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  1. Article: Iron Nitride Thin Films: Growth, Structure, and Properties.

    Wojciechowski, Paweł / Lewandowski, Mikołaj

    Crystal growth & design

    2022  Volume 22, Issue 7, Page(s) 4618–4639

    Abstract: The current state-of-the-art in the growth, structure, and physicochemical properties of iron nitride thin films is presented. First, different iron nitride phases are introduced based on their crystallographic structure and the Fe-N phase diagram. ... ...

    Abstract The current state-of-the-art in the growth, structure, and physicochemical properties of iron nitride thin films is presented. First, different iron nitride phases are introduced based on their crystallographic structure and the Fe-N phase diagram. Second, preparation methods for thin iron nitride films are described. Next, the structure, electronic, and magnetic properties of the films are discussed. Finally, potential applications of iron nitride films, as well as the challenges to be faced in the field, are highlighted. This Review constitutes a starting point for anyone who would like to conduct research on these fascinating materials, the scientific and technological potential of which has not been fully explored to date.
    Language English
    Publishing date 2022-05-25
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1528-7483
    ISSN 1528-7483
    DOI 10.1021/acs.cgd.1c01528
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  2. Article: Editorial: Resolving the complexity of plant genomes and transcriptomes with long reads, volume II.

    Zmienko, Agnieszka / Wojciechowski, Paweł / Figlerowicz, Marek

    Frontiers in plant science

    2023  Volume 14, Page(s) 1326500

    Language English
    Publishing date 2023-11-16
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1326500
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  3. Article ; Online: The correctness of large scale analysis of genomic data

    Wojciechowski Pawel / Krause Karol / Lukasiak Piotr / Blazewicz Jacek

    Foundations of Computing and Decision Sciences, Vol 46, Iss 4, Pp 423-

    2021  Volume 436

    Abstract: Implementing a large genomic project is a demanding task, also from the computer science point of view. Besides collecting many genome samples and sequencing them, there is processing of a huge amount of data at every stage of their production and ... ...

    Abstract Implementing a large genomic project is a demanding task, also from the computer science point of view. Besides collecting many genome samples and sequencing them, there is processing of a huge amount of data at every stage of their production and analysis. Efficient transfer and storage of the data is also an important issue. During the execution of such a project, there is a need to maintain work standards and control quality of the results, which can be difficult if a part of the work is carried out externally. Here, we describe our experience with such data quality analysis on a number of levels - from an obvious check of the quality of the results obtained, to examining consistency of the data at various stages of their processing, to verifying, as far as possible, their compatibility with the data describing the sample.
    Keywords genomic data ; large scale analysis ; processing pipeline ; Electronic computers. Computer science ; QA75.5-76.95
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Sciendo
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Editorial: Resolving the Complexity of Plant Genomes and Transcriptomes With Long Reads.

    Zmienko, Agnieszka / Wojciechowski, Pawel / Figlerowicz, Marek

    Frontiers in plant science

    2022  Volume 12, Page(s) 832257

    Language English
    Publishing date 2022-01-21
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2021.832257
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  5. Article: Transcript-Level Dysregulation of

    Handschuh, Luiza / Wojciechowski, Pawel / Kazmierczak, Maciej / Lewandowski, Krzysztof

    Cancers

    2021  Volume 13, Issue 13

    Abstract: The expression of apoptosis- ... ...

    Abstract The expression of apoptosis-related
    Language English
    Publishing date 2021-06-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers13133175
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  6. Article ; Online: Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.

    Samelak-Czajka, Anna / Wojciechowski, Pawel / Marszalek-Zenczak, Malgorzata / Figlerowicz, Marek / Zmienko, Agnieszka

    Functional & integrative genomics

    2023  Volume 23, Issue 2, Page(s) 120

    Abstract: MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental ...

    Abstract MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis/metabolism ; DNA Copy Number Variations ; Genes, Plant ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Genomics ; RNA, Plant/genetics ; Gene Expression Regulation, Plant ; Conserved Sequence
    Chemical Substances MicroRNAs ; RNA, Plant
    Language English
    Publishing date 2023-04-10
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2014670-X
    ISSN 1438-7948 ; 1438-793X
    ISSN (online) 1438-7948
    ISSN 1438-793X
    DOI 10.1007/s10142-023-01043-x
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  7. Article: Augmentation Therapies as Treatments for Coexisting Somatic Problems in Schizophrenia-A Systematic Review.

    Dróżdż, Wiktor / Wiciński, Michał / Szota, Anna Maria / Szambelan, Monika / Radajewska, Izabela / Popławski, Igor / Wojciechowski, Paweł

    Journal of clinical medicine

    2023  Volume 12, Issue 12

    Abstract: The aim of this review is to appraise the data from available randomized clinical trials (RCT) regarding the possible combinations of neuroleptic and non-antipsychotic treatment which could enhance antipsychotic therapy efficacy whilst simultaneously ... ...

    Abstract The aim of this review is to appraise the data from available randomized clinical trials (RCT) regarding the possible combinations of neuroleptic and non-antipsychotic treatment which could enhance antipsychotic therapy efficacy whilst simultaneously addressing somatic symptoms in individuals with schizophrenia. A systematic search of the PubMed database up to February 2022 was conducted. Inclusion criteria: randomized controlled trials using augmentation therapy in chronic schizophrenia in adults, written in English, and only studies with psychometric assessments of schizophrenia were incorporated. Exclusion criteria: non-clinical, first episode of schizophrenia, patients on medication other than antipsychotics augmented, and not adjunctive therapy. Overall, 37 studies of 1931 patients with schizophrenia who received a combination of antipsychotic medication with other drugs were selected. A statistically significant reduction of negative and positive symptoms of schizophrenia, measured with the PANSS scale, when using a combination of antipsychotic treatment along with aspirin, simvastatin, N-acetylcysteine, or pioglitazone was found. A combination of antipsychotic medication with aspirin, simvastatin, N-acetylcysteine, or pioglitazone seems to be effective in the reduction of symptoms of schizophrenia in adults, but long-term studies are required to confirm this effect.
    Language English
    Publishing date 2023-06-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm12124012
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  8. Article: Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members.

    Marszalek-Zenczak, Malgorzata / Satyr, Anastasiia / Wojciechowski, Pawel / Zenczak, Michal / Sobieszczanska, Paula / Brzezinski, Krzysztof / Iefimenko, Tetiana / Figlerowicz, Marek / Zmienko, Agnieszka

    Frontiers in plant science

    2023  Volume 14, Page(s) 1104303

    Abstract: Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number ... ...

    Abstract Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four
    Language English
    Publishing date 2023-01-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1104303
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  9. Article ; Online: Proving Opacity of Transactional Memory with Early Release

    Siek Konrad / Wojciechowski Paweł T.

    Foundations of Computing and Decision Sciences, Vol 40, Iss 4, Pp 317-

    2015  Volume 335

    Abstract: Transactional Memory (TM) is an alternative way of synchronizing concurrent accesses to shared memory by adopting the abstraction of transactions in place of low-level mechanisms like locks and barriers. TMs usually apply optimistic concurrency control ... ...

    Abstract Transactional Memory (TM) is an alternative way of synchronizing concurrent accesses to shared memory by adopting the abstraction of transactions in place of low-level mechanisms like locks and barriers. TMs usually apply optimistic concurrency control to provide a universal and easy-to-use method of maintaining correctness. However, this approach performs a high number of aborts in high contention workloads, which can adversely affect performance. Optimistic TMs can cause problems when transactions contain irrevocable operations. Hence, pessimistic TMs were proposed to solve some of these problems. However, an important way of achieving efficiency in pessimistic TMs is to use early release. On the other hand, early release is seemingly at odds with opacity, the gold standard of TM safety properties, which does not allow transactions to make their state visible until they commit. In this paper we propose a proof technique that makes it possible to demonstrate that a TM with early release can be opaque as long as it prevents inconsistent views.
    Keywords concurrency ; parallel programming ; software transactional memory ; safety ; early release ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 005
    Language English
    Publishing date 2015-12-01T00:00:00Z
    Publisher Sciendo
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Jiffy

    Kobus, Tadeusz / Kokociński, Maciej / Wojciechowski, Paweł T.

    A Lock-free Skip List with Batch Updates and Snapshots

    2021  

    Abstract: In this paper we introduce Jiffy, the first lock-free, linearizable ordered key-value index that offers both (1) batch updates, which are put and remove operations that are executed atomically, and (2) consistent snapshots used by, e.g., range scan ... ...

    Abstract In this paper we introduce Jiffy, the first lock-free, linearizable ordered key-value index that offers both (1) batch updates, which are put and remove operations that are executed atomically, and (2) consistent snapshots used by, e.g., range scan operations. Jiffy is built as a multiversioned lock-free skip list and relies on CPU's Time Stamp Counter register to generate version numbers at minimal cost. For faster skip list traversals and better utilization of the CPU caches, key-value entries are grouped into immutable objects called revisions. Moreover, by changing the size of revisions and thus modifying the synchronization granularity, our index can adapt to varying contentions levels (smaller revisions are more suited for write-heavy workloads whereas large revisions benefit read-dominated workloads, especially when they feature many range scan operations). Structure modifications to the index, which result in changing the size of revisions, happen through (lock-free) skip list node split and merge operations that are carefully coordinated with the update operations. Despite rich semantics, Jiffy offers highly scalable performance, which is comparable or exceeds the performance of the state-of-the-art lock-free ordered indices that feature linearizable range scan operations. Compared to its (lock-based) rivals that also support batch updates, Jiffy can execute large batch updates up to 7.4x more efficiently.
    Keywords Computer Science - Data Structures and Algorithms
    Publishing date 2021-02-01
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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