasma isolates, the Panamanian strain G186A and the NAm 2 strain G217B. We determined that WU24 is a chemotype II strain and requires cell wall α-(1,3)-glucan for successful in vitro infection of macrophages. In a mouse model of histoplasmosis, WU24 exhibited a disease profile that was very similar to that of strain G186A at a high sublethal dose; however, at this dose G217B had markedly different kinetics. Surprisingly, infection with a lower dose mitigated many of the differences during the course of infection. The observed differences in fungal burden, disease kinetics, symptomology, and cytokine responses all indicate that there is a sophisticated relationship between host and fungus that drives the development and progression of histoplasmosis.IMPORTANCEHistoplasmosis has a wide range of clinical manifestations, presenting as mild respiratory distress, acute respiratory infection, or a life-threatening disseminated disease most often seen in immunocompromised patients. Additionally, the outcome appears to be dependent on the amount and strain of fungus inhaled. In this study, we characterized a recent clinical H.capsulatum isolate that was collected from an HIV+ individual in North America. In contrast to other isolates from the same lineage, this strain, WU24, infected both macrophages and wild-type mice. We determined that in contrast to many other North American strains, WU24 infection of macrophages is dependent on the presence of cell wall α-(1,3)-glucan. Surprisingly, comparison of WU24 with two previously characterized isolates revealed that many conclusions regarding relative strain virulence and certain hallmarks of histoplasmosis are dependent on the inoculum size.
Dual Role for Inflammasome Sensors NLRP1 and NLRP3 in Murine Resistance to Toxoplasma gondii
Creators: name: Saeij, J. P. J.
name: Cirelli, K. M.
name: Melo, M. B.
name: Grigg, M. E.
name: Leppla, S. H.
name: Sher, A.
name: Masters, S.
name: Crown, D.
name: Gorfu, G.
name: Mayer-Barber, K.
name: Koller, B. H.
name: Moayeri, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: ABSTRACTInduction of immunity that limits Toxoplasma gondii infection in mice is critically dependent on the activation of the innate immune response. In this study, we investigated the role of cytoplasmic nucleotide-binding domain and leucine-rich repeat containing a pyrin domain (NLRP) inflammasome sensors during acute toxoplasmosis in mice. We show that in vitro Toxoplasma infection of murine bone marrow-derived macrophages activates the NLRP3 inflammasome, resulting in the rapid production and cleavage of interleukin-1β (IL-1β), with no measurable cleavage of IL-18 and no pyroptosis. Paradoxically, Toxoplasma-infected mice produced large quantities of IL-18 but had no measurable IL-1β in their serum. Infection of mice deficient in NLRP3, caspase-1/11, IL-1R, or the inflammasome adaptor protein ASC led to decreased levels of circulating IL-18, increased parasite replication, and death. Interestingly, mice deficient in NLRP1 also displayed increased parasite loads and acute mortality. Using mice deficient in IL-18 and IL-18R, we show that this cytokine plays an important role in limiting parasite replication to promote murine survival. Our findings reveal T.gondii as a novel activator of the NLRP1 and NLRP3 inflammasomes in vivo and establish a role for these sensors in host resistance to toxoplasmosis.IMPORTANCEInflammasomes are multiprotein complexes that are a major component of the innate immune system. They contain “sensor” proteins that are responsible for detecting various microbial and environmental danger signals and function by activating caspase-1, an enzyme that mediates cleavage and release of the proinflammatory cytokines interleukin-1β (IL-1β) and IL-18. Toxoplasma gondii is a highly successful protozoan parasite capable of infecting a wide range of host species that have variable levels of resistance. We report here that T. gondii is a novel activator of the NLRP1 and NLRP3 inflammasomes in vivo and establish a role for these sensors in host resistance to toxoplasmosis. Using mice deficient in IL-18 and IL-18R, we show that the IL-18 cytokine plays a pivotal role by limiting parasite replication to promote murine survival.
Analysis of Magnetic Fields in Inertial Alfven Wave Collisions
Creators: name: Drake, Dereth J.
name: Schroeder, James W. R.
name: Shanken, Brian C.
name: Howes, Gregory G.
name: Skiff, Frederick
name: Kletzing, Craig A.
name: Carter, Troy A.
name: Dorfman, Seth
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Turbulence in astrophysical and space plasmas is dominated by the nonlinear interaction of counterpropagating Alfven waves. Most Alfven wave turbulence theories have been based on ideal plasma models, such as incompressible MHD, for Alfven waves at large scales. However, in the inertial Alfven wave regime (vA > vthe), relevant to magnetospheric plasmas, how the turbulent nonlinear interactions are modified by the dispersive nature of the waves remains to be explored. Here we present the first laboratory evidence of the nonlinear interaction in the inertial regime. A comparison is made with the theory for MHD Alfven waves.
description: 2 pages, 1 figure
Additional file 11 of Adiposity and mortality among intensive care patients with COVID-19 and non-COVID-19 respiratory conditions: a cross-context comparison study in the UK
Creators: name: Bell, Joshua A.
name: Carslake, David
name: Hughes, Amanda
name: Tilling, Kate
name: Dodd, James W.
name: Doidge, James C.
name: Harrison, David A.
name: Rowan, Kathryn M.
name: Davey Smith, George
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 11: Figure S11 Acute severity, physiological severity and respiratory severity profiles of ICU patients with COVID-19 (1 March 2020 to 31 July 2021) and non-COVID-19 respiratory conditions (1 Feb 2018 to 31 Aug 2019), by admission date.
Supporting Information from Life-history speed, population disappearances and noise-induced ratchet effects
Creators: name: Greyson-Gaito, Christopher J.
name: Gellner, Gabriel
name: McCann, Kevin S.
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Nature is replete with variation in the body sizes, reproductive output and generation times of species that produce life-history responses known to vary from small and fast to large and slow. Although researchers recognize that life-history speed likely dictates fundamental processes in consumer-resource interactions like productivity and stability, theoretical work remains incomplete in this critical area. Here, we examine the role of life-history speed on consumer–resource interactions by using a well-used mathematical approach that manipulates the speed of the consumer's growth rate in a consumer–resource interaction. Importantly, this approach holds the isocline geometry intact, allowing us to assess the impacts of altered life-history speed on stability (coefficient of variation, CV) without changing the underlying qualitative dynamics. Although slowing life history can be initially stabilizing, we find that in stochastic settings slowing ultimately drives highly destabilizing population disappearances, especially under reddened noise. Our results suggest that human-driven reddening of noise may decrease species stability because the autocorrelation of red noise enlarges the period and magnitude of perturbations, overwhelming a species' natural compensatory responses via a ratchet-like effect. This ratchet-like effect then pushes species’ population dynamics far away from equilibria, which can lead to precipitous local extinction.
Additional file 1 of Structured implementation of digital, systematically updated guideline recommendations for enhanced adherence in schizophrenia (SISYPHOS)—protocol of a cluster-randomized trial
Creators: name: Lorenz, Carolin
name: Gaigl, Gabriele
name: Güler, Duygu
name: Halms, Theresa
name: Khorikian-Ghazari, Naiiri
name: Röh, Astrid
name: Schneider, Marco
name: Wagner, Elias
name: Schneider-Axmann, Thomas
name: Kapfhammer, Angelika
name: Flick, Marisa
name: Pielenz, Charline
name: Salveridou-Hof, Eva
name: Falkai, Peter
name: Gaebel, Wolfgang
name: Hasan, Alkomiet
name: Leucht, Stefan
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: Additional file 1. SPIRIT Checklist for Trials.
Polymicrobial Infection and Bacterium-Mediated Epigenetic Modification of DNA Tumor Viruses Contribute to Pathogenesis
Creators: name: Webster-Cyriaque, J.
name: Doolittle, J. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: ABSTRACTThe human body plays host to a wide variety of microbes, commensal and pathogenic. In addition to interacting with their host, different microbes, such as bacteria and viruses, interact with each other, sometimes in ways that exacerbate disease. In particular, gene expression of a number of viruses, including Kaposi’s sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV), is known to be regulated by epigenetic modifications induced by bacteria. These viruses establish latent infection in their host cells and can be reactivated by bacterial products. Viral reactivation has been suggested to contribute to periodontal disease and AIDS. In addition, bacterium-virus interactions may play a role in cancers, such as Kaposi’s sarcoma, gastric cancer, and head and neck cancer. It is important to consider the effects of coexisting bacterial infections when studying viral diseases in vivo.
Statistical Thermodynamics of Clustered Populations
Creators: name: Matsoukas, Themis
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: We present a thermodynamic theory for a generic population of $M$ individuals distributed into $N$ groups (clusters). We construct the ensemble of all distributions with fixed $M$ and $N$, introduce a selection functional that embodies the physics that governs the population, and obtain the distribution that emerges in the scaling limit as the most probable among all distributions consistent with the given physics. We develop the thermodynamics of the ensemble and establish a rigorous mapping to thermodynamics. We treat the emergence of a so-called "giant component" as a formal phase transition and show that the criteria for its emergence are entirely analogous to the equilibrium conditions in molecular systems. We demonstrate the theory by an analytic model and confirm the predictions by Monte Carlo simulation.
description: Minor edits to text
Additional file 1 of Factors influencing health workers’ compliance with the WHO intermittent preventive treatment for malaria in pregnancy recommendations in the Northern Region, Ghana
Creators: name: Mohammed, Abdul Gafaru
name: Duah, Dwomoh
name: Kenu, Ernest
name: Nonvignon, Justice
name: Manu, Alex
name: Bonful, Harriet Affran
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Questionnaire on factors influencing health workers compliance with the WHO IPTp-SP recommendation, Northern region, Ghana.
Posttranscriptional Regulation of the Yersinia pestis Cyclic AMP Receptor Protein Crp and Impact on Virulence
Creators: name: Ritzert, J. T.
name: Lathem, W. W.
name: Koo, J. T.
name: Bellows, L. E.
name: Price, P. A.
name: Schroeder, J. A.
name: Caulfield, A. J.
name: Goldman, W. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: ABSTRACTThe cyclic AMP receptor protein (Crp) is a transcriptional regulator that controls the expression of numerous bacterial genes, usually in response to environmental conditions and particularly by sensing the availability of carbon. In the plague pathogen Yersinia pestis, Crp regulates the expression of multiple virulence factors, including components of the type III secretion system and the plasminogen activator protease Pla. The regulation of Crp itself, however, is distinctly different from that found in the well-studied Escherichia coli system. Here, we show that at physiological temperatures, the synthesis of Crp in Y.pestis is positively regulated at the posttranscriptional level. The loss of the small RNA chaperone Hfq results in decreased Crp protein levels but not in steady-state Crp transcript levels, and this regulatory effect occurs within the 5′ untranslated region (UTR) of the Crp mRNA. The posttranscriptional activation of Crp synthesis is required for the expression of pla, and decoupling crp from Hfq through the use of an exogenously controlled promoter and 5′ UTR increases Pla protein levels as well as partially rescues the growth defect associated with the loss of Hfq. Finally, we show that both Hfq and the posttranscriptional regulation of Crp contribute to the virulence of Y.pestis during pneumonic plague. The Hfq-dependent, posttranscriptional regulation of Crp may be specific to Yersinia species, and thus our data help explain the dramatic growth and virulence defects associated with the loss of Hfq in Y.pestis.IMPORTANCEThe Crp protein is a major transcriptional regulator in bacteria, and its synthesis is tightly controlled to avoid inappropriate induction of the Crp regulon. In this report, we provide the first evidence of Crp regulation in an Hfq-dependent manner at the posttranscriptional level. Our discovery that the synthesis of Crp in Yersinia pestis is Hfq dependent adds an additional layer of regulation to catabolite repression in this bacterium. Our work provides a mechanism by which the plague pathogen links not just the sensing of glucose or other carbon sources but also other signals that influence Crp abundance via the expression of small RNAs to the induction of the Crp regulon. In turn, this allows Y.pestis to fine-tune Crp levels to optimize virulence gene expression during plague infection and may allow the bacterium to adapt to its unique environmental niches.
Additional file 22 of Adiposity and mortality among intensive care patients with COVID-19 and non-COVID-19 respiratory conditions: a cross-context comparison study in the UK
Creators: name: Bell, Joshua A.
name: Carslake, David
name: Hughes, Amanda
name: Tilling, Kate
name: Dodd, James W.
name: Doidge, James C.
name: Harrison, David A.
name: Rowan, Kathryn M.
name: Davey Smith, George
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 22: Table S7 Associations of confounding/selection factors with all-cause mortality among ICU patients with COVID-19, by admission region
Effetti degli acidi grassi polinsanturi sui processi di sviluppo e progressione tumorale
Creators: name: Rescigno, Tania
Publisher: name: Universita degli studi di Salerno
Year: 2015
Subjects: subject: BIO/10 BIOCHIMICA
subject: Omega-3
subject: Carcinoma mammario

description: 2013 - 2014
description: Molteplici analisi in vitro e in vivo hanno evidenziato la capacità di diversi fattori nutrizionali di influenzare i processi di carcinogenesi e di progressione tumorale. Gli acidi grassi polinsaturi (PUFA) della serie Omega 3, come l’acido eicosapentanoico (EPA) e l’acido docosaesanoico (DHA), di cui sono abbondanti i prodotti ittici, hanno mostrato molti effetti benefici nella prevenzione delle malattie cardiovascolari. D’altra parte, diverse attività biochimiche e cellulari di questi nutrienti suggeriscono che essi potrebbero interferire anche sull’insorgenza e sull’evoluzione di diversi tipi di neoplasie, incluso il carcinoma mammario. Tuttavia, i meccanismi molecolari attraverso i quali questi composti potrebbero influenzare i processi di carcinogenesi mammaria non sono stati ancora completamente chiariti. Dunque, lo scopo di questo progetto è stato quello di approfondire gli effetti degli Omega 3 sui meccanismi alla base dello sviluppo e della progressione del carcinoma mammario. In seguito al trattamento con diverse concentrazioni di DHA, è stata esaminata la vitalità e la mortalità cellulare e la progressione del ciclo cellulare in linee cellulari mammarie con diverso grado di trasformazione e con diverse caratteristiche biochimiche (MCF-10A, MCF-7, SK-BR-3, ZR-75-1). Le linee MCF-7 e ZR-75-1 hanno mostrato una bassa sensibilità al trattamento con DHA in termini di vitalità cellulare, mentre un elevato effetto antiproliferativo è stato indotto da questo nutriente nelle linee cellulari MCF-10A e SK-BR-3. In particolare, il DHA ha indotto un forte blocco del ciclo cellulare delle MCF-10A nella fase G0/G1 che non è stato evidenziato nelle altre linee cellulari mammarie esaminate. Alcuni dei possibili fattori molecolari responsabili degli effetti osservati sono stati esaminati a livello di proteina e di mRNA. L’attivazione dei pathway di ERK 1/2 e di STAT3 e l’espressione di alcune molecole coinvolte nella regolazione del ciclo cellulare (p21Waf1/Cip1 e p53) sono risultate regolate in maniera differenziale dai trattamenti con DHA in ciascuna linea cellulare. I dati ottenuti hanno mostrato che il DHA è in grado di influenzare la vitalità, il ciclo cellulare e l’attività di fattori che regolano la proliferazione, attraverso modalità differenti in ciascuna linea cellulare mammaria esaminata. Nonostante i diversi meccanismi coinvolti, il nutriente ha indotto una rilevante inibizione della crescita in due linee cellulari mammarie con diverso grado di trasformazione e con diverse caratteristiche biochimico-molecolari. Questi risultati suggeriscono un possibile ruolo inibitorio del DHA nell’eziologia e nello sviluppo del carcinoma mammario, che potrebbe essere dipendente dalle proprietà molecolari e dal grado di malignità del singolo caso clinico considerato. [a cura dell'autore]
title: Large-Scale Morphodynamic Impact of Groups of Piers on Low-Land Rivers
Creators: name: Abdou, Abdelrahman
name: Valero, Daniel
name: Crosato, Alessandra
Publisher: name: Utah State University
Year: 2022

description:  This study explores the morphodynamic impact of groups of piers with different configurations (i.e., span characteristics, number of piers, and different reach locations) in a river cross section. It focuses on sandy low-land rivers presenting steady alternate bars and low Froude numbers. A 2DH (vertically integrated) numerical physics-based model (Delft3D) is used to simulate a straight channel, which is inspired from a Nile River reach in Egypt, downstream of the High Aswan Dam. The results show the formation of a forced bar upstream and downstream of the piers and increased deposition over the existing steady bars with different intensities. The nearest bars to the structures are the most affected ones. Large spans between bridge piers and more uniform pier distribution are found to decrease the deposition and its extension, hence reducing dredging investments for navigability.
Viral Profiling Identifies Multiple Subtypes of Kaposi's Sarcoma
Creators: name: Damania, B.
name: Mwafongo, A.
name: Dittmer, D. P.
name: Nyirenda, M.
name: Chiwoko, L.
name: Sweet, K. M.
name: Namarika, D.
name: Vahrson, W.
name: Xiong, J.
name: Hosseinipour, M. C.
name: Phiri, S.
name: Kamwendo, D.
name: Hoffman, I.
name: Lee, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: ABSTRACTKaposi’s sarcoma (KS), caused by KS-associated herpesvirus (KSHV), is the most common cancer among HIV-infected patients in Malawi and in the United States today. In Malawi, KSHV is endemic. We conducted a cross-sectional study of patients with HIV infection and KS with no history of chemo- or antiretroviral therapy (ART). Seventy patients were enrolled. Eighty-one percent had T1 (advanced) KS. Median CD4 and HIV RNA levels were 181cells/mm3 and 138,641 copies/ml, respectively. We had complete information and suitable plasma and biopsy samples for 66 patients. For 59/66 (89%) patients, a detectable KSHV load was found in plasma (median, 2,291 copies/ml; interquartile range [IQR], 741 to 5,623). We utilized a novel KSHV real-time quantitative PCR (qPCR) array with multiple primers per open reading frame to examine KSHV transcription. Seventeen samples exhibited only minimal levels of KSHV mRNAs, presumably due to the limited number of infected cells. For all other biopsy samples, the viral latency locus (LANA, vCyc, vFLIP, kaposin, and microRNAs [miRNAs]) was transcribed abundantly, as was K15 mRNA. We could identify two subtypes of treatment-naive KS: lesions that transcribed viral RNAs across the length of the viral genome and lesions that displayed only limited transcription restricted to the latency locus. This finding demonstrates for the first time the existence of multiple subtypes of KS lesions in HIV- and KS-treatment naive patients.IMPORTANCEKS is the leading cancer in people infected with HIV worldwide and is causally linked to KSHV infection. Using viral transcription profiling, we have demonstrated the existence of multiple subtypes of KS lesions for the first time in HIV- and KS-treatment-naive patients. A substantial number of lesions transcribe mRNAs which encode the viral kinases and hence could be targeted by the antiviral drugs ganciclovir or AZT in addition to chemotherapy.
A Hierarchical Cascade of Second Messengers Regulates Pseudomonas aeruginosa Surface Behaviors
Creators: name: Wong, Gerard C. L.
name: Wolfgang, Matthew C.
name: Kuchma, Sherry L.
name: Luo, Yun
name: Zhao, Kun
name: Coggan, Kimberly A.
name: O’Toole, George A.
name: Baker, Amy E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Biofilms are surface-attached multicellular communities. Using single-cell tracking microscopy, we showed that a pilY1 mutant of Pseudomonas aeruginosa is defective in early biofilm formation. We leveraged the observation that PilY1 protein levels increase on a surface to perform a genetic screen to identify mutants altered in surface-grown expression of this protein. Based on our genetic studies, we found that soon after initiating surface growth, cyclic AMP (cAMP) levels increase, dependent on PilJ, a chemoreceptor-like protein of the Pil-Chp complex, and the type IV pilus (TFP). cAMP and its receptor protein Vfr, together with the FimS-AlgR two-component system (TCS), upregulate the expression of PilY1 upon surface growth. FimS and PilJ interact, suggesting a mechanism by which Pil-Chp can regulate FimS function. The subsequent secretion of PilY1 is dependent on the TFP assembly system; thus, PilY1 is not deployed until the pilus is assembled, allowing an ordered signaling cascade. Cell surface-associated PilY1 in turn signals through the TFP alignment complex PilMNOP and the diguanylate cyclase SadC to activate downstream cyclic di-GMP (c-di-GMP) production, thereby repressing swarming motility. Overall, our data support a model whereby P.aeruginosa senses the surface through the Pil-Chp chemotaxis-like complex, TFP, and PilY1 to regulate cAMP and c-di-GMP production, thereby employing a hierarchical regulatory cascade of second messengers to coordinate its program of surface behaviors. IMPORTANCEBiofilms are surface-attached multicellular communities. Here, we show that a stepwise regulatory circuit, involving ordered signaling via two different second messengers, is required for Pseudomonas aeruginosa to control early events in cell-surface interactions. We propose that our studies have uncovered a multilayered “surface-sensing” system that allows P.aeruginosa to effectively coordinate its surface-associated behaviors. Understanding how cells transition into the biofilm state on a surface may provide new approaches to prevent formation of these communities.
Additional file 10 of Adiposity and mortality among intensive care patients with COVID-19 and non-COVID-19 respiratory conditions: a cross-context comparison study in the UK
Creators: name: Bell, Joshua A.
name: Carslake, David
name: Hughes, Amanda
name: Tilling, Kate
name: Dodd, James W.
name: Doidge, James C.
name: Harrison, David A.
name: Rowan, Kathryn M.
name: Davey Smith, George
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 10: Figure S10 Comorbidity and acute severity profiles of ICU patients with COVID-19 (5 Feb 2020 to 1 Aug 2021) or non-COVID-19 respiratory conditions (1 Feb 2018 to 31 Aug 2019), by geographical region.
Thermal heritage on the ways to Rome. The role of knowledge for enriching tourism experiences along three Italian pilgrimage ways
Creators: name: Mariotti, Alessia
Publisher: name: La Rivista di Engramma
Year: 2023
Subjects: subject: Thermal Heritage
subject: Pilgrimage
subject: Tourism
subject: FOS: Economics and business
subject: Argenta Marshes

description: Pilgrimage is nowadays gaining in popularity as a new form of slow tourism, combining outdoor exercises with spiritual and cultural experiences along established transnational and transregional itineraries. Pilgrimage ways have great potential as territorial development tools, enabling new economic activities and enterprises mainly in peripheral rural areas. Within the rurAllure H2020 project aiming at the promotion of rural museums and heritage sites in the vicinity of European pilgrimage routes, three pilgrimage routes leading to Rome, supported by three Italian universities and a Spanish one, have joined forces to test and experiment new meaningful contents on thermal and water-related heritage to enrich the educational potential of walking tourism. After a short research context introduction, the present contribution summarises the activities carried out in each pilot area, while in the conclusions we will underline the main takeaways as well as potential further research lines that have emerged from the cooperation between experts in archaeology and thermal heritage, tourism and the civil society here represented by municipalities, the managing bodies of the pilgrimage trails and the pilgrims themselves.
Spin Axes and Shape Models of Asteroid Pairs: Fingerprints of YORP and a Path to the Density of Rubble Piles
Creators: name: Polishook, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: An asteroid pair consists of two unbound objects with almost identical heliocentric orbital elements that were formed when a single "rubble pile" asteroid failed to remain bound against an increasing rotation rate. Models suggest that the pairs' progenitors gained the fast rotation due to the YORP effect. Since it was shown that the spin axis vector can be aligned by the YORP effect, such a behavior should be seen on asteroid pairs, if they were indeed formed by the described mechanism. Alternatively, if the pairs were formed by a collision, the spin axes should have a random direction and small or young bodies might have a tumbling rotation. Here I apply the lightcurve inversion method on self-obtained photometric data, in order to derive the rotation axis vectors and shape models of the asteroid pairs 2110, 3749, 5026, 6070, 7343 and 44612. Three asteroids resulted with polar-directed spin axes and three objects with ambiguous results. In addition, the secondary member 44612 presents the same sense of rotation as its primary member 2110, and its spin is not tumbling. Finally, I use a rotational fission model, based on the assumption of an angular momentum conservation, and match it to the measured spin, shape, and mass ratio parameters in order to constrain the density of the primary members in the pairs. Using this method, low density values that are expected from a "rubble pile" are derived. All these results lead to the conclusion that the disruption of these asteroid pairs was most likely the outcome of the YORP effect that spun-up "rubble pile" asteroids.
description: 20 Pages, 41 figures, 5 tables. Accepted for publication in Icarus
A New Quaternary Structure Epitope on Dengue Virus Serotype 2 Is the Target of Durable Type-Specific Neutralizing Antibodies
Creators: name: Widman, D. G.
name: Baric, R. S.
name: Wahala, W. M.
name: Gallichotte, E. N.
name: Yount, B. L.
name: Durbin, A.
name: Crowe, J. E.
name: Sariol, C. A.
name: Whitehead, S.
name: de Silva, A. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACT Dengue virus serotype 2 (DENV2) is widespread and responsible for severe epidemics. While primary DENV2 infections stimulate serotype-specific protective responses, a leading vaccine failed to induce a similar protective response. Using human monoclonal antibodies (hMAbs) isolated from dengue cases and structure-guided design of a chimeric DENV, here we describe the major site on the DENV2 envelope (E) protein targeted by neutralizing antibodies. DENV2-specific neutralizing hMAb 2D22 binds to a quaternary structure epitope. We engineered and recovered a recombinant DENV4 that displayed the 2D22 epitope. DENV2 neutralizing antibodies in people exposed to infection or a live vaccine tracked with the 2D22 epitope on the DENV4/2 chimera. The chimera remained sensitive to DENV4 antibodies, indicating that the major neutralizing epitopes on DENV2 and -4 are at different sites. The ability to transplant a complex epitope between DENV serotypes demonstrates a hitherto underappreciated structural flexibility in flaviviruses, which could be harnessed to develop new vaccines and diagnostics. IMPORTANCE Dengue virus causes fever and dengue hemorrhagic fever. Dengue serotype 2 (DENV2) is widespread and frequently responsible for severe epidemics. Natural DENV2 infections stimulate serotype-specific neutralizing antibodies, but a leading DENV vaccine did not induce a similar protective response. While groups have identified epitopes of single monoclonal antibodies (MAbs), the molecular basis of DENV2 neutralization by polyclonal human immune sera is unknown. Using a recombinant DENV displaying serotype 2 epitopes, here we map the main target of DENV2 polyclonal neutralizing antibodies induced by natural infection and a live DENV2 vaccine candidate. Proper display of the epitope required the assembly of viral envelope proteins into higher-order structures present on intact virions. Despite the complexity of the epitope, it was possible to transplant the epitope between DENV serotypes. Our findings have immediate implications for evaluating dengue vaccines in the pipeline as well as designing next-generation vaccines.
Changes in Expression Induced by Epstein-Barr Virus LMP1-CTAR1: Potential Role of bcl3
Creators: name: Marquitz, Aron R.
name: Raab-Traub, Nancy
name: Edwards, Rachel Hood
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: ABSTRACTThe Epstein-Barr virus protein latent membrane protein 1 (LMP1) has two NF-κB activating domains within its intracellular carboxy terminus (carboxy-terminal activating region 1 [CTAR1] and CTAR2). LMP1-CTAR1 is required for B-lymphocyte transformation, is capable of transforming rodent fibroblasts, and uniquely activates phosphoinositol (PI3) kinase, the noncanonical NF-κB pathway, and expression of the epidermal growth factor receptor (EGFR). In this study, the effects of LMP1-CTAR1 on cellular gene expression were determined by high-throughput sequencing. Additionally, the binding of bcl3 was determined using chromatin immunoprecipitation (ChIP) and sequencing. LMP1-CTAR1 induced few changes in transcription with more genes showing decreased expression. Ingenuity pathway analysis indicated significant enrichment for genes involved in cancer and cellular movement, survival, growth, and proliferation pathways. ChIP in combination with high-throughput sequencing (ChIP-Seq) identified bcl3 binding for more than 2,000 genes in LMP1-CTAR1-expressing cells with more than 90% of the peaks at genes detected within the probable promoter region. Only a small subset of the genes with significant changes in expression had corresponding peaks in the bcl3 ChIP. However, both NFKB2 and PI3 kinase were identified in the bcl3 ChIP. Additionally, many of the predicted upstream regulators for the changes in expression were identified in the bcl3 ChIP. Analysis of the proteins in the NF-κB pathway revealed many changes identified by the high-throughput RNA sequencing (RNA-Seq) and bcl3 ChIP that would likely activate noncanonical NF-κB signaling and possibly inhibit canonical NF-κB signaling. These findings suggest that the two LMP1 signaling domains modulate their combined activity and that the bcl3 transcription factor is likely responsible for some of the unique effects of CTAR1 on cellular expression.IMPORTANCEThe Epstein-Barr virus protein latent membrane protein 1 (LMP1) has potent effects on cell growth. LMP1 has two regions, carboxy-terminal activating region 1 (CTAR1) and CTAR2, that distinctly activate NF-κB, a transcription factor complex involved in activation of important host genes. In this study, analysis of the effects on cellular gene expression revealed that CTAR1 significantly affected cellular expression in part through effects on a specific form of NF-κB. The data suggest that LMP1 can activate a distinct subset of host gene expression through its CTAR1 domain which in combination with other signaling effects induced by the CTAR2 domain likely affects cell movement, survival, and growth.
Black holes and Boyle's law -- the thermodynamics of the cosmological constant
Creators: name: Dolan, Brian P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: When the cosmological constant, $Λ$, is interpreted as a thermodynamic variable in the study of black hole thermodynamics a very rich structure emerges. It is natural to interpret $Λ$ as a pressure and define the thermodynamically conjugate variable to be the thermodynamic volume of the black hole (which need not bear any relation to the geometric volume). Recent progress in this new direction for black hole thermodynamics is reviewed.
description: Review article; 31 pages, 3 figures
Additional file 12 of Adiposity and mortality among intensive care patients with COVID-19 and non-COVID-19 respiratory conditions: a cross-context comparison study in the UK
Creators: name: Bell, Joshua A.
name: Carslake, David
name: Hughes, Amanda
name: Tilling, Kate
name: Dodd, James W.
name: Doidge, James C.
name: Harrison, David A.
name: Rowan, Kathryn M.
name: Davey Smith, George
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 12: Figure S12 Physiological and respiratory severity profiles of ICU patients with COVID-19 (5 Feb 2020 to 1 Aug 2021) or non-COVID-19 respiratory conditions (1 Feb 2018 to 31 Aug 2019), by geographical region.
Additional file 2 of Factors influencing health workers’ compliance with the WHO intermittent preventive treatment for malaria in pregnancy recommendations in the Northern Region, Ghana
Creators: name: Mohammed, Abdul Gafaru
name: Duah, Dwomoh
name: Kenu, Ernest
name: Nonvignon, Justice
name: Manu, Alex
name: Bonful, Harriet Affran
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Checklist for health worker IPTp-SP compliance with WHO IPTp-SP treatment guidelines.