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As aquatic hypoxia worsens on a global scale, fishes will become increasingly challenged by low oxygen, and understanding the molecular basis of their response to hypoxia may help to better define the capacity of fishes to cope with this challenge. The hypoxia inducible factor (HIF) plays a critical role in the molecular response to hypoxia by activating the transcription of genes that serve to improve oxygen delivery to the tissues or enhance the capacity of tissues to function at low oxygen. The current study examines the molecular evolution of genes encoding the oxygen-dependent HIFα subunit (HIFA) in the ray-finned fishes (Actinopterygii). Genomic analyses demonstrate that several lineages retain four paralogs of HIFA predicted from two rounds of genome duplication at the base of vertebrate evolution, broaden the known distribution of teleost-specific HIFA paralogs, and provide evidence for salmonid-specific HIFA duplicates. Evolution of the HIFA gene family is characterized by widespread episodic positive selection at amino acid sites that potentially mediate protein stability, protein–protein interactions, and transcriptional regulation. HIFA transcript abundance depends upon paralog, tissue, and fish lineage. A phylogenetically-informed gene nomenclature is proposed along with avenues for future research on this critical family of transcription factors. [ABSTRACT FROM AUTHOR]

Stratovolcanoes are commonly characterised by cyclic eruptive activity marked by transitions between dome-forming, Vulcanian, Subplinian and Plinian eruptions. Guagua Pichincha volcano (Ecuador) has been a location of such cyclicity for the past ~ 2000 years, with Plinian eruptions in the first and tenth centuries AD (Anno Domini/after Christ), and CE (Common Era) 1660, which were separated by dome-forming to Subplinian eruptions, such as the recent 1999–2001 eruption. These cycles are therefore a prominent example of effusive-explosive transitions at varying timescales. Here, we investigate the reasons for such shifts in activity by focusing on degassing and outgassing processes within the conduit. We have coupled a petrophysical and textural analysis of dacites from the CE 1660 Plinian eruption and the 1999–2001 dome-forming/Vulcanian eruption, with different percolation models in order to better understand the role of degassing on eruptive style. We demonstrate that the transition from dome-forming to Plinian activity is correlated with differences in phenocryst content and consequently in bulk viscosity. A lower initial phenocryst content and viscosity is inferred for the Plinian case, which promotes faster ascent, closed-system degassing, fragmentation and explosive activity. In contrast, dome-forming phases are promoted by a higher magma viscosity due to higher phenocryst content, with slower ascent enhancing gas escape and microlite crystallization, decreasing explosivity and yielding effusive activity. Resumen: Los estratovolcanes se caracterizan comúnmente por presentar actividad eruptiva cíclica, marcada por transiciones entre erupciones formadoras de domos y erupciones de tipo Vulcanianas, Subplinianas y Plinianas. El volcán Guagua Pichincha (Ecuador) ha dado lugar a tal ciclicidad durante los últimos ~ 2000 años, con erupciones Plinianas tanto en los siglos Primero y Décimo, como en el año 1660, las cuales estuvieron intercaladas por erupciones formadoras de domos y de tipo Subplinianas, tal como ocurrió durante la erupción reciente de 1999–2001. Estos ciclos son, por lo tanto, ejemplos destacados de transiciones eruptivas de tipo efusiva-explosiva a escalas de tiempo variadas. En este trabajo, investigamos las razones de tales cambios de actividad enfocándonos en procesos de exsolución y pérdida de gases del magma en el conducto (desgasificación en sistemas cerrado y abierto). Hemos acoplado análisis petrofísicos y texturales tanto de dacitas de la erupción Pliniana de 1660, como de la erupción formadora de domos/Vulcaniana de 1999–2001, junto con diferentes modelos de percolación, para así comprender mejor el rol de la exsolución de volátiles en el estilo eruptivo. Demostramos que la transición desde una actividad efusiva formadora de domos a una Pliniana está correlacionada con diferencias en el contenido de fenocristales y, subsecuentemente, con la viscosidad total del magma. Un contenido inicial menor de fenocristales y una menor viscosidad se infiere para el caso Pliniano, lo que promueve un ascenso más rápido, desgasificación en sistema cerrado, fragmentación y finalmente actividad explosiva. Por el contrario, las fases formadoras de domos son promovidas por una viscosidad mayor debido a un contenido mayor de fenocristales, con ascenso más lento promoviendo a su vez el escape de gases y la cristalización de microlitos, disminuyendo la explosividad y produciendo actividad efusiva. [ABSTRACT FROM AUTHOR]

Pulmonary arteriovenous malformations (PAVMs) are uncommon, predominantly congenital direct fistulous connections between the pulmonary arteries and pulmonary veins, resulting in a right to left shunt. Patients with PAVMs are usually asymptomatic with lesions detected incidentally when radiological imaging is performed for other indications. In this review, we discuss the classification and radiological features of PAVMs as well as their treatment and follow-up options, with a particular focus on percutaneous endovascular techniques and the evolution of the available equipment for treatment. [ABSTRACT FROM AUTHOR]

One of the most common power problems today is communication and control delays. This can adversely affect decision interaction in grid security management. This paper focuses on communication signal delays and how to identify and address communication system failure issues in the context of grid monitoring and control, with emphasis on communication signal delay. An application to solve this problem uses a thyristor switch capacitor (TSC) and a thyristor-controlled reactor (TCR) to improve the power quality of the Rwandan National Grid (RNG) with synchronous and PV generators. It is to counteract the negative effects of time delays. To this end, the TSC and TCR architectures use two methods: the fuzzy logic controller (FLC) method and the modified predictor method (MPM). The experiment was performed using the Simulink MATLAB tool. The power quality of the system was assessed using two indicators: the voltage index and total harmonic distortion. The FLC-based performance was shown to outperform the MPM for temporary or permanent failures if the correct outcome was found. As a result, we are still unsure if TSC and TCR can continue to provide favorable results in the event of a network cyber-attack. [ABSTRACT FROM AUTHOR]

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes. ancestral reconstruction | gene duplication | genome rearrangements

Author(s): Jer-Yuan Hsu; Suzanne Crawley; Michael Chen; Dina A. Ayupova; Darrin A. Lindhout; Jared Higbee; Alan Kutach; William Joo; Zhengyu Gao; Diana Fu; Carmen To; Kalyani Mondal; Betty Li; Avantika [...]

Author(s): Jer-Yuan Hsu (corresponding author) [1]; Suzanne Crawley [1]; Michael Chen [1]; Dina A. Ayupova [1]; Darrin A. Lindhout [1]; Jared Higbee [1]; Alan Kutach [1]; William Joo [1]; Zhengyu [...]

Author(s): Andrew R. Klekociuk (corresponding author) [1]; Peter G. Brown [2]; Dee W. Pack [3]; Douglas O. ReVelle [4]; W. N. Edwards [2]; Richard E. Spalding [5]; Edward Tagliaferri [3]; [...]

The role of oxygen in regulating patterns of gene expression in mammalian development, physiology, and pathology has received increasing attention, especially after the discovery of the hypoxia-inducible factor (HIF), a transcription factor that has been likened to a 'master switch' in the transcriptional response of mammalian cells and tissues to low oxygen. At present, considerably less is known about the molecular responses of nonmammalian vertebrates and invertebrates to hypoxic exposure. Because many animals live in aquatic habitats that are variable in oxygen tension, it is relevant to study oxygen-dependent gene expression in these animals. The purpose of this review is to discuss hypoxia-induced gene expression in fishes from an evolutionary and ecological context. Recent studies have described homologs of HIF in fish and have begun to evaluate their function. A number of physiological processes are known to be altered by hypoxic exposure of fish, although the evidence linking them to HIF is less well developed. The diversity of fish presents many opportunities to evaluate if inter- and intraspecific variation in HIF structure and function correlate with hypoxia tolerance. Furthermore, as an aquatic group, fish offer the opportunity to examine the interactions between hypoxia and other stressors, including pollutants, common in aquatic environments. It is possible, if not likely, that results obtained by studying the molecular responses of fish to hypoxia will find parallels in the oxygen-dependent responses of mammals, including humans. Moreover, novel responses to hypoxia could be discovered through studies of this diverse and species-rich group. hypoxia-inducible factor; teleost fish; hypoxia; transcription factor; hypoxia response element

With an increased immunocompromised population as a result of AIDS and widespread immunosuppressive therapy, Cryptococcus neoformans has emerged as a major pathogenic microbe in patients with impaired immunity (1). C. [...], Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its ~20-megabase genome, which contains ~6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which duster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.

Salt tectonism in the Gulf of Mexico hydrocarbon province controls the development of reservoirs and faults that allow oil and gas to escape at the sea floor (1). More than [...], In the Campeche Knolls, in the southern Gulf of Mexico, lava-like flows of solidified asphalt cover more than 1 square kilometer of the rim of a dissected salt dome at a depth of 3000 meters below sea level. Chemosynthetic tubeworms and bivalves colonize the sea floor near the asphalt, which chilled and contracted after discharge. The site also includes oil seeps, gas hydrate deposits, locally anoxic sediments, and slabs of authigenic carbonate. Asphalt volcanism creates a habitat for chemosynthetic life that may be widespread at great depth in the Gulf of Mexico.

Although classified as an AIDS-defining illness, several reports show histoplasmosis also affects patients living with cancers including haematological malignancies and solid tumours. However, reviews describing cases of histoplasmosis in malignancies are lacking in the literature. We identified a total of thirty-four cases with twenty (58.8 %) cases reported from the USA, four from Brazil (11.8 %), three from India (8.8 %), and one each from Singapore (2.9 %), France (2.9 %), Netherlands (2.9 %), Colombia (2.9 %), Canada (2.9 %), Morocco (2.9 %), and Malaysia (2.9 %). 82.4 % (n = 28) of the cases were adults. Presenting symptoms were majorly fever (61.7 %), lymphadenopathy (50.0 %) and weight loss (29.4 %). Essential haematologic findings were pancytopaenia (n = 7, 20.6 %), neutropenia (n = 2, 5.9 %) and anaemia (n = 5, 14.7 %). The associated cancers were predominantly haematological and comprised 73.5 % (n = 25) of all cases. The diagnosis of histoplasmosis was via histopathology (n = 23, 67.6%), culture (n = 13, 38.2%), Histoplasma antigen assay (n = 13, 38.2%), anti- Histoplasma antibody assay (n = 5, 14.7%), PCR and sequencing (n = 2, 5.9%), peripheral blood film/direct microscopy (n = 4, 11.8%) and cytology (n = 1, 2.9%). Of the thirty-four cases, twenty-four (70.6%) had favourable outcomes, eight (23.5%) died, one (2.9%) was lost to follow-up and in one (2.9%) case, the outcome was not stated. Histoplasmosis is not an uncommon opportunistic disease complicating malignancies but is paradoxically underdiagnosed in Africa given the huge burden of cancers in that region. Besides following chemotherapy and the use of steroids, tumour necrosis factor-α antagonists therapy, hematopoietic stem cell transplantation and environmental exposure were factors associated with Histoplasma infection in patients with malignancies. A resolution to promptly screen suspected or confirmed cases of malignancies for histoplasmosis will improve diagnosis and clinical outcomes. [ABSTRACT FROM AUTHOR]