bluuebunny/crossref_metadata_2025_split huggingface dataset:
Сторонники соборной экклесиологии в мире греческого православия с 2018 г.
Authors: Шлёнов Дионисий 
Published: January 2025

В статье анализируются взгляды грекоязычных богословов, которые, начиная с 2018 г., то есть после предоставления автокефалии украинским раскольникам Константинопольским Патриархатом, стали поддерживать соборную позицию Русской Православной Церкви. В начале излагаются взгляды иерархов Элладской Православной Церкви, а также выдающихся представителей Кипрской и Албанской Поместных Церквей, а именно митр. Никифора и архиеп. Анастасия соответственно. Отдельно рассматриваются ключевые публикации и высказывания клириков и мирян Элладской Православной Церкви как менее, так и более радикальные. Следует отметить, что в настоящее время дискуссия ослабла в силу очень сильного давления официальной государственной и церковной власти, хотя неприятие неправомочных мер остаётся достаточно большим и среди подвизающихся на Святой Афонской Горе, и среди духовенства и прихожан храмов Греции и Кипра. Значительная часть представителей официальной иерархии не приняла во внимание данные призывы, что не означает поражения истины, которая остаётся таковой при любых обстоятельствах.
The article analyzes the views of Greek-speaking theologians who, starting in 2018, that is, after the granting of autocephaly to Ukrainian schismatics by the Patriarchate of Constantinople, began to support the conciliar position of the Russian Orthodox Church. At the beginning, the views of the hierarchs of the Greek Orthodox Church, as well as prominent representatives of the Cypriot and Albanian Local Churches, namely Met. Nicephorus and Archbishop. Anastasia accordingly. Key publications and statements of clergy and laity of the Greek Orthodox Church, both less and more radical, are examined separately. It should be noted that at present the discussion has weakened due to very strong pressure from the official state and church authorities, although the rejection of unauthorized measures remains quite large among those who labor on Mount Athos, and among the clergy and parishioners of the temples of Greece and Cyprus. A significant part of the representatives of the official hierarchy did not take these calls into account, which does not mean a defeat of the truth, which remains so under any circumstances.
Протоирей Александр Павлович Смирнов как ректор Московских духовных школ
Authors: Кечкин Иоанн / Иван Эдуардович 
Published: January 2025

В статье исследуется малоизученная деятельность митрофорного протоиерея Александра Павловича Смирнова на посту ректора Московских духовных школ (1949–1950). Известный московский пастырь являлся одним из ближайших помощников патриарха Сергия (Страгородского) и патриарха Алексия I (Симанского). Главными источниками для статьи послужили малоизученные архивные материалы, сохранившие сведения о жизни московских духовных школ того времени: протоколы заседаний Учёного совета академии и семинарии, годовые отчёты и личные дела преподавателей. Определяющим источником стало личное дело протоиерея А. П. Смирнова, хранящееся в архиве Московской духовной академии. С помощью сравнительного метода изучения архивных данных, воспоминаний современников и других источников в статье была предпринята попытка восстановить максимально полную картину деятельности протоиерея А. П. Смирнова в должности ректора Московских духовных школ.
The article is devoted to the little-studied activity of the famous Moscow pastor Archpriest Alexander Pavlovich Smirnov as Rector of the Moscow Theological Schools (1949–1950). Mitred Archpriest A. P. Smirnov (1888–1950) was one of the closest aides of Patriarch Sergius (Stragorodsky) and Patriarch Alexy I (Simansky) in the 1940s. In the last period of his life Fr. Alexander headed the Moscow Theological Schools. For the theological school, it was a time of formation and development within the walls of the Trinity-Sergius Lavra, and the rector's work continued the best endeavors of his predecessors. The main sources for the article were little-studied archival materials that preserved information about the life of Moscow theological schools of that time: minutes of meetings of the Academic Council of the Academy and Seminary, annual reports and personal files of teachers. The determining source was the personal file of Fr. A. P. Smirnov, kept in the archives of the Moscow Theological Academy, on the basis of which it was possible to learn the details of his early biography and activities at the Academy. Based on a comparative method of studying archival data, memoirs of contemporaries, and other sources, the article attempts to reconstruct the fullest possible picture of Fr. A. P. Smirnov’s activities as rector of the Moscow Theological Schools.
Текстология списков памятника славяно-русской гимнографии XV в. «Кондаки и Икосы свт. Иоанну Златоусту»
Authors: Перминов Иоанн 
Published: January 2025

Целью статьи является рассмотрение характера отношений между списками литературного памятника «Кондаки и Икосы свт. Иоанну Златоусту». В результате изучения списков автор делает вывод, что текст довольно стабилен, лишь один список имеет признаки редакторской правки. Среди остальных списков выявлен ряд незначительных изменений текста, позволяющих выделить два извода памятника. Два старших списка происходят от одного протографа и имеют прямую родственную связь. Группа младших списков происходит от одного протографа и не имеет признаков систематической правки, однако заметна тенденция к грамматической архаизации текста и к прояснению смыслов через изменение книжных форм церковнославянского текста на формы разговорного русского языка.
The purpose of the article is to consider the nature of the relationship between the lists of the literary monument «Kontakions and Oikoi to St. John Chrysostom». As a result of studying the lists, the author concludes that the text is rather stable, only one list has signs of editorial editing. Among the other folios a number of insignificant changes in the text are revealed, which allow us to distinguish two varieties of the monument. The two older lists come from the same protograph and have a direct kinship. The group of younger folios comes from one protograph and has no signs of systematic editing, but there is a tendency to grammatical archaisation of the text and to clarification of meanings by changing the book forms of the Church Slavonic text into the forms of colloquial Russian.
PENINGKATAN PRODUKTIVITAS SPINNING MELALUI PERANCANGAN ALAT CLEANING DRAFTING ROLL MODEL BARU PADA MESIN RING SPINNING
Authors: Supriatna Nandang , Rochman Didit Damur 
Published: January 2025

Perancangan alat cleaning drafting roll model baru pada mesin ring spinning, guna meningkatkan efektivitas dan efisiensi kerja karyawan di PT Danar Mas-2, merupakan tujuan dari penelitian ini proses pembersihan area drafting roll yang dilakukan secara manual menggunakan bambu kilik terbukti kurang efektif dan efisien, sehingga diperlukan inovasi dalam bentuk alat baru yang mampu menyelesaikan tugas ini dengan lebih baik. Pengumpulan informasi awal, perancangan alat, pengembangan alat, pengetesan awal, perbaikan rancangan alat, pengetesan di produksi dan evaluasi keefektifan alat, ini semua merupakan diantaranya beberapa tahapan yang harus dijalankan pada penelitian ini. Uji coba dilakukan pada mesin Ring Spinning Frame dengan pengambilan sampel cleaning area 100 spindle per orang. Effisiensi kerja karyawan dan dampak alat terhadap kualitas benang yang dihasilkan diukur dan dianalisa menggunakan dua data yaitu quantitave analysis serta qualitative analysis. Hasil penelitian menunjukkan bahwa alat cleaning drafting roll model baru yang berbasis pneumatik ini dapat meningkatkan efisiensi kerja karyawan dan memberikan dampak positif terhadap kualitas produksi benang. Kontribusi secara efektif untuk perusahaan dalam meningkatkan jumlah produksi dan kualitas yang dihasilkan merupakan salah satu alasan sehingga alat ini rancang.
On improving the performance of utility‐based wireless fair scheduling through a combination of adaptive FEC and ARQ
Authors: Gao Xia , Nandagopal Thyagarajan , Bharghavan Vaduvur 
Published: January 2025

The increasing number of wireless data users and the deployment of broadband wireless networks have brought the issue of providing fair channel access to the forefront. Wireless fair scheduling algorithms must deal with unique domain‐specific issues such as location‐dependent and bursty channel error. In the past, a number of scheduling disciplines have been proposed for approximating fluid fair queueing in wireless channels, but using only the ARQ‐based link‐layer retransmit model (Bhagwat et al., in: IEEE INFOCOM, 1996; Lu et al., in: ACM SIGCOMM, 1997; Ng et al., in: IEEE INFOCOM, 1998; Lu et al., WINET 6, 2000, pp. 323–343; Nandagopal et al., in: ACM MOBICOM, 1999). In this work, we generalize past work in three key ways: (a) we use the notion of ‘utility‐based’ fair scheduling, wherein the goal of the scheduler is to serve flows in a way that maximizes the aggregate utility of the system, (b) we combine the techniques of FEC and ARQ in a generalized framework in which different scheduling disciplines can be realized by mixing and matching component algorithms within the framework, and (c) we support the notion of ‘application level fairness’ when flows see different channel error probabilities. Specifically, we explore the combination of adaptive FEC and ARQ‐based schemes within the utility‐based wireless fair scheduling paradigm. We show through simulation and analysis that this combination enables the scheduling disciplines to optimize the aggregate system utility and achieve application level fairness, while handling varying channel errors effectively.
Network security policy refinement process: Expression and analysis
Authors: Laborde Romain , Barrère François , Benzekri Abdelmalek 
Published: January 2025

Today, users need to access their granted services from anywhere and at any time. Network security management must evolve to satisfy these requirements. The policy based network management approach proposes to separate the rules that govern the system from the functionalities provided by it. Nevertheless, the policy rules should be consistent, correct against the objectives and enforceable onto the devices. This problem becomes complex considering the dependencies of the rules – each rule on a device can impact another rule on another device – and each device needs specific configuration according to the technologies implemented. This article presents a formal framework for the refinement of network security management information. It includes three abstraction levels: the network security objectives, the network security tactics and the network security devices configurations. The information models of each abstraction level are formally specified and analysed (consistency, correctness and feasibility). A WBEM implementation of the formal refinement framework proves its feasibility in management architectures.
Analysis of the burst loss rate in OBS rings with depth limited optical buffers
Authors: Xu Huadong , Fan Ge 
Published: January 2025

Optical Burst Switching (OBS) is considered as the promised solution for next generation backbone networks, but the high burst loss rate caused by the burst contention is a great hindrance to the practical use. The authors proposed a new way to solve the burst contentions in OBS rings. As illustrated in the paper, basing the optical buffers with depth about the maximum Data Burst (DB) size and a proper wavelengths selection strategy for the local DBs the burst loss rate in an OBS ring can be decreased to a negligible level. So buffer insertion, the most successful method for asynchronous packet switching, can be adopted in OBS ring by an acceptable cost.
Comparison of Protein Structures Reveals Monophyletic Origin of	the AdoMet-Dependent Methyltransferase Family and Mechanistic Convergence	Rather than Recent Differentiation of N4-Cytosine and N6-Adenine DNA	Methylation
Authors: Bujnicki Janusz M. 
Published: January 2025

Phylogenetic analysis of the S-adenosyl-L-methionine-dependent methyltransferases was performed based on similarity of positions of main chain á-carbon atoms in published structures of members of this superfamily. The evolutionary tree was inferred and the problem of mono/polyphyletic origin of DNA methyltransferases from the Rossmann-fold enzymes was solved, bridging two seemingly antithetical hypotheses. The comparison of protein structures provides evidence for an evolutionary link between widely diverged subfamilies of RNA and DNA N6-adenine methyltransferases and argues against the close homology of N6-adenine and N4-cytosine methyltransferases, apparent from biochemical data and comparison of fragments of sequences. Such evolutionary analysis of methyltransferases has never been published yet in the literature and will guide further phylogenetical studies based on both sequence and structure comparison.
Curved DNA in Promoter Sequences
Authors: Gabrielian Andrei E. , Landsman David , Bolshoy Alexander 
Published: January 2025

Sequence-dependent DNA curvature is known to play an important role in initiation of transcription of many genes. We compared the distribution of predicted intrinsic curvature of Escherichia coli and human promoter sequences with the distribution of curvature of randomly selected coding and non-coding fragments from these organisms. Different methods of curvature calculation were found to yield mostly similar overall tendencies of DNA curvature in all groups of sequences. According to all methods of calculation, E. coli promoters were found to be more curved than coding sequences from the same genome and random sequences with the same nucleotide composition. By contrast, the average curvature of human promoter sequences was only marginally greater than the average curvature of human coding sequences. Non-coding intron sequences were found to be the most curved of the human sequences examined. Based on these observations, we hypothesize about the role of DNA curvature in promoter sequences.
Using Prior Knowledge to Improve Genetic Network Reconstruction	from Microarray Data
Authors: Le Phillip P. , Bahl Amit , Ungar Lyle H. 
Published: January 2025

The use of Bayesian Network methods to recover transcriptional regulatory networks from static microarray data is an active area of bioinformatics research. However, early work in this area lacked realistic analysis of the effects of data set size on learning performance and ignored the potentially immense benefits of using prior biological knowledge. More recent work which has utilized such information has tended to focus on qualitative descriptions of the results. In this paper, we construct a detailed, realistic model for glucose homeostasis and use this model to generate static, synthetic gene expression data. We then use a Bayesian Network method to reconstruct this genetic network from the synthetic microarray data utilizing various amounts and types of prior knowledge. By quantitatively analyzing the effects of data set size and the incorporation of different types of prior biological knowledge on our ability to reconstruct the original network, we show that characteristic portions of genetic networks can be reconstructed from microarray data. Incorporating prior knowledge into the learning scheme greatly reduces the data required, allowing these reverse engineering techniques to be used to learn regulatory interactions from microarray data sets of realistic size.
Selecting SNPs for Association Studies Based on Population Frequencies: A Novel Interactive Tool and Its Application to Polygenic Diseases
Authors: Möller Steffen , Koczan Dirk , Serrano-Fernandez Pablo , Zettl Uwe K. , Thiesen Hans-Jürgen , Ibrahim Saleh M. 
Published: January 2025

Common complex polygenic diseases as autoimmune diseases have not been completely understood on a molecular level. While many genes are known to be involved in the pathways responsible for the phenotype, explicit causes for the susceptibility of the disease remain to be elucidated. The susceptibility to disease is thought to be the result of genetic epistatic interactions between common polymorphic genes. This polymorphism is mostly caused by single nucleotide polymorphisms (SNPs). Human subpopulations are known to differ in the susceptibility to the diseases and generally in the distribution of single nucleotide polymorphisms. The here presented approach retrieves SNPs with the most divergent frequencies for selected human subpopulations to help defining properties for the experimental verification of SNPs within defined regions. A web-accessible program implementing this approach was evaluated for multiple sclerosis (MS), a common human polygenic disease. A link to a summary of data from "The SNP Consortium" (TSC) with sex-dependencies of SNPs is available. Associations of SNPs to genes, genetic markers and chromosomal loci are retrieved from the Ensembl project. This tool is recommended to be used in conjunction with microarray analyses or marker association studies that link genes or chromosomal loci to particular diseases.
FASSM: Enhanced Function Association in Whole Genome Analysis	Using Sequence and Structural Motifs
Authors: Gaurav Kumar , Gupta Nitin , Sowdhamini Ramanathan 
Published: January 2025

We present an algorithm to detect remote homology, which arises through circular permutation and discontinuous domains. It is also helpful in detecting small domain proteins that are characterized by few conserved residues. The input to the algorithm is a set of multiply aligned protein sequence profiles. This method, coded as FASSM, examines the sequence conservation and positions of protein family signatures or motifs for the annotation of protein sequences and to facilitate the analysis of their domains. The overall coverage of FASSM is 93% in comparison to other validation tools like HMM and IMPALA. The method is especially useful for difficult relationships such as discontinuous domains during whole-genome surveys and is demonstrated to perform accurate family associations at sequence identities as low as 15%. Availability: Available upon request from the authors.
RANDNA: A Random DNA Sequence Generator
Authors: Piva Francesco , Principato Giovanni 
Published: January 2025

Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.
Protein Subcellular Localization Prediction Using a Hybrid of	Similarity Search and Error-Correcting Output Code Techniques That Produces	Interpretable Results
Authors: Doderer Mark , Yoon Kihoon , Salinas John , Kwek Stephen 
Published: January 2025

In silico prediction of protein subcellular localization based on amino acid sequence can reveal valuable information about the protein's innate roles in the cell. Unfortunately, such prediction is made difficult because of complex protein sorting signals. Some prediction methods are based on searching for similar proteins with known localization, assuming that known homologs exist. However, it may not perform well on proteins with no known homolog. In contrast, machine learning-based approaches attempt to infer a predictive model that describes the protein sorting signals. Alas, in doing so, it does not take advantage of known homologs (if they exist) by doing a simple "table lookup". Here, we capture the best of both worlds by combining both approaches. On a dataset with 12 locations, similarity-based and machine learning independently achieve an accuracy of 83.8% and 72.6%, respectively. Our hybrid approach yields an improved accuracy of 85.9%. We compared our method with three other methods' published results. For two of the methods, we used their published datasets for comparison. For the third we used the 12 location dataset. The Error Correcting Output Code algorithm was used to construct our predictive model. This algorithm gives attention to all the classes regardless of number of instances and led to high accuracy among each of the classes and a high prediction rate overall. We also illustrated how the machine learning classifier we use, built over a meaningful set of features can produce interpretable rules that may provide valuable insights into complex protein sorting mechanisms.
Theoretical Study of Escherichia Coli Peptide Deformylase	Inhibition by Several Drugs
Authors: Chikhi Abdelouahab , Bensegueni Abderrahmane , Boulahrouf Abderrahmane , Bencharif Mustapha 
Published: January 2025

Because peptide deformylase (PDF) is essential for the initiation of translation in eubacteria but not in eukaryotes, it is a potentially interesting target for antibiotics. Computer simulation using docking software can be used to model protein-ligand interactions, and in this brief report we describe its use in optimizing the design in PDF-directed inhibitors. PDF was used as target for a set of five inhibitors with substantial structural differences. Docking results show that the compound 1BB2 (actinonin) binds with high affinity to the enzyme and produces the most stable complex, forming nine hydrogen bonds with the enzyme active site. Its binding energy is ΔG=−31.880 kJ/mol. The modeling study shows that when the methyl group of 1BB2 is replaced with an amine group, the binding energy is increased to −35.316 kJ/mole. This enhancement is more marked (ΔG=−41.141 kJ/mol) when the propyl group and the five-membered ring of 1BB2 are replaced by an amide group and a phenyl ring, respectively. We describe an attempt to design better antibiotics on the basis of a computer-aided simulation of the interaction between a drug and its target molecule.