Creation Of Libraries Research Articles

Building a Library for Catalysts Research Using High‐Throughput Approaches

AbstractThe development of new catalysts is an urgent task in chemistry research because of the increasing demands for higher productivity and efficiency in modern industrial chemistry. High‐throughput (HT) technologies have emerged as powerful accelerators for the discovery of new catalytic materials. Generally, HT techniques involve HT computational screening of catalytic materials and HT experimental approaches. Significant progress has been made in discovering and optimizing catalysts, which demonstrates the speed and economic advantages of HT methods in a matter of process within days and even hours, in contrast with traditional time‐consuming trial and error experiments. From this perspective, the key processes of HT technologies for building a catalysts library are highlighted, including the virtual lab construction based on informatics tools and experimental data lab involving the following processes: 1) design of experiments; 2) reactants prepared manually or automatically; 3) constructing reactor that can well control the variations including materials diversity and reaction conditions (e.g., temperature and reaction time); 4) parallel characterization of fabricated catalysts. Moreover, the correlation between virtual lab and experimental data is discussed to inspire explorations in this field. Furthermore, several remaining challenges of HT technologies accompanied by possible research directions are presented to promote efforts in catalysts library creation.

Curation Principles Derived from the Analysis of the SBOL iGEM Data Set.

As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use. The aim of this work was to improve this situation by creating a curated library of parts from the International Genetically Engineered Machines (iGEM) registry data set. To this end, an analysis of the Synthetic Biology Open Language (SBOL) version of the iGEM registry was carried out using four different approaches-simple statistics, SnapGene autoannotation, SYNBICT autoannotation, and expert analysis-the results of which are presented herein. Key challenges encountered include the use of free text, insufficient part provenance, part duplication, lack of part removal, and insufficient continuous curation. On the basis of these analyses, the focus has shifted from the creation of a curated iGEM part library to instead the extraction of a set of lessons, which are presented here. These lessons can be exploited to facilitate the creation and curation of other part libraries using a simpler and less labor intensive process.

Digitalization as a trend in library development

The purpose of this article is to introduce into the scientific circulation the results of the research work started in 2019 by the Russian State Library (RSL) with the aim to identify, analyze and characterize processes of digitalization of public libraries of the Russian Federation as well as to make the forecast of their further development. In the course of the research, there was done the analysis of normative documents, publications in the professional press and on the sites of Russian and foreign journals, other net actors, accumulating and testing scientific information about digitalization of librarianship; examination of libraries’ sites as points of access to distant library services.The summarization of the significant empirical base made it possible to identify and characterize the main trends in the process of digitalization of public libraries, as well as to conduct a comparative analysis of international and domestic experience in the introduction of digital technologies into library practice.During the first two stages of this scientific project, there was defined the concept of “library digitalization”, studied the content of the process of library digitalization, identified the main avenues and analyzed forms and areas of application of new information technologies in library practice.The results of the research have indicated that digitalization affects the development of all the main areas of library activities. The introduction of digital technologies leads to significant changes in the forms and methods of library work and library communications.There have been identified several main vectors of library digitalization development: digitization of library collections and creation of digital resources; development of the remote user services via the Internet, robotization of library processes and implementation of mobile communication technologies, augmented reality and radio frequency identification. The objectives of the introduction of digital technologies into library practice have been formulated as follows: liberation of library specialists from routine library work for to perform processes that require intellectual and creative abilities. The results of this research have important theoretical and practical significance.

Prospects of Digital Dostoevsky

There were several epochs in history that have altered the life of mankind. The first epoch was when the oral text was written down. The second was when the German scribe Guttenberg invented the printing press, and the handwritten text became printed. Now text is becoming digital, and there is a natural digitalization of all spheres of human activity, including the legacy of Dostoevsky. Modern information technologies create a new type of text that not only preserves the advantages of oral, handwritten and printed text, but also acquires new capabilities. The digital text expands the range of sources, the volume of information, and stimulates new methods of studying the writer's creative work. Despite the fact that electronic libraries, which currently dominate the Internet, present digital copies of Dostoevsky's printed publications, new types of electronic publications and new tools for analyzing not only handwritten and printed, but also digital text, are emerging. The idea of Digital Dostoevsky is being implemented in Petrozavodsk University projects (since 1995), the Institute of Russian Literature of the Russian Academy of Sciences (since 2016), and the University of Toronto (since 2019). Lexicographic work on Dostoevsky's vocabulary is being carried out in digital format at the Russian Language Institute of the Russian Academy of Sciences. The article provides an overview and outlines the prospects for the development of Digital Dostoevsky. An important task of the global Digital Dostoevsky is the creation of national bibliographies and electronic libraries and publication of new sources related to the writer's life and work. It is necessary to create the conditions for optimizing and integrating the existing resources. The digital format allows to actively use new text analysis tools and information technology capabilities for research and educational purposes.

TRANSFORMATION OF NOMADIC EXISTENCE

Annotation. When conducting a study of the national mentality of Kazakhstan, it became necessary to analyze the transformation of the society of the Kazakh people since the formation of the Kazakh Khanate and the modern, independent Republic of Kazakhstan. The determination is made on the basis of the perception of information from the surrounding reality by society. This is the division into auditory and visual (oculocentrism) culture of the Kazakh society. This is confirmed by changes in all forms of culture. The world-setting of the Kazakhs is aimed at contemplating nature, the surrounding reality without changing it, but living with it in complete harmony, respecting and preserving natural resources. Cattle breeding was the main source of livelihood. However, there is a noticeable respect for the animal. We know everything about the culture of Kazakhs from oral folk art. Associations arise primarily related to the nomadic way of life, in unconditional creation of libraries, somehow fixing knowledge. Reflecting on this, there is a need for a return, to the determination of the Turkic culture, to the late and modern, the need to speak about the principle of this division. It should be noted that Kazakh culture, as is clear, did not survive these stages in an instant. This process took place gradually, settling on the subconscious side of the human mind. Listening to being by the Turkic nomads opens before us a whole world full of features associated with the perception of reality, and its no less interesting embodiment in folklore. Key words: oculocentrism, transformations, mentality, visual culture, nomadism, determination.

The role of compaction simulator equipment in formulation design

The assessment of the compaction performances of pharmaceutical powders is an important aspect of tablet product design, development and manufacturing. Compaction simulators have potential applications in pharmaceutical research and development in terms of studying basic compaction mechanisms, troubleshooting, various process variables, compaction data library creation, scale-up parameters, and fingerprinting of new active pharmaceutical ingredients (APIs) or excipients. The upscaling of the compaction process between early R&D and production can be time-consuming and costly, resulting in a long time-to-market and shorter commercial lifecycles. Due to the limited availability and high price of a new APIs during early drug development phases, compaction simulators have proven highly valuable as the dwell time and punch speed can be set accurately to mimic bottom and upper punch movement on a rotary tablet press. Many issues inherent in the formula ingredients or acquired from previous processes can be avoided or reduced if applied correctly. However, if adequate attention is not paid to understanding the compaction behaviour of what is being pressed, this process may also be the source of several other problems. Pharmaceutical scientists now use a variety of instrumented presses to produce robust tablet formulations. They allow scientists to conduct experiments for in-depth analysis of compaction characteristics of pharmaceutical materials with great efficiency in terms of time, expense, and knowledge gained. The ability to use simulators for anything from early formulation studies to manufacturing troubleshooting makes them invaluable, particularly in light of the recent Process Analytical Technology (PAT)/Ouality by design (QbD) phenomenon.

LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design.

Because of the strong relationship between the desired molecular activity and its structural core, the screening of focused, core-sharing chemical libraries is a key step in lead optimization. Despite the plethora of current research focused on in silico methods for molecule generation, to our knowledge, no tool capable of designing such libraries has been proposed. In this work, we present a novel tool for de novo drug design called LibINVENT. It is capable of rapidly proposing chemical libraries of compounds sharing the same core while maximizing a range of desirable properties. To further help the process of designing focused libraries, the user can list specific chemical reactions that can be used for the library creation. LibINVENT is therefore a flexible tool for generating virtual chemical libraries for lead optimization in a broad range of scenarios. Additionally, the shared core ensures that the compounds in the library are similar, possess desirable properties, and can also be synthesized under the same or similar conditions. The LibINVENT code is freely available in our public repository at https://github.com/MolecularAI/Lib-INVENT. The code necessary for data preprocessing is further available at: https://github.com/MolecularAI/Lib-INVENT-dataset.

Transcript expression profiling of fibromelanosis-related genes in black-bone chickens

ABSTRACT 1. The aim of the present study was to identify differentially expressed genes (DEGs) and metabolic pathways involved in this phenotype. Fibromelanosis is the most striking feature of black-bone chickens, such as the Silkie and Dongxiang indigenous breeds. Due to the accumulation of eumelanin in connective tissues, fibromelanosis manifests as black colouration of the skin, muscles, gut, and periosteum. Studies on fibromelanosis can provide useful information pertaining to human diseases and offer commercial value to the poultry industry. However, the genetic basis of fibromelanosis remains unclear. 2. Digital gene expression analysis was performed on black and white skin samples collected from the HW1 black-bone chicken line to detect differences in genome-wide expression patterns. A total of >30 billion bp were sequenced, and 2,707,926,466 bp and 2,948,782,964 bp of clean data obtained for creation of libraries for black and white skin, respectively. In total, 252 DEGs from 15,508 mapped genes were identified with 83 up-regulated in white skin and 169 up-regulated in black skin. 3. Gene ontology analysis highlighted that genes from the extracellular region and associated components were abundant among the DEGs. Pathway analysis revealed that many DEGs were linked to amino acid metabolism and the immune system. qRT-PCR validation using 14 genes showed good conformity with the sequence analysis of fibromelanosis-related genes. 4. The results showed that L-dopachrometautomerase precursor (DCT), tyrosine aminotransferase (TAT), 4-hydroxyphenylpyruvate dioxygenase (HPD) from the tyrosine metabolism pathway, coagulation factor II (F2), fibrinogen beta chain (FGB), plasminogen (PLG) and complement component 7 (C7) from the complement and coagulation cascades were important genes in the fibromelanosis process in black-bone chickens. These candidate genes require further correlation analysis and functional verification.

Model Libraries: Historical Outline of the Project

The article presents the history of interaction between the government authorities and the library and information sector in the project of development of municipal libraries. The project resulted in the “model libraries”. The project has been operating since the early 2000s. The purpose of the article is to reveal the implementation and analyse the support at the level of federal and regional government management of the program until 2018 (the start of work within the frames of the National project “Culture”). The author presents periodization of the project, as well as quantitative characteristics and approaches to the understanding the concept of “model library”.Model library is a public library of municipal level that has standard and optimal set of material and information resources. At the same time, there is no approved definition of this phenomenon. It is assumed that the model rural library in its functions, content and equipment meets international and domestic standards and serves as a model for other institutions. The “model” indicators are reflected in the “Model Standard for Public Library Services”.The project on creation of model libraries on the basis of municipal public libraries in rural areas of Russia started in 2002 with the emergence of the all-Russian project “Creation of model public libraries in rural areas”. Since 2012, funding under the federal target program “Culture of Russia (2012—2018)” is carried out in the form of subsidies allocated on a competitive basis. The project became a “catalyst” for modernization processes in rural libraries of Russian regions. The transformation program included the following stages: repair and equipment of the library premises; acquisition of books and electronic publications; conducting training seminars for staff. The rural model library targeted the goals of ensuring equal and free access to information, creation of a comfortable library space, etc.After the approval of the “Model Standard for Public Library Services” (2014), it was decided to test its feasibility by creating so-called “pilot libraries of a new type”. According to this document, model libraries are intellectual centres equipped with high speed Internet, access to modern domestic information resources, which should provide access points to the National Electronic Library.The regional leaders in creation of model libraries are the Republic of Chuvashia, the Belgorod Region, the Republic of Bashkortostan, the Kursk Region and the Republic of Mari El. As of January 1, 2019, there were 3,310 model libraries operating in the country. The creation of model municipal libraries has become one of the departmental projects of the National project “Culture”.

Methods for enzyme library creation: Which one will you choose?: A guide for novices and experts to introduce genetic diversity.

Enzyme engineering allows to explore sequence diversity in search for new properties. The scientific literature is populated with methods to create enzyme libraries for engineering purposes, however, choosing a suitable method for the creation of mutant libraries can be daunting, in particular for the novices. Here, we address both novices and experts: how can one enter the arena of enzyme library design and what guidelines can advanced users apply to select strategies best suited to their purpose? Section I is dedicated to the novices and presents an overview of established and standard methods for library creation, as well as available commercial solutions. The expert will discover an up-to-date tool to freshen up their repertoire (Section I) and learn of the newest methods that are likely to become a mainstay (Section II). We focus primarily on in vitro methods, presenting the advantages of each method. Our ultimate aim is to offer a selection of methods/strategies that we believe to be most useful to the enzyme engineer, whether a first-timer or a seasoned user.

Abstract 272: Glycomics: Protein glycosylation changes in the pathogenesis of head and neck cancer

Abstract Background: Glycosylation is the most common post-translational modification of proteins, and glycosylation changes at cell surfaces are frequently associated with malignant epithelia. These affect many functions including proliferation, motility and invasiveness, increasing the propensity to metastasise. Many head & neck squamous cell carcinomata (HNSCC), especially those originating in the lymphoid mucosa of the oropharynx, are driven by so-called high risk genotypes of Human Papillomavirus (HPV). Five-year survival remains poor, averaging around 50% globally: this is partly related to late diagnosis. Specific protein glycosylation signatures on malignant keratinocytes have promise as diagnostic and prognostic markers and as therapeutic targets. Here we begin creation of a glyco-fingerprint library mapping the glyco-space of HNSCC. Materials and methods: Six established HNSCC cell lines were used to capture the qualitative and semi-quantitative profile of the N- and O-glycome using the well-established porous graphitized carbon (PGC) glycomics approach. Furthermore, we attempted to evaluate the effect sialylation has on HNSCC cell migration by enzymatically removing sialic acid residues from cell surface glycoconjugates. Therefore, we used the enzyme neuraminidase to remove sialic acids from HNSCC cells and measured cell proliferation rates by using incucyte. Results: In Human Papillomavirus (HPV) negative HNSCC cell lines, 37-41% of cells carried oligomannoses on their surfaces compared to 45% in HPV+ cell lines. Sialylated N-glycan were the most abundant type of N-glycan, contributing to >40% of the N-glycome in the HPV negative cell lines: but just 32-38% in HPV+ cell lines; di- and tri-sialylated forms were most frequent. The majority of complex type N-glycans (33%) carried core-fucose residues with just minor levels (<3%) of Lewis-type fucosylation identified. We also observed unusual types of oligomannose N-glycans carrying core-fucose residues. Enzymatic sialic acid removal resulted in 40% reduction in cell doubling numbers. Conclusion: This first systematic mapping reveals diverse glycosylation of head and neck cancer cell lines with high levels of core fucosylation and sialylation. Differences between HPV positive and negative cells may partly explain the comparatively good prognosis of HPV-driven HNC. This mapping forms the basis of histopathological profiling of real tumours which might have prognostic potential and suggest targets for immunotherapy. Removal of sialic acids resulted in decreased cell proliferation in vitro, indicating the fundamental role of protein glycosylation in the pathogenesis of HNC. Citation Format: Mohammad Rasheduzzaman, Xi Zhang, Riccardo Dolcetti, Liz Kenny, Newell W. Johnson, Daniel Kolarich, Chamindie Punyadeera. Glycomics: Protein glycosylation changes in the pathogenesis of head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 272.

Supercomputing in Python With Legate

Legate is a recently developed software system for constructing scalable simulation and data analysis programs using convenient, familiar notation. It demonstrates how coupling Python, with a runtime system originally designed for high-performance computing, can enable the creation of libraries that mimic the familiar interface of NumPy and Pandas for execution on both desktops and supercomputers.

Роль информационно-ресурсных центров в развитии мировоззрения общества

The article reveals the predominance of university libraries, which took on an educational function and played a significant role in the dissemination of knowledge and the development of society. The author lists the history and sequence of the creation of university libraries in the world and in Uzbekistan, where he also points to the library of the Turkestan People’s University, which became the ancestor of higher education in Middle Asia and Kazakhstan. About the current stage of development of information resource centers in the country and abroad, and also indicates the main directions that contribute to the full implementation of the role and tasks of information resource centers

Diastereoselective Synthesis of Spirocyclic Ether from ortho‐Carbonylarylacetylenols via Silver‐Catalyzed Cyclization under Acidic Conditions

Abstractortho‐Carbonylarylacetylenol, can be utilized for the synthesis of several important core structures. In this work, a method is developed for the diastereoselective synthesis of spirocyclic ethers using a silver catalyst under the presence of acid. This protocol can be applied to a variety of substrates resulting in the corresponding products in 35–97% yields with good diastereoselectivity. The proposed reaction mechanisms and stereoselectivity outcome of the corresponding products are investigated using DFT calculation. This current protocol can be applied to a broad range of substrates which would be useful for the creation of libraries of spirocylic ethersmagnified image

Rapid Assessment of Anthocyanins Content of Onion Waste through Visible-Near-Short-Wave and Mid-Infrared Spectroscopy Combined with Machine Learning Techniques

A sustainable process for valorization of onion waste would need to entail preliminary sorting out of exhausted or suboptimal material as part of decision-making. In the present study, an approach for monitoring red onion skin (OS) phenolic composition was investigated through Visible Near-Short-Wave infrared (VNIR-SWIR) (350–2500 nm) and Fourier-Transform-Mid-Infrared (FT-MIR) (4000–600 cm−1) spectral analyses and Machine-Learning (ML) methods. Our stepwise approach consisted of: (i) chemical analyses to obtain reference values for Total Phenolic Content (TPC) and Total Monomeric Anthocyanin Content (TAC); (ii) spectroscopic analysis and creation of OS spectral libraries; (iii) generation of calibration and validation datasets; (iv) spectral exploratory analysis and regression modeling via several ML algorithms; and (v) model performance evaluation. Among all, the k-nearest neighbors model from 1st derivative VNIR-SWIR spectra at 350–2500 nm resulted promising for the prediction of TAC (R2 = 0.82, RMSE = 0.52 and RPIQ = 3.56). The 2nd derivative FT-MIR spectral fingerprint among 600–900 and 1500–1600 cm−1 proved more informative about the inherent phenolic composition of OS. Overall, the diagnostic value and predictive accuracy of our spectral data support the perspective of employing non-destructive spectroscopic tools in real-time quality control of onion waste.

Flynn’s Reconciliation

A large portion of the recent performance increase in the High Performance Computing (HPC) and Machine Learning (ML) domains is fueled by accelerator cards. Many popular ML frameworks support accelerators by organizing computations as a computational graph over a set of highly optimized, batched general-purpose kernels. While this approach simplifies the kernels’ implementation for each individual accelerator, the increasing heterogeneity among accelerator architectures for HPC complicates the creation of portable and extensible libraries of such kernels. Therefore, using a generalization of the CUDA community’s warp register cache programming idiom, we propose a new programming idiom (CoRe) and a virtual architecture model (PIRCH), abstracting over SIMD and SIMT paradigms. We define and automate the mapping process from a single source to PIRCH’s intermediate representation and develop backends that issue code for three different architectures: Intel AVX512, NVIDIA GPUs, and NEC SX-Aurora. Code generated by our source-to-source compiler for batched kernels, borG, competes favorably with vendor-tuned libraries and is up to 2× faster than hand-tuned kernels across architectures.

Library Creation of Ultrasmall Multi‐metallic Nanoparticles Confined in Mesoporous MFI Zeolites

AbstractThe development of materials integrated with ultrasmall multi‐metal nanoparticles (UMMNs) and mesoporous zeolite is a considerable challenge in chemistry and materials science. We designed a trifunctional surfactant, in which the pyridyl benzimidazole in the hydrophobic tail generates the mesopores through π–π stacking; the diquaternary ammonium in the hydrophilic headgroup direct the formation of MFI zeolite sheets and the nitrogen atoms in the heterocyclic rings coordinate with various metal ions to form UMMNs confined in the zeolite matrix after calcination and reduction. A library of 56 UMMNs confined within both micropores and mesopores of MFI zeolites (MMZs) with 4 mono‐, 14 bi‐ and 38 tri‐metallic nanoparticles (sizes of 1.3–4.7 nm) of combinations of Rh, Pd, Pt, Au, Fe, Co, Ni, Cu and Zn were made. An improved catalytic performance was exhibited in the sequence of Rh‐MMZ<Rh/Pt‐MMZ<Rh/Pt/Ni‐MMZ for the mild oxidation of methane to methanol or liquid acid.

Library Creation of Ultrasmall Multi-metallic Nanoparticles Confined in Mesoporous MFI Zeolites.

The development of materials integrated with ultrasmall multi-metal nanoparticles (UMMNs) and mesoporous zeolite is a considerable challenge in chemistry and materials science. We designed a trifunctional surfactant, in which the pyridyl benzimidazole in the hydrophobic tail generates the mesopores through π-π stacking; the diquaternary ammonium in the hydrophilic headgroup direct the formation of MFI zeolite sheets and the nitrogen atoms in the heterocyclic rings coordinate with various metal ions to form UMMNs confined in the zeolite matrix after calcination and reduction. A library of 56 UMMNs confined within both micropores and mesopores of MFI zeolites (MMZs) with 4 mono-, 14 bi- and 38 tri-metallic nanoparticles (sizes of 1.3-4.7 nm) of combinations of Rh, Pd, Pt, Au, Fe, Co, Ni, Cu and Zn were made. An improved catalytic performance was exhibited in the sequence of Rh-MMZ<Rh/Pt-MMZ<Rh/Pt/Ni-MMZ for the mild oxidation of methane to methanol or liquid acid.

Electrosynthesis of Stable Betulin‐Derived Nitrile Oxides and their Application in Synthesis of Cytostatic Lupane‐Type Triterpenoid‐Isoxazole Conjugates

AbstractNovel lupane‐type triterpenoid‐isoxazole conjugates were designed by direct placing of isoxazole linker at C(17) of triterpenoid. The suggested synthetic sequence demonstrates successful combination of electro‐organic synthesis and conventional approaches. TEMPO‐mediated electrooxidation of betulin to betulinal was developed and optimized at boron‐doped diamond anodes with potassium acetate as inexpensive supporting electrolyte. Betulinal‐derived oxime was further selectively electro‐oxidized at a graphite anode to nitrile oxide, which proved to be stable and isolable species. The same reaction sequence was performed with 3β‐lupane‐3,28‐diol. Nitrile oxides were characterized by 15N NMR and X‐ray crystallography. The isolable nitrile oxides allowed creation of isoxazole library by 1,3‐dipolar cycloaddition reactions with various alkynes. Some of the title conjugates exhibit cytostatic properties against breast cancer cell line MCF7, glioblastoma multiform cell line U‐87 MG and lung carcinoma cell line A549 with growth inhibition (GI50) concentrations up to 11 μm, while being harmless to immortalized human fibroblasts hTERT (GI50 &gt;100 μm).

A NUMERICAL STUDY ON POLAR RING GALAXY (PRG) FORMATION

The association between galaxies is a phenomenon frequently occurring in the universe. Systems called Polar Ring Galaxies (PRGs) can be built for certain interactions. These structures consist of a galaxy known as a host and a ring of gas and stars surrounding a plane nearly perpendicular to its main axis. This research has contributed to the creation of a first library of N-body simulations, to study the parameters required to construct PRGs. A library of this kind is continuously expanding with new simulations based on these first findings. The inherent secular processes of isolated galaxies cannot give rise to this PRG geometry. Such systems are (i) created by galaxy interactions or (ii) by the introduction of cold gas from interstellar filaments within a galaxy. The most popular mechanisms are thought to be (i), and we are interested in this project, particularly where gas from one galaxy to another is introduced, without the need for a fusion. For formation of interaction, orbits with particular geometries are required in order to attach matter to form a polar ring. We review various mass ratios, inclinations and orbital energies in our society. The database which will be developed with the simulation results will contribute to future research on the interaction between galaxies, especially polar rings.