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Innovators, deep fermentation and antibiotics: promoting applied science before and after the Second World War
Bud,Robert;
Dynamis , 2011, DOI: 10.4321/S0211-95362011000200004
Abstract: the historiography of penicillin has tended to overlook the importance of developing and disseminating know-how in fermentation technology. a focus on this directs attention to work before the war of a network in the us and europe concerned with the production of organic acids, particularly gluconic and citric acids. at the heart of this network was the german-czech konrad bernhauer. other members of the network were a group of chemists at the us department of agriculture who first recognized the production possibilities of penicillin. the pfizer corporation, which had recruited a leading department of agriculture scientist at the end of the first world war, was also an important centre of development as well as of production. however, in wartime bernhauer was an active member of the ss and his work was not commemorated after his death in 1975. after the war new processes of fermentation were disseminated by penicillin pioneers such as jackson foster and ernst chain. because of its commercial context his work was not well known. the conclusion of this paper is that the commercial context, on the one hand, and the nazi associations of bernhauer, on the other, have submerged the significance of know-how development in the history of penicillin.
Comparing De Novo Genome Assembly: The Long and Short of It
Giuseppe Narzisi,Bud Mishra
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019175
Abstract: Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium.
The qualitative assessment of Crasna River in terms of Water Framework Directive 2000/60/EC and Directive 78/659/EC
Giana Popa,Ioan Bud
Aquaculture, Aquarium, Conservation & Legislation , 2010,
Abstract: It is the central objective of the Water Framework Directive of the EC to achieve “good status”for all bodies of water, both surface and ground waters, but with the exception of heavily modified andartificial bodies. For the latter ones, the central objective is defined as "good environmental potential". Inessence, environmental goals by 2015 include: 1) for surface water bodies: achieving good ecologicalstatus and good chemical state, or good ecological potential and good chemical status for heavilymodified water and artificial bodies; 2) for underground water bodies: achieving good chemical statusand good quantitative status; 3) protected areas: environmental objectives under specific legislation; 4)keeping the surface water and ground water away of deterioration status. In this context, our studyhighlights aspects of water resource management of the Crasna catchment, sub-catchment of Some Tisa, to ensure compliance with the contents of the EU Framework Directive 2000/60/EC, in the year2008, and prospects achieving the objectives set, by processing synthetic data created by the Some Tisa Water Directorate, through monitoring quality and quantity of surface resources. Structuralfunctionalpeculiarities of Crasna on the flow velocity, the nature of substrate, flow and water levelvariations, the influence of the structure and the functioning of plant and animal populations, which inturn determine the physical-chemical properties of water, are analysed. Deteriorating environmentalconditions, especially following acute pollution of aquatic organisms, is producing shocks, which areaffecting parts of or all trophic structures, so the result is a decrease in aquatic ecosystems’ diversity,critical for populational survival.
Effects of hydrogen peroxide on Compsopogon caeruleus (Rhodophycophyta) and two superior plants
Vass Levente,Ioan Bud
Aquaculture, Aquarium, Conservation & Legislation , 2010,
Abstract: Hydrogen peroxide was investigated as a potential algaecide for the filamentous epiphyticalga, Compsopogon caeruleus (Balbis ex C.Agardh). The goal was to determine if hydrogen peroxidecould be used to eliminate C. caeruleus, without affecting two other aquatic plants, Ceratopteris thalictroides, and Hygrophila rosanervis. A zebrafish (Danio rerio) was also exposed during thetreatment, to observe the effects of hydrogen peroxide on fish. Concentrations between 1mM and 6 mM l-2were tested for their ability to induce bleaching or tissue disintegration in plant and algal tissues. 1mM l-2 hydrogen peroxide had no major effect on the alga, or on the plants. The 3 mM solution inducedpartial bleaching in C. thalictroides and damaged significantly de filamentous alga. The 6 mM solutionkilled completely the alga and damaged significantly the C. thalictroides. H. rosanervis suffered minorlesions during the treatment. D. rerio wasn’t affected by the mentioned concentrations of hydrogenperoxide.
Significant punctiform and diffuse pressure in upper Crasna river basin
Giana Popa,Ioan Bud
Aquaculture, Aquarium, Conservation & Legislation , 2011,
Abstract: t. The preservation of healthy ecosystems which are biological valuable, whose actual status is convenient, as well as the improvement or transformation of those partially or heavily modified by anthropic interventions, should be targeted to achieve objectives of the ecological balance of any watercourse. The pressure on aquatic environment are generated by agglomerations, industry and agriculture, but also by hydromorphological area. In the upper of the Crasna basin the level of nutrient impurification due to human agglomeration sets a “sensitive” character for Crasna area and ranks the Crasna river in a lower class of quality. IPPC and NON IPPC industry generates dangerous substances, especially those on List II, which establishes the low state of the Crasna river. Dangerous substances cause toxicity, persistence and bioaccumulation in the aquatic environment. Impact of non-priority and priority pollutants, in terms of environmental impact is not distinct, therefore there is a tendency to pay attention to priority poluttants, even if non-priority substances create the gratest damages. Lack of clean technologies or non compliance with Best Available Technologies is the main cause of surface resource contamination by dangerous substances.
Contributions concerning the quality indices? appreciation in main aquatic organisms, which fall under human consumption
Ioan Bud,Vioara Mire?an
Aquaculture, Aquarium, Conservation & Legislation , 2008,
Abstract: In present work paper, the authors broach a theme of top modernity concerning the fish and other aquatic organisms? quality, in the context of more and more demand from the consumers? side. To put into evidence the meat quality proceeded from fishes and other aquatic organisms, were effected physical-chemical studies to emphasize the value of some parameters and their evolution depending on species, age and body weight. Also, were done comparisons between fish meat quality and other provenance sources respectively meat from farm animals. The obtained results put into evidence superior qualitative values of aquatic organism meat to those terrestrial ones, especially as regard the protein and decreased fat content. The researches emphasized also the fact that meat production indices have an evolution in direct correspondence with body weight and age on the one hand, and on the other one, they are different also depending on species, those predacious ones having superior values in all cases. Other studied aquatic organisms, unless fishes, have emphasized a very reduced content of fats and carbohydrates that reveals the especial biological and chemical value, in conditions of alimentary components? demand to provide a rational alimentation and an alimentary insurance.
Superconductivity In K- And Na- Doped Bafe2as2: What Can We Learn From Heat Capacity And Pressure Dependence of Tc
Sergey L. Bud'ko
Physics , 2014, DOI: 10.1142/S0217984914300191
Abstract: A brief overview of changes in the superconducting transition temperature under pressure and evolution of specific heat capacity jump at Tc for two related families of iron - based superconductors, Ba{1-x}KxFe2As2 (0.2 < x < 1.0) and Ba{1-x}NaxFe2As2 (0.2 < x < 0.9) will be given. For Ba{1-x}KxFe2As2 the specific heat capacity jump at Tc measured over the whole extent of the superconducting dome shows clear deviation from the empirical, Delta Cp (Tc) ~ Tc^3, scaling (known as the BNC scaling) for x > 0.7. At the same concentrations range apparent equivalence of effects of pressure and K- substitution on Tc fails. These observations suggests a significant change of the superconducting state for x > 0.7. In contrast, the data for the large portion of Ba{1-x}NaxFe2As2 (0.2 < x < 0.9) series follow the BNC scaling. However, the pressure dependence of Tc (measured up to ~ 12 kbar) have clear non-linearities for Na concentration in 0.2 - 0.25 region, that may be consistent with Tc crossing the phase boundaries of the emergent, narrow, antiferromagnetic/tetragonal phase. Results will be discussed in context other studies of these two and related families of iron-based superconductors.
The Temporal Logic of Causal Structures
Samantha Kleinberg,Bud Mishra
Computer Science , 2012,
Abstract: Computational analysis of time-course data with an underlying causal structure is needed in a variety of domains, including neural spike trains, stock price movements, and gene expression levels. However, it can be challenging to determine from just the numerical time course data alone what is coordinating the visible processes, to separate the underlying prima facie causes into genuine and spurious causes and to do so with a feasible computational complexity. For this purpose, we have been developing a novel algorithm based on a framework that combines notions of causality in philosophy with algorithmic approaches built on model checking and statistical techniques for multiple hypotheses testing. The causal relationships are described in terms of temporal logic formulae, reframing the inference problem in terms of model checking. The logic used, PCTL, allows description of both the time between cause and effect and the probability of this relationship being observed. We show that equipped with these causal formulae with their associated probabilities we may compute the average impact a cause makes to its effect and then discover statistically significant causes through the concepts of multiple hypothesis testing (treating each causal relationship as a hypothesis), and false discovery control. By exploring a well-chosen family of potentially all significant hypotheses with reasonably minimal description length, it is possible to tame the algorithm's computational complexity while exploring the nearly complete search-space of all prima facie causes. We have tested these ideas in a number of domains and illustrate them here with two examples.
Lifting the Veil on al Qaeda: an Inside Story
Valentin-Gabriel Bud?u
Sfera Politicii , 2012,
Abstract: Review of: Omar Nasiri, Inside the Jihad: My Life with Al Qaeda
Feature-by-Feature – Evaluating De Novo Sequence Assembly
Francesco Vezzi, Giuseppe Narzisi, Bud Mishra
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031002
Abstract: The whole-genome sequence assembly (WGSA) problem is among one of the most studied problems in computational biology. Despite the availability of a plethora of tools (i.e., assemblers), all claiming to have solved the WGSA problem, little has been done to systematically compare their accuracy and power. Traditional methods rely on standard metrics and read simulation: while on the one hand, metrics like N50 and number of contigs focus only on size without proportionately emphasizing the information about the correctness of the assembly, comparisons performed on simulated dataset, on the other hand, can be highly biased by the non-realistic assumptions in the underlying read generator. Recently the Feature Response Curve (FRC) method was proposed to assess the overall assembly quality and correctness: FRC transparently captures the trade-offs between contigs' quality against their sizes. Nevertheless, the relationship among the different features and their relative importance remains unknown. In particular, FRC cannot account for the correlation among the different features. We analyzed the correlation among different features in order to better describe their relationships and their importance in gauging assembly quality and correctness. In particular, using multivariate techniques like principal and independent component analysis we were able to estimate the “excess-dimensionality” of the feature space. Moreover, principal component analysis allowed us to show how poorly the acclaimed N50 metric describes the assembly quality. Applying independent component analysis we identified a subset of features that better describe the assemblers performances. We demonstrated that by focusing on a reduced set of highly informative features we can use the FRC curve to better describe and compare the performances of different assemblers. Moreover, as a by-product of our analysis, we discovered how often evaluation based on simulated data, obtained with state of the art simulators, lead to not-so-realistic results.
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