Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Error in Gas Chromatography-Mass Spectrometry–Based Quantification of Hydrolyzed Urinary Steroids

Gas chromatography-mass spectrometry–based metabolite profiling can lead to an understanding of various disease mechanisms as well as to identifying new diagnostic biomarkers by comparing the metabolites related in quantification. However, the unexpected transformation of urinary steroids during enzymatic hydrolysis with Helix pomatia could result in an underestimation or overestimation of their concentrations. A comparison of β-glucurondase extracted from Escherichia coli revealed 18 conversions of 84 steroids tested as an unexpected transformation under hydrolysis with β-glucuronidase/arylsulfatase extracted from Helix pomatia. In addition to the conversion of 3β-hydroxy-5-ene steroids into 3-oxo-4-ene steroids, which has been reported, the transformation of 3β-hydroxy-5α–reduced and 3β-hydroxy-5β–reduced steroids to 3-oxo-5α–reduced and 3-oxo-5β–reduced steroids, respectively, was newly observed. The formation of by-products was in proportion to the concentration of substrates becoming saturated against the enzyme. The substances belonging to these three steroid groups were undetectable at low concentrations, whereas the corresponding by-products were overestimated. These results indicate that the systematic error in the quantification of urinary steroids hydrolyzed with Helix pomatia can lead to a misreading of the clinical implications. All these hydrolysis procedures are suitable for study purposes, and the information can help prevent false evaluations of urinary steroids in clinical studies. Cancer Epidemiol Biomarkers Prev; 19(2); 388–97
Tissue Requirements and DNA Quality Control for Clinical Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Samples: A Mini-Review of Practical Issues

Most molecular pathology laboratories perform mutational analyses to diagnose somatic cancer mutations and evaluate therapeutic options on formalin fixed paraffin embedded (FFPE) samples as daily practice using various methods. Recent studies show that targeted next-generation sequencing (NGS) is a promising diagnostic method with many benefits including simultaneous detection of multiple mutations in various genes in a single test. High quality DNA is essential for an efficient and successful NGS performance. However, low tumor tissue percentage and low DNA quality are the main limitations to use FFPE DNA for NGS assay. We reviewed and discussed the required tissue amount for the NGS assay, the effect of formalin fixation on DNA integrity, and the method for reduction of formalin-induced sequencing artifacts. We also review DNA extraction methods, DNA quality control methods and quality control workflow for nucleic acids and libraries. This review provides an overview for molecular pathology laboratories or researcher considering NGS to detect somatic cancer mutations using small FFPE samples.
In Vitro Model for Studying Malignancy Associated Changes

Malignancy associated changes (MAC) can be defined as subtle morphological and physiologic changes that are found in ostensibly normal cells of patients harboring malignant disease. It has been postulated that MAC have a potential to become a useful tool in detection, diagnosis and prognosis of malignant diseases. An in vitro cell culture model system was designed to study interactions between non‐small cell lung cancer (NSCLC) and the normal bronchial epithelium of the human respiratory tract in vivo to see if the MAC‐like phenomenon can be detected in such a system. In this study we examined changes in nuclear features of normal human bronchial epithelial cells (NHBE) when they were co‐cultured with cells derived from a lung cancer cell line NCI‐H460. Using discriminant function analysis, nuclear features were determined which allow maximal discrimination between normal cells incubated with or without cancerous cells. Our results demonstrate that MAC appear to be specific to changes induced by malignancy, and that these changes differ from those induced by growth factors in the serum. This study provides evidence in support to the hypothesis that MAC are induced by a soluble factor(s) released by malignant cells. Colour figure can be viewed on http://www.esacp. org/acp/2003/25‐2/sun.htm.
Analysis of Gene Expression Data Based on Density and Biological Knowledge

Cluster analysis of gene expression data is one of the most useful tools for identifying biologically relevant groups of genes, however, gene expression data suffer severely from the problems of measurement noise, dimension curse, high redundancy between genes, and the functional annotation of genes is incomplete and imprecise. These properties lead to most of the traditional clustering algorithms are very sensitive to the initialization, and are likely to get the local result, and also made the analysis results lacking of stability, reliability and biological interpretability. In the present article, we propose incorporating the data density and gene functions into distance-based clustering method, which can get more stable and reliable results, especially in discovering gene set with completely unknown function.
The politics of the Earth: Environmental discourses

With its hundred-year history; its global reach; its local interests; its implications for government and industry, science, and humanity; and organizations that range from the mildest of reformers to the most radical of protesters, environmentalism is a difficult subject to organize and elucidate. This is the task John S. Dryzek sets out to accomplish in the second edition of his book The Politics of the Earth: Environmental Discourses. Dryzek understands the challenge. In his introduction, he positions his book as offering a "bigger territory" view of environmental political discourse. He writes, "I will be guided by some analytical devices and distinctions . that give me some confidence in painting such large and complex discursive terrain in broad strokes. I seek vindication only in the plausibility of the stories I tell" (p. 11 ). As backing for these narratives, he offers his impressive 25 years of teaching and writing in the environmental field. Dryzek begins his first chapter with a sharp-eyed introduction to environmental problems. With a snapshot approach, he illustrates the changing political context for environmental concerns: swamps have become wetlands, people have become populations, and the Earth may, after all, be a finite resource. This introduction to environmental issues is simply written and compelling an excellent vehicle for discussion in an upper division environmental studies class. For his "analytical devices and distinctions," Dryzek classifies environmental discourses into a matrix, with the horizontal dimension characterizing the discourse as either reformist or radical in its departure from industrialism. The vertical dimension describes whether the discourse is prosaic (forming assumptions from the
An Evaluation of a Booklet of Ideas to Support Teachers in Thinking About How to Increase the Independence of Dyslexic Children.

Six primary school teachers and two secondary schoolteachers completed a questionnaire asking them to definedyslexia and to rate their confidence levels in supportingdyslexic pupils. Classroom observations were made in theprimary classrooms to look at the strategies already used byteachers and teachers were able to comment on the strategiesthat they found useful. A booklet of ideas was provided andfive of the primary school teachers completed a secondquestionnaire to evaluate its usefulness in guiding theirclassroom practice. A follow-up observation was made in twoclassrooms to compare the strategies being used. Teacherswere found to define dyslexia using constructs that weredifferent to those they used when considering pupils withreading or spelling difficulties. The booklet was found to leadto a significant increase in confidence amongst teachers(p=0.043) and to an increase in the number of strategiesreported to being used. Observations revealed an increase instrategies used by teachers and an increase in pupil on-taskbehaviour in the two classes observed.
Hand-based Interface for Augmented Reality

Augmented reality (AR) is a highly interdisciplinary field which has received increasing attention since late 90s. Basically, it consists of a combination of the real scene viewed by a user and a computer generated image, running in real time. So, AR allows the user to see the real world supplemented, in general, with some information considered as useful, enhancing the users perception and knowledge of the environment. Benefits of reconfigurable hardware for AR have been explored by Luk et al. [4]. However, the wide majority of AR systems have been based so far on PCs or workstations.
Specific regions of the intervening sequences of ,3-globin RNA are resistant to nuclease in 50S heterogeneous nuclear RNA-protein complexes

The specific assembly of heterogeneous nu- clear RNA-protein complexes (hnRNPs) containing precursor (3-globin RNA was Investigated by using the 50S hnRNP released from chicken reticulocyte nuclei by endogenous nuclease. The nuclease-resistant regions were mapped on adult ,8-globin intervening sequences (IYS) at the resolution of nucleotides with an RNA mapping method [Patton, J. R. and Chae, C. -B. (1983) J. Biol. Chem. 258, 3991-3995]. We found that there is one 28-nudeotide-long nuclease-resistant region in the first IVS and there are four nuclease-resistant regions in the second IVS. Of particular interest is the presence in 50S hnRNP of a nuclease-resistant region (24-28 nucleotides long) in both IVS immediately upstream from the putative lariat branch site in an RNA splicing intermediate. Our results demonstrate that hnRNPs containing precursor (3-globin RNA are, like those containing mature (3-globin RNA, assembled in a site-specific manner.
Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory tumor necrosis factor (TNF). The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steady-state total RNA and should be useful in many biological settings.
Controlling size and uniformity of molecularly imprinted nanoparticles using auxiliary template

Molecularly imprinted nanomaterials are gaining substantial importance. As a simple and efficient synthetic method, precipitation polymerization has been used to prepare uniform molecularly imprinted microspheres for numerous template compounds. Despite of its general applicability, the difficulty of obtaining uniform particles for some difficult templates by precipitation polymerization has been reported. In this work, we attempted to produce uniform atrazine‐imprinted nanoparticles using propranolol as an auxiliary template under standard precipitation polymerization condition. When propranolol was added in the prepolymerization mixture for atrazine imprinting, it displayed a significant effect on particle size and size distribution of atrazine‐imprinted polymers. The molecular binding characteristics of the molecularly imprinted polymer (MIP) nanoparticles were found to be dependent on the relative ratios of the two templates. Under an optimal template propranolol–atrazine ratio of 1:3 mol/mol, very uniform imprinted nanoparticles (dH = 106 nm) with a polydispersity index of 0.07 were obtained. The loading of the auxiliary template (propranolol) could be reduced to as low as 5% without sacrificing the uniformity of the MIP nanoparticles. The uniform MIP nanoparticles could be easily encapsulated into polyethylene terephthalate nanofibers using a simple electrospinning technique. The composite nanofibers containing the MIP nanoparticles maintained specific molecular binding capability for both atrazine and propranolol. Copyright © 2012 John Wiley & Sons, Ltd.
Path tracking by a mobile robot equipped with only a downward facing camera

This paper presents a practical path-tracking method for a mobile robot with only a downward camera facing the passage plane. A unique algorithm for tracking and searching ground images with natural texture is used to localize the robot without a feature-point extraction scheme commonly used in other visual odometry methods. In our tracking algorithm, groups of reference pixels are used to detect the relative translation and rotation between frames. Furthermore, a reference pixel group of another shape is registered both to record a path and to correct errors accumulated during localization. All image processing and robot control operations are carried out with low memory consumption for image registration and fast calculation times for completing the searches on a laptop PC. We also describe experimental results in which a vehicle developed by the proposed method repeatedly performed precise path tracking under indoor and outdoor environments.
Are Risky Choices Actually Guided by a Compensatory Process? New Insights from fMRI

The dominant theories about risky decision-making assume that decision conflicts are solved by a compensatory process involving a trade-off of probability against payoff, but it is unclear whether these theories actually represent the events that occur when people make a risky decision. By contrasting a preferential choice with a judgment-based choice that required a compensatory process, we explored the mechanisms underlying risky decision-making. First, using parametric analyses, we identified the dorsomedial prefrontal cortex (dMPFC) as the specific region in charge of task-related conflict in risky decision-making tasks. We also showed that the dMPFC was activated less when judgment-based choices were being made, implying that the conflict experienced during a judgment-based choice was not as strong as the conflict that was experienced during the preferential choice. Our results provide neural evidence that preferential choice cannot be characterized solely as a compensatory process. Thus, questions were raised about whether existing compensatory theories could adequately describe individual risky decisions.
Rifampin-resistant replication of pBR322 derivatives in Escherichia coli cells induced for the SOS response

Replication of plasmid pBR322 in Escherichia coli cells normally requires RNA synthesis and thus is sensitive to rifampin, an inhibitor of RNA polymerase. In cells induced for the SOS response, however, derivatives of pBR322 were found to replicate in the presence of rifampin. This rifampin-resistant replication of pBR322 requires the insertion of certain sequences of DNA. The replication depends on recF+ and DNA polymerase I.
Iterated multi-swarm: a multi-swarm algorithm based on archiving methods

Usually, Multi-Objective Evolutionary Algorithms face serious challengers in handling many objectives problems. This work presents a new Particle Swarm Optimization algorithm, called Iterated Multi-Swarm (I-Multi Swarm), which explores specific characteristics of PSO to face Many-Objective Problems. The algorithm takes advantage of a Multi-Swarm approach to combine different archiving methods aiming to improve convergence to the Pareto-optimal front and diversity of the non-dominated solutions. I-Multi Swarm is evaluated through an empirical analysis that uses a set of many-Objective problems, quality indicators and statistical tests.
Stochasticity and negative feedback lead to pulsed dynamics and distinct gene activity patterns

Gene expression is an inherently stochastic process that depends on the structure of the biochemical regulatory network in which the gene is embedded. Here we study the interplay between stochastic gene switching and the widespread negative feedback regulatory loop. Using a simple hybrid model, we find that stochasticity in gene switching by itself can induce pulses in the system. Furthermore, we find that our simple model is able to reproduce both exponential and peaked distributions of gene active and inactive times similar to those that have been observed experimentally. Our hybrid modelling approach also allows us to link these patterns to the dynamics of the system for each gene state.
The algorithmic imaginary: exploring the ordinary affects of Facebook algorithms

ABSTRACT This article reflects the kinds of situations and spaces where people and algorithms meet. In what situations do people become aware of algorithms? How do they experience and make sense of these algorithms, given their often hidden and invisible nature? To what extent does an awareness of algorithms affect people's use of these platforms, if at all? To help answer these questions, this article examines people's personal stories about the Facebook algorithm through tweets and interviews with 25 ordinary users. To understand the spaces where people and algorithms meet, this article develops the notion of the algorithmic imaginary. It is argued that the algorithmic imaginary – ways of thinking about what algorithms are, what they should be and how they function – is not just productive of different moods and sensations but plays a generative role in moulding the Facebook algorithm itself. Examining how algorithms make people feel, then, seems crucial if we want to understand their social power.
SLCO1A2, SLCO1B1 and SLCO2B1 polymorphisms influences chloroquine and primaquine treatment in Plasmodium vivax malaria

Aim: The association of transporters gene polymorphisms with chloroquine/primaquine malaria treatment response was investigated in a Brazilian population. Patients & methods: Totally, 164 Plasmodium vivax malaria infected patients were included. Generalized estimating equations were performed to determine gene influences on parasitemia and/or gametocytemia clearance over treatment time. Results: Significant interaction between SLCO2B1 genotypes and treatment over time for parasitemia clearance rate on day 2 were observed (p FDR = 0.002). SLCO1A2 and SLCO1B1 gene treatment over time interactions were associated with gametocytemia clearance rate (p FDR = 0.018 and p FDR = 0.024). ABCB1, ABCC4 and SLCO1B3 were not associated with treatment response. Conclusion: The present work presents the first pharmacogenetic report of an association between chloroquine/primaquine responses with OATP transporters.
Antioxidant and Antimicrobial Activities of Ethanol Extracts of Cynara Scolymus (Cynarae folium, Asteraceae Family)

Purpose: Cynara scolymus is a medicinal plant frequently used in traditional medicine for stomach and liver diseases. The purpose of the study was to identify the most suitable extraction solvent for maximum antioxidant and antimicrobial effect of fluidized bed extracts. Methods: The extracts were obtained by conventional maceration and fluidized bed extraction using 25, 50, 75 and 97 % v/v ethanol as solvent. The antioxidant effect of the extracts was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. The quantities of phenols and flavonoids, and the reducing power of the extracts were also determined. The antimicrobial activity of the extracts was tested against different microbial strains using agar well diffusion method. The minimum inhibiting concentration (MIC) of the fluidized bed extract was also determined. Results: The ethanol extract showed the highest antioxidant activity as well as yielded the largest quantity of polyphenolic compounds. For the extract obtained by fluidized bed technique, the optimum concentration of 10 mg/ml gave maximum antioxidant activity of 65.15 %. The MIC values obtained using the freeze-dried extract ranged from 5.0 mg/ml – 15.0 mg/ml. The extracts showed significant inhibitory activity against the tested strains of Listeria innocua CMGB 218, Bacillus cereus CMGB 215 with MIC of 5 mg/ml but showed MIC of 15 mg/ml for the other strains. Conclusion: The results indicate that the freeze-dried extract from Cynara scolymus is capable of yielding nutritional supplements with antioxidant and antimicrobial activities. Keywords: Artichoke, Freeze-drying, Fluidized bed extract, MIC
Hypothesis Test-based Similarity Matching algorithm of time-series data

There were many deficiencies in traditional sequences distance and similarity matching algorithm dealing with multivariate time-series. The paper firstly expounded the definition of time-series, furthermore proposed a new distance measure aimed at multivariate time-series. Secondly it advanced the HTbSM (Hypothesis Test-based Similarity Matching algorithm of multivariate time-series data). The algorithm included two parts: Transform, Hypothesis Test. Finally, an experiment was conducted, showing that the algorithm could do well in the multivariate time-series, as it has advantage of effectiveness, simplicity, robustness, and controllability.
Catenation and specialization for Tcl virtual machine performance

We present techniques for eliminating dispatch overhead in a virtual machine interpreter using a lightweight just-in-time native-code compilation. In the context of the Tcl VM, we convert bytecodes to native Sparc code, by concatenating the native instructions used by the VM to implement each bytecode instruction. We thus eliminate the dispatch loop. Furthermore, immediate arguments of bytecode instructions are substituted into the native code using runtime specialization. Native code output from the C compiler is not amenable to relocation by copying; fix-up of the code is required for correct execution. The dynamic instruction count improvement from eliding dispatch depends on the length in native instructions of each bytecode opcode implementation. These are relatively long in Tcl, but dispatch is still a significant overhead. However, their length also causes our technique to overflow the instruction cache. Furthermore, our native compilation consumes runtime. Some benchmarks run up to three times faster, but roughly half slow down, or exhibit little change.