Squid – a simple bioinformatics grid

BACKGROUND: BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. RESULTS: Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. CONCLUSION: Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example

A Tail-Anchored Myotonic Dystrophy Protein Kinase Isoform Induces Perinuclear Clustering of Mitochondria, Autophagy, and Apoptosis

Contains fulltext : 79678.pdf (publisher's version ) (Open Access)BACKGROUND: Studies on the myotonic dystrophy protein kinase (DMPK) gene and gene products have thus far mainly concentrated on the fate of length mutation in the (CTG)n repeat at the DNA level and consequences of repeat expansion at the RNA level in DM1 patients and disease models. Surprisingly little is known about the function of DMPK protein products. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrate here that transient expression of one major protein product of the human gene, the hDMPK A isoform with a long tail anchor, results in mitochondrial fragmentation and clustering in the perinuclear region. Clustering occurred in a variety of cell types and was enhanced by an intact tubulin cytoskeleton. In addition to morphomechanical changes, hDMPK A expression induces physiological changes like loss of mitochondrial membrane potential, increased autophagy activity, and leakage of cytochrome c from the mitochondrial intermembrane space accompanied by apoptosis. Truncation analysis using YFP-hDMPK A fusion constructs revealed that the protein's tail domain was necessary and sufficient to evoke mitochondrial clustering behavior. CONCLUSION/SIGNIFICANCE: Our data suggest that the expression level of the DMPK A isoform needs to be tightly controlled in cells where the hDMPK gene is expressed. We speculate that aberrant splice isoform expression might be a codetermining factor in manifestation of specific DM1 features in patients

Disentangling superconducting and magnetic orders in NaFe_1-xNi_xAs using muon spin rotation

Muon spin rotation and relaxation studies have been performed on a "111" family of iron-based superconductors NaFe_1-xNi_xAs. Static magnetic order was characterized by obtaining the temperature and doping dependences of the local ordered magnetic moment size and the volume fraction of the magnetically ordered regions. For x = 0 and 0.4 %, a transition to a nearly-homogeneous long range magnetically ordered state is observed, while for higher x than 0.4 % magnetic order becomes more disordered and is completely suppressed for x = 1.5 %. The magnetic volume fraction continuously decreases with increasing x. The combination of magnetic and superconducting volumes implies that a spatially-overlapping coexistence of magnetism and superconductivity spans a large region of the T-x phase diagram for NaFe_1-xNi_xAs . A strong reduction of both the ordered moment size and the volume fraction is observed below the superconducting T_C for x = 0.6, 1.0, and 1.3 %, in contrast to other iron pnictides in which one of these two parameters exhibits a reduction below TC, but not both. The suppression of magnetic order is further enhanced with increased Ni doping, leading to a reentrant non-magnetic state below T_C for x = 1.3 %. The reentrant behavior indicates an interplay between antiferromagnetism and superconductivity involving competition for the same electrons. These observations are consistent with the sign-changing s-wave superconducting state, which is expected to appear on the verge of microscopic coexistence and phase separation with magnetism. We also present a universal linear relationship between the local ordered moment size and the antiferromagnetic ordering temperature TN across a variety of iron-based superconductors. We argue that this linear relationship is consistent with an itinerant-electron approach, in which Fermi surface nesting drives antiferromagnetic ordering.Comment: 20 pages, 14 figures, Correspondence should be addressed to Prof. Yasutomo Uemura: [email protected]

Determinação simultânea de ácido ascórbico e ácido acetilsalicílico usando análise por injeção em fluxo com detecção amperométrica pulsada

A simple flow system with multiple pulse amperometric detection using a single working electrode is proposed for simultaneous determination of ascorbic (AA) and acetylsalicylic (AAS) acids in pharmaceutical formulations. The procedure is based on application of two potential pulses: 0.90 V/50 ms: oxidation and determination of AA without the interference of AAS; 1.35 V/50 ms: oxidation of both compounds and quantification of AAS by current subtraction using a correction factor. Sampling rate was estimated as 125 injections per hour and the limits of detection were 0.17 and 0.16 µmol L-1 for AA and AAS, respectively. Results for commercial samples agreed with those obtained using HPLC

Digging deeper into colonial palaeontological practices in modern day Mexico and Brazil

Scientific practices stemming from colonialism, whereby middle- and low-income countries supply data for high-income countries and the contributions of local expertise are devalued, are still prevalent today in the field of palaeontology. In response to these unjust practices, countries such as Mexico and Brazil adopted protective laws and regulations during the twentieth century to preserve their palaeontological heritage. However, scientific colonialism is still reflected in many publications describing fossil specimens recovered from these countries. Here, we present examples of ‘palaeontological colonialism’ from publications on Jurassic–Cretaceous fossils from NE Mexico and NE Brazil spanning the last three decades. Common issues that we identified in these publications are the absence of both fieldwork and export permit declarations and the lack of local experts among authorships. In Mexico, access to many fossil specimens is restricted on account of these specimens being housed in private collections, whereas a high number of studies on Brazilian fossils are based on specimens illegally reposited in foreign collections, particularly in Germany and Japan. Finally, we outline and discuss the wider academic and social impacts of these research practices, and propose exhaustive recommendations to scientists, journals, museums, research institutions and government and funding agencies in order to overcome these practices

Venom alkaloids against Chagas disease parasite: search for effective therapies

Chagas disease is an important disease affecting millions of patients in the New World and is caused by a protozoan transmitted by haematophagous kissing bugs. It can be treated with drugs during the early acute phase; however, effective therapy against the chronic form of Chagas disease has yet to be discovered and developed. We herein tested the activity of solenopsin alkaloids extracted from two species of fire ants against the protozoan parasite Trypanosoma cruzi, the aetiologic agent of Chagas disease. Although IC50 determinations showed that solenopsins are more toxic to the parasite than benznidazole, the drug of choice for Chagas disease treatment, the ant alkaloids presented a lower selectivity index. As a result of exposure to the alkaloids, the parasites became swollen and rounded in shape, with hypertrophied contractile vacuoles and intense cytoplasmic vacuolization, possibly resulting in osmotic stress; no accumulation of multiple kinetoplasts and/or nuclei was detected. Overexpressing phosphatidylinositol 3-kinase—an enzyme essential for osmoregulation that is a known target of solenopsins in mammalian cells—did not prevent swelling and vacuolization, nor did it counteract the toxic effects of alkaloids on the parasites. Additional experimental results suggested that solenopsins induced a type of autophagic and programmed cell death in T. cruzi. Solenopsins also reduced the intracellular proliferation of T. cruzi amastigotes in infected macrophages in a concentration-dependent manner and demonstrated activity against Trypanosoma brucei rhodesiense bloodstream forms, which is another important aetiological kinetoplastid parasite. The results suggest the potential of solenopsins as novel natural drugs against neglected parasitic diseases caused by kinetoplastids.Fil: Silva, Rafael C. M. Costa. Universidade Federal do Rio de Janeiro; BrasilFil: Fox, Eduardo G. P.. Universidade Federal do Rio de Janeiro; Brasil. South China Agricultural University; ChinaFil: Gomes, Fabio M.. Universidade Federal do Rio de Janeiro; Brasil. National Institutes of Health; Estados UnidosFil: Feijó, Daniel F.. Universidade Federal do Rio de Janeiro; BrasilFil: Ramos, Isabela. Universidade Federal do Rio de Janeiro; BrasilFil: Koeller, Carolina M.. Universidade Federal do Rio de Janeiro; Brasil. University at Buffalo; Estados UnidosFil: Costa, Tatiana F. R.. Universidade Federal do Rio de Janeiro; BrasilFil: Rodrigues, Nathalia S.. Universidade Federal do Rio de Janeiro; BrasilFil: Lima, Ana P.. Universidade Federal do Rio de Janeiro; BrasilFil: Atella, Georgia C.. Universidade Federal do Rio de Janeiro; BrasilFil: Rocha de Miranda, Kildare. Universidade Federal do Rio de Janeiro; Brasil. Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem; BrasilFil: Schoijet, Alejandra Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Alonso, Guillermo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: de Alcântara Machado, Ednildo. Universidade Federal do Rio de Janeiro; BrasilFil: Heise, Norton. Universidade Federal do Rio de Janeiro; Brasi

ULEEN: A Novel Architecture for Ultra Low-Energy Edge Neural Networks

The deployment of AI models on low-power, real-time edge devices requires accelerators for which energy, latency, and area are all first-order concerns. There are many approaches to enabling deep neural networks (DNNs) in this domain, including pruning, quantization, compression, and binary neural networks (BNNs), but with the emergence of the "extreme edge", there is now a demand for even more efficient models. In order to meet the constraints of ultra-low-energy devices, we propose ULEEN, a model architecture based on weightless neural networks. Weightless neural networks (WNNs) are a class of neural model which use table lookups, not arithmetic, to perform computation. The elimination of energy-intensive arithmetic operations makes WNNs theoretically well suited for edge inference; however, they have historically suffered from poor accuracy and excessive memory usage. ULEEN incorporates algorithmic improvements and a novel training strategy inspired by BNNs to make significant strides in improving accuracy and reducing model size. We compare FPGA and ASIC implementations of an inference accelerator for ULEEN against edge-optimized DNN and BNN devices. On a Xilinx Zynq Z-7045 FPGA, we demonstrate classification on the MNIST dataset at 14.3 million inferences per second (13 million inferences/Joule) with 0.21 $\mu$s latency and 96.2% accuracy, while Xilinx FINN achieves 12.3 million inferences per second (1.69 million inferences/Joule) with 0.31 $\mu$s latency and 95.83% accuracy. In a 45nm ASIC, we achieve 5.1 million inferences/Joule and 38.5 million inferences/second at 98.46% accuracy, while a quantized Bit Fusion model achieves 9230 inferences/Joule and 19,100 inferences/second at 99.35% accuracy. In our search for ever more efficient edge devices, ULEEN shows that WNNs are deserving of consideration.Comment: 14 pages, 14 figures Portions of this article draw heavily from arXiv:2203.01479, most notably sections 5E and 5F.

The Origin of Primordial Magnetic Fields

(abridged) We suggest here that the large scale fields $\sim \mu$G, observed in galaxies at both high and low redshifts by Faraday Rotation Measurements (FRMs), have their origin in the electromagnetic fluctuations that naturally occurred in the dense hot plasma that existed just after the QHPT. We evolve the predicted fields to the present time. The size of the region containing a coherent magnetic field increased due to the fusion (polymerization) of smaller regions. Magnetic fields (MFs) $\sim 10 \mu G$ over a comoving $\sim 1$ pc region are predicted at redshift z $\sim 10$. These fields are orders of magnitude greater than those predicted in previous scenarios for creating primordial magnetic fields. Line-of-sight average magnetic fields (MFs) $\sim$ $10^{-2}$ $\mu$G, valid for FRMs, are obtained over a 1 Mpc comoving region at the redshift z $\sim$ 10. In the collapse to a galaxy (comoving size $\sim$ 30 kpc) at z $\sim$ 10, the fields are amplified to $\sim 10 \mu$G. This indicates that the MFs created immediately after the QHPT, predicted by the Fluctuation-Dissipation Theorem, could be the origin of the $\sim \mu G$ fields observed by FRMs in galaxies at both high and low redshifts.Comment: 34 pages, 8 figure

Uso de árvores nativas em pastagens agroecológicas

O conhecimento tradicional tem sido a base da parceria entre o Centro de Tecnologias Alternativas, as organizações dos agricultores familiares da Zona da Mata de Minas Gerais e as Universidades Federais de Viçosa e, mais recentemente, de Lavras. O objetivo desse trabalho foi identificar o conhecimento tradicional sobre os usos comuns de árvores nativas em pastagens de famílias agricultoras dos municípios de Divino e Araponga, aplicando metodologias participativas (observação participante e entrevista semi-estruturada). O principal uso da terra na região é com café e pastagens. Foi observado pelas famílias que os animais comem ramos de Solanum mauritianum, Senna macranthera, Aegiphila sellowiana e Inga edulis. De acordo com as famílias, a maioria das árvores já estava na pastagem antes do capim. É necessário aprofundamento que dialogue com o aprendizado de famílias agricultoras.Traditional knowledge has been the main base of the partnership among the Center of Alternative Technologies, the organizations of family farmers of Zona da Mata of Minas Gerais and the Federal Universities of Viçosa and, more recently, of Lavras. The objective was to identify the traditional knowledge about the common uses of native trees in the pastures of the properties of family farmers in the municipalities of Divino and Araponga, applying qualitative methodologies (participant observation and semi-structured interviews). The land use in the region is mainly coffee and pastures. Was observed by the families that the animals feed themselves with branches of Solanum mauritianum, Senna macranthera, Aegiphila sellowiana and Inga edulis. According to the families the majority of the trees was already in the field before the grass. It is necessary to deep the dialogue to keep leaning and exchange knowledge with smallholders families.Eje A1 Sistemas de producción de base agroecológica (Trabajos científicos)Facultad de Ciencias Agrarias y Forestale