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1

The transverse arch collapse correction as a path to foot toes alignment

Dygut J., Piwowar P., Kogut W., Boroń W., Piwowar M.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 3

art. no. 20180014

EN

The study presents a fragment of pilot studies showing the reconstruction of the transverse arch of the foot using a specially constructed orthosis for this purpose. It involves the mechanical reinforcement of the effect by an orthosis, which pushes down the I, IV, and V metatarsal bones while elevating or blocking the fall of the near-immobile II and III metatarsal bones according to the “three-force” rule. The correction of the transverse arch of the foot runs simultaneously with the correction of hallux valgus (HV). As a result, the significant correction of HV and associated toe deformities was achieved. In stage I foot deformity, the reduction of HV was reduced from 19.1° before to 15.1° after putting on orthosis (p = 0.024). In stage II, the reduction was from 20.1° (before) to 16.2° (after; p = 0.032). Equally satisfactory results were obtained for the remaining angles of the metatarsal bones. In the future, the method can be suitable for patients undergoing preparation for corrective HV surgery and for maintaining postoperative HV results. It can be used preventively, for example, by women who frequently wear high-heeled shoes and by those who need to remain standing for prolonged periods of time.

2

The similarity of selected statins - a comparative analysis

Dreyer C., Placha W., Zgajewski J., Dygut J., Stangel-Wójcikiewicz K., Piwowar M.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 4

art. no. 20180034

EN

The paper presents the physicochemical and structural characteristics as well as the comparison of selected statins. Statins are relatively popular compounds used in modern medicine. They are increasingly often combined with other medications to improve the effectiveness of therapy. We analyzed the characteristics of pravastatin, simvastatin, atorvastatin, pitavastatin, lovastatin, mevastatin, fluvastatin, and rosuvastatin obtained from the PubChem Substance database. On the basis of data related to chemical structure and physicochemical properties, the statins were grouped into more and less similar ones. Statins are not homogeneous in terms of physicochemical properties and structure. Three groups of statins were identified. Mevastatin, lovastatin, and simvastatin are the most similar to each other, while pravastatin shows a slightly lower similarity to them. Pitavastatin and fluvastatin are also highly similar, while atorvastatin and rosuvastatin, because of their properties, are the most different from other statin groups.

3

Missing data in open-data era - a barrier to multiomics integration

Piwowar M., Jurkowski W.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 1

art. no. 20170026

EN

The exploration of complex interactions in biological systems is one of the main aims in nature science nowadays. Progress in this area is possible because of high-throughput omics technologies and the computational surge. The development of analytical methods “is trying to keep pace” with the development of molecular biology methods that provide increasingly large amounts of data - omics data. Specialized databases consist of ever-larger collections of experiments that are usually conducted by one next-generation sequencing technique (e.g. RNA-seq). Other databases integrate data by defining qualitative relationships between individual objects in the form of ontologies, interactions, and pathways (e.g. GO, KEGG, and String). However, there are no open-source complementary quantitative data sets for the biological processes studied, including information from many levels of the organism organization, which would allow the development of multidimensional data analysis methods (multiscale and insightful overviews of biological processes). In the paper, the lack of omics complementary quantitative data set, which would help integrate the defined qualitative biological relationships of individual biomolecules with statistical, computational methods, is discussed.

4

Genetic traces of never born proteins

Piwowar M., Matczyńska E., Malawski M., Szapieniec T., Roterman-Konieczna I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 2

79--87

EN

The presented results cover issues related to proteins that were “never born in nature”. The paper is focused on identifying genetic information stretches of protein sequences that were not identified to be existing in nature. The aim of the work was finding traces of “never born proteins” (NBP) everywhere in completely sequenced genomes including regions not expected as carrying the genetic information. The results of analyses relate to the search of the genetic material of species from different levels of the evolutionary tree from yeast through plant organisms up to the human genome. The analysis concerns searching the genome sequences. There are presented statistical details such as sequence frequencies, their length, percent identity and similarity of alignments, as well as E value of sequences found. Computations were performed on gLite-based grid environment. The results of the analyses showed that the NBP genetic record in the genomes of the studied organisms is absent at a significant level in terms of identity of contents and length of the sequences found. Most of the found sequences considered to be similar do not exceed 50% of the length of the NBP output sequences, which confirms that the genetic record of proteins is not accidental in terms of composition of gene sequences but also as regards the place of recording in genomes of living organisms.

5

Simulations in orthopedics and rehabilitation - Part 2: Computer simulations

Dygut J., Piwowar P., Gołda M., Popławski K., Jakubas R., Gonzales G., Piwowar M.

Bio-Algorithms and Med-Systems

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2016

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Vol. 12, no. 4

159--168

EN

Simulations in medicine have already become the mainstream trend in the field of research and education. It includes simulations on simulators through which students are afforded the opportunity to train manual skills as well as series of simulations that enable one to train not just motor and manual skills alone. Some of these offer the student the basis to train decision-making process and conduct experiments that visualize biological phenomena that are important from a doctor’s perspective. The authors have done a review of medical computer simulations and found that simulations in medicine focus, in respect of the issues raised, on techniques and computer science aspects. The first one is discussed in the paper “Simulations in orthopedics and rehabilitation – Part I: Simulators.” The second one is discussed in this paper. In the paper, the authors focus on computer simulations, in the broadest sense, presenting them while taking into consideration the distinction between simulations used for the following purposes: test (conducted under laboratory conditions), training (incorporated into school, universities syllabus), and diagnostic and therapeutic (within the hospital, clinics, private medical practice).

6

Simulations in orthopedics and rehabilitation - Part 1: Simulators

Dygut J., Piwowar P., Gołda M., Popławski K., Jakubas R., Gonzales G., Piwowar M.

Bio-Algorithms and Med-Systems

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2016

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Vol. 12, no. 4

147--157

EN

Nowadays, medical simulators and computer simulation programs are used to train various skills required in medicine. The development of medicine, including orthopedics and rehabilitation, has meant that resident physicians, within a much shorter period of time, must acquire the knowledge and skills that their older colleagues gained over years, learning as they operated on patients. For this reason, simulation very often helps the doctor and others engaged in health care train some techniques necessary during the work before they start working in a clinical environment. They have a chance of fine-tuning certain skills under nonclinical environment. On the other hand, simulation techniques are used in medical scientific research to know and explain the different biological processes that can be used for better patient treatment in the future. In this paper (Part I), the authors focused on the presentation of different types of simulators for the following purposes: test (conducted under laboratory conditions), training (incorporated into school, universities syllabus), diagnostic and therapeutic (within the hospital, clinics, private medical practice).

7

Detecting Security Violations Based on Multilayered Event Log Processing

Malec P., Piwowar M., Kozakiewicz A., Lasota K.

Journal of Telecommunications and Information Technology

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2015

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nr 4

30--36

EN

The article proposes a log analysis approach to detection of security violations, based on a four layer design. First layer, named the event source layer, describes sources of information that can be used for misuse investigation. Transport layer represents the method of collecting event data, preserving it in the form of logs and passing it to another layer, called the analysis layer. This third layer is responsible for analyzing the logs' content, picking relevant information and generating security alerts. Last layer, called normalization layer, is custom software which normalizes and correlates produced alerts to raise notice on more complex attacks. Logs from remote hosts are collected by using rsyslog software and OSSEC HIDS with custom decoders and rules is used on a central log server for log analysis. A novel method of handling OSSEC HIDS alerts by their normalization and correlation is proposed. The output can be optionally suppressed to protect the system against alarm flood and reduce the count of messages transmitted in the network.

8

Genetic background of urinary incontinence - state-of-the-art and perspectives

Stangel-Wójcikiewicz K., Piwowar M.

Bio-Algorithms and Med-Systems

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2015

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Vol. 11, no. 4

197--203

EN

The paper presents an overview of the current studies attempting to determine the genetic background of urinary incontinence (UI) problems. The overview referred to the adaptations of biomedical literature from Medline, life science journals, and online books were searched from the earliest date possible to March 2015. Genetic variability studies (mostly with the use of single nucleotide polymorphism) in the context of UI are discussed. The authors indicate the variability of polymorphic forms of proteins, whose modified function may be related to the observed phenotypic symptoms: UI. The paper includes a discussion of the varied level of gene expression and the issue of defective process of the development of the urinary system in the context of UI disorders. The literature does not present any general, unequivocal description of the relationship between the genetic background and phenotype as UI. It is suggested that the methods of integration of data from various techniques (e.g. high throughputs) in reference to social, demographic, and other data may be the way of the approach used for the effective description of the relationship between genetic background and observed UI.

9

ePBLmed: application supporting classes in medical colleges conducted with the problem based learning method

Lipiak T., Piwowar M., Markiewicz M., Nowakowski M.

Bio-Algorithms and Med-Systems

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2015

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Vol. 11, no. 1

69--75

EN

This paper reviews the available e-learning applications used in teaching medicine and presents the functionalities of the Web application developed to support classes conducted with the problem-based learning (PBL) method. The application is a form of e-learning platform that allows posting as well as archiving content stored during PBL sessions; it is made up of three modules: the administration module, the teacher module, and the student module. The presented Web application is flexible in operation; it allows designing the number of groups and PBL sessions. The user, apart from using the system during PBL sessions, can access it at any place and time to supplement and update the content. The materials collected during individual PBL sessions constitute sets of content unique for each group because the learning objectives are different for them. With this approach, students can study considerably larger batches of material than it would be possible during classes conducted with other methods.

10

Virtual patient case: study of a urinary incontinence therapy procedure in a woman

Stangel-Wójcikiewicz K., Piwowar M., Migdał M., Skotniczny K.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 3

151--157

EN

The aim of the study was to present a case of virtual patient with urinary incontinence (UI), the treatment especially based on the new muscle-derived stem cell (MDSC) procedure. With the use of e-learning systems, the UI patient’s classical follow-up as well as MDSC sphincter injection therapy are shown. The “Virtual Patient” case allowed us to demonstrate the main results and the creation of a robotic system from the MDSC study. In this way, the authors will disseminate the new procedure developed in Collegium Medicum JU in UI patients. The “Virtual Patient” case may help students get involved in this new procedure along the main program.

11

Operative procedures supported with robotics systems and available endoscope procedures in operative gynecology

Stangel-Wójcikiewicz K., Basta A., Piwowar M., Petko M., Karpiel G., Panek D., Ludwin I., Jach R.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 3

139--149

EN

Minimally invasive surgery revolutionized operative procedures in the last 20 years. Much of the progress in minimally invasive surgery can be attributed to the development of robot-based systems. The most apparent changes are found in laparoscopy procedures. Procedures in which only small skin incisions are made have revolutionized operating theaters. The learning curve, although long in itself, allows for the development of procedures with reduced perioperative risk (i.e., bleeding, pain) or shorter postoperative period. Convalescence after endoscopy procedures is significantly shorter compared with classic laparotomy. However, certain limitations apply to laparoscopy. Apart from the long learning curve, movements executed with long and rigid tools cannot strictly translate the precision of an operator’s hand. The body position of the surgeon is often forced by the reach of the endoscope instrument. It is related to a significant physical load of personnel, especially during long operating procedures. For this reason, some therapeutic procedures are still executed using the laparotomy approach.

12

Attempt at a systemic outlook on aging and carcinogenesis

Piwowar M., Dygut J., Piwowar P., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2014

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Vol. 10, no. 3

101--115

EN

Two of the key problems plaguing humanity – aging and carcinogenesis – are inexorably linked. While their nature seems different, their mechanisms have a lot in common. Evidence suggests that aging is the result of spontaneous synthesis and accumulation of improperly folded proteins in cells, leading to a variety of pathologies. As for carcinogenesis, it is tied to genetic mutations – permanent, covalent changes in the DNA. Both processes are random in character; however, unlike mutations, the accumulation of malformed proteins is not genetically determined. Instead, control over this process hinges upon regulating the protein exchange rate – a phenomenon that seems a likely candidate for the basic aging control mechanism. Although mutations themselves may be counteracted in a controlled manner, their effects typically cannot. The mechanisms of aging and carcinogenesis, while functionally different, remain correlated: an aging cell is rendered more susceptible to mutational changes. The rapidly growing body of information regarding aging and carcinogenesis enables a systemic approach to both these phenomena – an approach that is attempted in this review.

13

Structural role of exons in hemoglobin

Piwowar M., Banach M., Konieczny L., Chomilier J., Roterman I.

Bio-Algorithms and Med-Systems

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2013

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Vol. 9, no. 2

81--90

EN

The role of exons can be studied on many levels, one of which pertains to protein structure. It is a well-known fact that secondary structural motifs do not directly correspond to exons: helices, β-sheets and loops have all been identified as encoded by more than one exon. The relation between exon fragments and their involvement in shaping the three-dimensional (3D) structure of a protein body is subject to ongoing studies. In particular, the role of exons in stabilizing tertiary structures can be related to the structure of the hydrophobic core of the protein. Participation of specific polypeptide fragments (single exons) in hydrophobic stabilization reveals the role played by each fragment. In the course of the presented research, exons in selected proteins have been identified on the basis of GenBank files, imported from the nucleotide database at the National Center of Biotechnology Information. Amino acid sequences representing each exon were subsequently traced to parts of 3D structural forms. The participation of each exon fragment in shaping the hydrophobic core of the protein was measured using divergence entropy calculations. It was found that each protein contains at least one exon which encodes a structural fragment in accordance with the theoretical hydrophobic core model. This implies that the likely role of at least one exon in each protein is to generate a hydrophobic core which is, in turn, responsible for tertiary structural stabilization.

14

Structural role of exon-coded fragments in proteins

Piwowar M., Banach M., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2013

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Vol. 9, no. 3

103--114

EN

This article describes the role of protein fragments encoded by individual exons. Structural analysis of the hydrophobic core on the basis of the “fuzzy oil drop” model – in whole molecules as well as in fragments encoded by specific exons – indicates that, in each protein, at least one exon encodes a fragment, which is consistent with the theoretical distribution of hydrophobicity density. Quantitative assessment of the properties of such exons in selected proteins enables the model to be applied in identifying the structural (stabilizing) role of polypeptide chains encoded by individual exons. This is viewed as a preliminary step toward future exploitation of this technique in studying the alternative splicing phenomenon.

15

Laparoscopic colpopexy technique performed with laparoscopic supracervical hysterectomy, total laparoscopic hysterectomy, and following total abdominal hysterectomy

Stangel-Wójcikiewicz K., Wojtyś A., Piwowar M., Migdał M., Popławska A. M.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 1

43--48

EN

Study objective: Our purpose was to assess a modification of laparoscopic colpopexy technique. Design: Retrospective case analysis. Setting: University teaching hospital. Patients: A total of 28 patients with stage I, II and III organ prolapse. Interventions: The rectovaginal space was dissected at the superior aspect of the posterior vaginal fascia and a mesh was sutured to this fascia. Measurements and Main Results: 28 patients completed a 36 months follow-up. No recurrences of the vagina vault prolapse was observed. Three cases of abdominal pain at the level of the trocars placing were recorded in a first week after surgery. Two of these were found in the group of LSH and one in the group of a hysterectomy history. There was no significant difference in blood loss, length of hospital stay and surgical or postoperative complications. Conclusion: The modification of laparoscopic colpopexy, although technically challenging, may be learned quickly. It shows rapid improvement in operative time without subjecting the patient to undue risk. Further studies are required to determine the long-term tolerance and outcome of the procedure.

16

VoGE - Java application for presentation of never born proteins gene structure elements

Piwowar M., Matczyńska E., Pomański F., Kośmider A., Kość D., Swatowski M., Więcek P., Szepieniec T.

Bio-Algorithms and Med-Systems

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2009

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Vol. 5, no. 10

9--13

EN

VoGE application for visualizing gene structure elements in nucleotide sequences is presented in the paper. Genomic analyzing of genome sequences was continuation of proteomic efforts in the EuChinaGrid project that was oriented on the structure prediction of never born proteins, but probably with pharmacological application (there were 10**4 protein sequences generated which were used to create structures of that sequences). Finding of gene traces of never born proteins in all accessible sequenced genomes was one of the aim. As a results of searching genome materials there were found regions including protein-coding gene fragments that VoGE (Visualiser of Gene Elements) application presents. Graphical presentation of particular sequences enable user to see localization of coding NBP sequence and gene element composition in wider sequence context. Application interface and menu is intuitive so it seems to be easy to use.

17

GenFoSS - java application for presentation of coding stretches of never born proteins

Piwowar M., Matczyńska E., Ochlawski P., Kosibowicz M., Kość D., Swatowski M., Więcek P., Szepieniec T.

Bio-Algorithms and Med-Systems

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2008

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Vol. 4, no. 7

9--17

EN

Application of genomes analysis results with respect to project of "never born protein" (NBP) is presented in this paper. GenFoSS application concerns visualisation of genomic sequence stretches that could encode proteins that are not observed in the Nature. The sequences of these proteins were generated randomly aimed to recognize the proteins of potential pharmacological activity. Identification of sequences similar to these of NBP can be viewed by GenFoSS application. GenFoSS gives information about sequence frequencies, percent identity, percent of similarity of alignments and E-value for aligned sequences. Comparison between two chromosomes in common organism and between different genomes as well can be done by these applications. There are also possibilities to check codon frequencies of nucleotide sequences that were found as a stretch of NBP.

18

Association between the N-acetylation genetic polymorphism and aspirin-induced urticartia

Porębski G., Obtulowicz K., Piwowar M., Roterman-Konieczna I.

Bio-Algorithms and Med-Systems

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2008

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Vol. 4, no. 8

19--23

EN

N-acetylation represents one of the key pharmacogenetic traits in metabolism of xenobiotics, including drugs. Dominance of ‘slow-acetylators’ has been demonstrated in atopic patients, contact allergy and has been investigated in patients with sulfonamide hypersensitivity. The aim of this survey was to assess genotype of N-acetyltransferase2 (NAT2) polymorphism in patients with aspirin-induced urticaria (AIU). To the study we included 24 consecutive patients with medical history of urticaria induced by aspirin and 123 healthy controls. In the patients’ group oral provocation tests (OPT) up to 565mg cumulative dose of acetylsalicylic acid were performed. The NAT2 alleles (*4-wilde type, *5, *6 and *7) were determined by polymerase chain reaction-restriction fragment length polymorphism method with DNA extracted from peripherial blood. It was observed 53.7% of slow acetylators in the control group, and respectively 66.7%, 83.3% and 100% in the patients with AIU, in patients with positive OPT and in patients with positive reaction in OPT assessed as severe. Statistical significance association between NAT2*5/NAT2*6 genotype and aspirin-induced urticaria was revealed. The linkage of AIU and slow acetylation (NAT2*5/NAT2*6) seems to be highly probable in the patients with medical history of skin hypersensitivity to aspirin confirmed by positive oral provocation test.

19

Massive identification of similarities in DNA materials organized in GRID environment

Piwowar M., Szepieniec T., Roterman I.

Bio-Algorithms and Med-Systems

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2007

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Vol. 3, no. 5

51--52

EN

In this paper we presented, how computations related to Genomics, could be organize on gLite-grid. The grid environment gives opportunity to radically speed-up computational part in research on this field. The authors belive that similar methodology would be adapted to other applications as well.

20

An approach to protein folding on the grid – EuChinaGRID experience

Malawski M., Szepieniec T., Kochanczyk M., Piwowar M., Roterman I.

Bio-Algorithms and Med-Systems

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2007

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Vol. 3, no. 5

45--49

EN

Contemporary pharmacology in its quest for more relevant and effective drugs needs to examine large range of biological structures to identify biological active compounds. We consider large grid environment the only platform to face such a computational challenge. In our project, the search is focused on peptide-like molecules containing about 70 amino acids in a single polypeptide chain. The limited number of proteins existing in the nature will be extended to those, which have not been recognized in any organisms (“never born proteins”). The assumption is that those which do not exist in the nature may also render biological activity, which directed on pharmacological use may correct some pathological phenomena. As the function results from the structure, two approaches are applied to predict cartesian coordinates of proteins’ atoms: sophisticated Monte Carlo structure creation, elimination and refinement using the Rosetta program and our own program for simulation of the protein folding process. As a computing platform we use the EuChinaGRID project resources, which are currently a part of EGEE infrastructure and are expanding to include Chinese resources as well. We describe the approach for porting the application to the grid and the prototype portal developed for simulation management and results analysis.