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BackgroundMany important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences and under- or over-representation of certain taxa in a dataset. These schemes aim to assign high weights to sequences that are 'novel' compared to the others in the same dataset, and low weights to sequences that are over-represented.ResultsWe formalise this principle by rigorously defining the evolutionary 'novelty' of a sequence within an alignment. This results in new sequence weights that we call 'phylogenetic novelty scores'. These scores have various desirable properties, and we showcase their use by considering, as an example application, the inference of character frequencies at an alignment column-important, for example, in protein family profiling. We give computationally efficient algorithms for calculating our scores and, using simulations, show that they are versatile and can improve the accuracy of character frequency estimation compared to existing sequence weighting schemes.ConclusionsOur phylogenetic novelty scores can be useful when an evolutionarily meaningful system for adjusting for uneven taxon sampling is desired. They have numerous possible applications, including estimation of evolutionary conservation scores and sequence logos, identification of targets in conservation biology, and improving and measuring sequence alignment accuracy.

Antibiotics with significant environmental toxicity, e.g., tetracyclines (TCs), are often used in large quantities worldwide, with 50–80% of the applied dose ending up in the environment. This study aimed to investigate the effects of exposure to tetracycline hydrochloride (TC) and minocycline hydrochloride (MIN) on L. minor. Our research evaluated the phytotoxicity of the TCs by analyzing plant growth and biomass and evaluating assimilation pigment levels and fluorescence. The research was extended with the ability potential of duckweed as a tool for removing TCs from water/wastewater. The results demonstrated that both TCs influenced Ir, Iy, biomass, and photosynthetic efficiency. The uptake of TC and MIN by duckweed was proportional to the concentration in the growth medium. The TC was absorbed more readily, reaching up to 8.09 mg × g−1 of dry weight (DW) at the highest concentration (19.2 mg × L−1), while MIN reached 6.01 mg × g−1 of DW. As indicated, the consequences of the influence of TC on plants were slightly smaller, in comparison to MIN, while the plants could biosorb this drug, even at the lowest tested concentration. This study has shown that using plants for drug biosorption can be an effective standalone or complementary method for water and wastewater treatment.

Abstract Background Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds. A closed source implementation of a natural product-likeness score, that finds its application in virtual screening, library design and compound selection, has been previously reported by one of us. In this note, we report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications. Results The Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at http://www.myexperiment.org/packs/183.html. It is also available for download as executable standalone java package from http://sourceforge.net/projects/np-likeness/under Academic Free License. Conclusions Our open-source, open-data Natural-Product-Likeness scoring system can be used as a filter for metabolites in Computer Assisted Structure Elucidation or to select natural-product-like molecules from molecular libraries for the use as leads in drug discovery.

Does invention belong in the chemistry classroom? This article attempts to answer this question by describing how invention education first took root in a chemistry class at Ridgewood High School in Ridgewood, NJ, and then expanded to other students with diverse interests to find a solution to two worldwide problems: satisfying the need for safe drinking water and reducing plastic waste. Specifically, it describes the students' journey step-by-step during the COVID-19 pandemic to invent a self-sanitizing and sustainable Solar Aqua Tech water bottle. The concept underlying this invention was to quickly produce hydrogen peroxide (H[subscript 2]O[subscript 2]), a well-known sanitizing agent, on-demand within the confines of a bottle using only water, dissolved oxygen (O[subscript 2]), and solar power to eliminate pathogens in untreated water. Students had to convert this chemistry classroom concept into reality without a prescription and without knowing if their goal was even attainable. Since the journey did not take a linear path but veered in different directions as unexpected problems arose, the students sought guidance from academics, mentors, and local experts. Along the way, they acquired new knowledge with deepened understanding and overarching perspectives. Success was achieved only after many setbacks. In the end, the sense of accomplishment for finding a solution to two global problems instilled confidence in the students that, with empathy, perseverance, and resilience, they are equipped with essential skills to tackle 21st-century challenges. Invention, therefore, can be a valuable complement to the standard chemistry curriculum and is unparalleled in sparking a lifelong passion for learning.

Abstract Background The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego™-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public. Results The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios. Conclusions CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Taverna community and published on myexperiment.org enables molecular scientists to quickly calculate, process and analyse molecular data as typically found in e.g. today's systems biology scenarios.

Abstract Background Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences and under- or over-representation of certain taxa in a dataset. These schemes aim to assign high weights to sequences that are ‘novel’ compared to the others in the same dataset, and low weights to sequences that are over-represented. Results We formalise this principle by rigorously defining the evolutionary ‘novelty’ of a sequence within an alignment. This results in new sequence weights that we call ‘phylogenetic novelty scores’. These scores have various desirable properties, and we showcase their use by considering, as an example application, the inference of character frequencies at an alignment column—important, for example, in protein family profiling. We give computationally efficient algorithms for calculating our scores and, using simulations, show that they are versatile and can improve the accuracy of character frequency estimation compared to existing sequence weighting schemes. Conclusions Our phylogenetic novelty scores can be useful when an evolutionarily meaningful system for adjusting for uneven taxon sampling is desired. They have numerous possible applications, including estimation of evolutionary conservation scores and sequence logos, identification of targets in conservation biology, and improving and measuring sequence alignment accuracy.

Antibiotics with significant environmental toxicity, e.g., tetracyclines (TCs), are often used in large quantities worldwide, with 50–80% of the applied dose ending up in the environment. This study aimed to investigate the effects of exposure to tetracycline hydrochloride (TC) and minocycline hydrochloride (MIN) on L. minor. Our research evaluated the phytotoxicity of the TCs by analyzing plant growth and biomass and evaluating assimilation pigment levels and fluorescence. The research was extended with the ability potential of duckweed as a tool for removing TCs from water/wastewater. The results demonstrated that both TCs influenced Ir, Iy, biomass, and photosynthetic efficiency. The uptake of TC and MIN by duckweed was proportional to the concentration in the growth medium. The TC was absorbed more readily, reaching up to 8.09 mg × g−1 of dry weight (DW) at the highest concentration (19.2 mg × L−1), while MIN reached 6.01 mg × g−1 of DW. As indicated, the consequences of the influence of TC on plants were slightly smaller, in comparison to MIN, while the plants could biosorb this drug, even at the lowest tested concentration. This study has shown that using plants for drug biosorption can be an effective standalone or complementary method for water and wastewater treatment. [ABSTRACT FROM AUTHOR]

Changes in the retail prices of pasteurised milk, purchase prices, and the price relationship between retail prices for pasteurised milk and other food products are analysed for Poland during the period from 2004-2018. In addition, the paper presents factors affecting changes in milk prices in Poland and characterises the Common Agricultural Policy (CAP) on the milk market. The adoption of a long period of analysis allows for the study of periods of both high and low variability. The data analysis uses various methods including the Augmented Dickey-Fuller (ADF) test and the Autoregressive-Moving-Average Model (ARMA). The milk market showed significant response because it was one of the few that was strongly administered by the European Union. These policies led to a significant increase in milk prices in the analysed period. The average price of pasteurised food milk increased by 63% in 2003-2015, and the purchase farm price of milk increased by 91.74%. The situation changed when the production limits were eliminated after 2015. In the initial period after quotas ended, the price of milk decreased and then increased. Similar changes were observed in other EU countries. Even short-term fluctuations associated with economic crises did not significantly affect the milk market.

DuPont™ Exirel™ and Verimark™ insect control contain DuPont™ Cyazypyr™ insecticide, the second active ingredient from the anthranilic diamide class of chemistry, and the first to control a cross-spectrum of insect pests including Lepidoptera, Dipteran leafminers, fruit flies, beetles, whiteflies, thrips, aphids, leafhoppers, psyllids and weevils, while conserving key predators and parasitoids.  Exirel™ and Verimark™ deliver a novel mode of action that impacts insect behavior by impairing muscle function.  Intoxicated insects stop feeding rapidly, resulting in excellent plant protection.  Exirel™ is designed for foliar applications to optimize leaf penetration and spray coverage.  Exirel™ applied at the major flush periods provides excellent protection against Asian citrus psyllid adult and nymphs and citrus leafminer for extended periods, generally 3-4 weeks.

The article presents the subject of public communication in local self-governments in Poland. The possibility of including more inhabitants is the main advantage of the process. The main disadvantage is the difficulty of determining the person actually involved in the consultation. Therefore, the purpose of the article is to present the existing procedures of using the Internet in the process of public consultations. Legal acts and regulations of public consultations indicate the internet as an appropriate communication tool. Most documents do not specify the number of participants in this process. There are many risks when conducting online consultations. Therefore, the most often the quantitative factor is not essential. Online consultations are used to provide information about the project and to gather ideas from residents directly related to the place of planned investments. There are already voting procedures for a civic budget. They are much more difficult and more expensive. However, they give the opportunity to personalize the vote. This will be the main mechanism of social consultations in local self-governments and regional governments in the future.

In view of their advantageous properties (high hardness, good frictional wear resistance, chemical and thermal stability at elevated temperatures), cubic boron nitride (cBN) and tungsten carbide (WC) are commonly used for the fabrication of cutting tools. The composites were consolidated at a temperature of 1100°C under a load of 100 MPa for 10 min. The density of the thus produced material was close to the theoretical value (about 99.6%), and the hardness HV30 was about 1950. The phases identified in the composite were WC, Co, and cBN. Microstructural examinations revealed that numerous trans-crystalline fractures through the cBN particles occurred in the material. The present study is concerned with the wear of the WCCo and WCCo/cBN composites. Comparative tribological examinations were performed in a tribological tester using the ball-on-disc arrangement under the conditions of dry friction. The counterspecimens were steel and Al2O3 balls. The tests were conducted under a unit load of 10 N. After the tests, the surface of the samples was examined to describe the wear mechanisms active in various composite materials.

The first aerial survey conducted within the vicinity of the ancient city of Metsamor and its cemetery detected several promising anomalies in the aerial photos and processed images within and beyond the known limits of the burial ground. The survey results are discussed in this article along with a brief outline of the burial types found in this cemetery.

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Copyright of Annuals of the Administration & Law / Roczniki Administracji i Prawa is the property of Oficyna Wydawnicza Humanitas and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

PAX7 transcription factor plays a crucial role in embryonic myogenesis and in adult muscles in which it secures proper function of satellite cells, including regulation of their self renewal. PAX7 downregulation is necessary for the myogenic differentiation of satellite cells induced after muscle damage, what is prerequisite step for regeneration. Using differentiating pluripotent stem cells we documented that the absence of functional PAX7 facilitates proliferation. Such action is executed by the modulation of the expression of two proteins involved in the DNA methylation, i.e., Dnmt3b and Apobec2. Increase in Dnmt3b expression led to the downregulation of the CDK inhibitors and facilitated cell cycle progression. Changes in Apobec2 expression, on the other hand, differently impacted proliferation/differentiation balance, depending on the experimental model used.