TY  - JOUR
AU  - Bajić, Vladan P.
AU  - Salhi, Adil
AU  - Lakota, Katja
AU  - Radovanović, Aleksandar
AU  - Razali, Rozaimi
AU  - Živković, Lada
AU  - Spremo-Potparević, Biljana
AU  - Uludag, Mahmut
AU  - Tifratene, Faroug
AU  - Motwalli, Olaa
AU  - Marchand, Benoit
AU  - Bajić, Vladimir
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Essack, Magbubah
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10387
AB  - More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid net- work systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this infor- mation through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome- amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid- related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.
T2  - PLoS ONE
T1  - DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases
VL  - 17
IS  - 7
DO  - 10.1371/journal.pone.0271737
ER  - 

@article{
author = "Bajić, Vladan P. and Salhi, Adil and Lakota, Katja and Radovanović, Aleksandar and Razali, Rozaimi and Živković, Lada and Spremo-Potparević, Biljana and Uludag, Mahmut and Tifratene, Faroug and Motwalli, Olaa and Marchand, Benoit and Bajić, Vladimir and Gojobori, Takashi and Isenović, Esma R. and Essack, Magbubah",
year = "2022",
abstract = "More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid net- work systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this infor- mation through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome- amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid- related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.",
journal = "PLoS ONE",
title = "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases",
volume = "17",
number = "7",
doi = "10.1371/journal.pone.0271737"
}

Bajić, V. P., Salhi, A., Lakota, K., Radovanović, A., Razali, R., Živković, L., Spremo-Potparević, B., Uludag, M., Tifratene, F., Motwalli, O., Marchand, B., Bajić, V., Gojobori, T., Isenović, E. R.,& Essack, M.. (2022). DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE, 17(7).
https://doi.org/10.1371/journal.pone.0271737

Bajić VP, Salhi A, Lakota K, Radovanović A, Razali R, Živković L, Spremo-Potparević B, Uludag M, Tifratene F, Motwalli O, Marchand B, Bajić V, Gojobori T, Isenović ER, Essack M. DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE. 2022;17(7).
doi:10.1371/journal.pone.0271737 .

Bajić, Vladan P., Salhi, Adil, Lakota, Katja, Radovanović, Aleksandar, Razali, Rozaimi, Živković, Lada, Spremo-Potparević, Biljana, Uludag, Mahmut, Tifratene, Faroug, Motwalli, Olaa, Marchand, Benoit, Bajić, Vladimir, Gojobori, Takashi, Isenović, Esma R., Essack, Magbubah, "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases" in PLoS ONE, 17, no. 7 (2022),
https://doi.org/10.1371/journal.pone.0271737 . .

TY  - JOUR
AU  - Obradović, Milan M.
AU  - Zafirović, Sonja
AU  - Essack, Magbubah
AU  - Dimitrov, Jelena
AU  - Živković, Lada
AU  - Spremo-Potparević, Biljana
AU  - Radak, Đorđe J.
AU  - Bajić, Vladimir B.
AU  - Isenović, Esma R.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8487
AB  - To remedy carotid artery stenosis and prevent stroke surgical intervention is commonly used, and the gold standard being carotid endarterectomy (CEA). During CEA cerebrovascular hemoglobin oxygen saturation decreases and when this decrease reaches critical levels it leads to cerebral hypoxia that causes neuronal damage. One of the proposed mechanism that affects changes during CEA and contribute to acute brain ischemia (ABI) is oxidative stress. The increased production of reactive oxygen species and reactive nitrogen species during ABI may cause an unregulated inflammatory response and further lead to structural and functional injury of neurons. Antioxidant activity are involved in the protection against neuronal damage after cerebral ischemia. We hypothesized that neuronal injury and poor outcomes in patients undergoing CEA may be results of oxidative stress that disturbed function of antioxidant enzymes and contributed to the DNA damage in lymphocytes. © 2019 The Authors
PB  - Churchill Livingstone
T2  - Medical Hypotheses
T1  - Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy
VL  - 134
SP  - 109419
DO  - 10.1016/j.mehy.2019.109419
ER  - 

@article{
author = "Obradović, Milan M. and Zafirović, Sonja and Essack, Magbubah and Dimitrov, Jelena and Živković, Lada and Spremo-Potparević, Biljana and Radak, Đorđe J. and Bajić, Vladimir B. and Isenović, Esma R.",
year = "2020",
abstract = "To remedy carotid artery stenosis and prevent stroke surgical intervention is commonly used, and the gold standard being carotid endarterectomy (CEA). During CEA cerebrovascular hemoglobin oxygen saturation decreases and when this decrease reaches critical levels it leads to cerebral hypoxia that causes neuronal damage. One of the proposed mechanism that affects changes during CEA and contribute to acute brain ischemia (ABI) is oxidative stress. The increased production of reactive oxygen species and reactive nitrogen species during ABI may cause an unregulated inflammatory response and further lead to structural and functional injury of neurons. Antioxidant activity are involved in the protection against neuronal damage after cerebral ischemia. We hypothesized that neuronal injury and poor outcomes in patients undergoing CEA may be results of oxidative stress that disturbed function of antioxidant enzymes and contributed to the DNA damage in lymphocytes. © 2019 The Authors",
publisher = "Churchill Livingstone",
journal = "Medical Hypotheses",
title = "Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy",
volume = "134",
pages = "109419",
doi = "10.1016/j.mehy.2019.109419"
}

Obradović, M. M., Zafirović, S., Essack, M., Dimitrov, J., Živković, L., Spremo-Potparević, B., Radak, Đ. J., Bajić, V. B.,& Isenović, E. R.. (2020). Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy. in Medical Hypotheses
Churchill Livingstone., 134, 109419.
https://doi.org/10.1016/j.mehy.2019.109419

Obradović MM, Zafirović S, Essack M, Dimitrov J, Živković L, Spremo-Potparević B, Radak ĐJ, Bajić VB, Isenović ER. Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy. in Medical Hypotheses. 2020;134:109419.
doi:10.1016/j.mehy.2019.109419 .

Obradović, Milan M., Zafirović, Sonja, Essack, Magbubah, Dimitrov, Jelena, Živković, Lada, Spremo-Potparević, Biljana, Radak, Đorđe J., Bajić, Vladimir B., Isenović, Esma R., "Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy" in Medical Hypotheses, 134 (2020):109419,
https://doi.org/10.1016/j.mehy.2019.109419 . .

TY  - JOUR
AU  - Bajić, Vladan P.
AU  - Essack, Magbubah
AU  - Živković, Lada
AU  - Stewart, Alan J.
AU  - Zafirović, Sonja
AU  - Bajić, Vladimir B.
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Spremo-Potparević, Biljana
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8825
AB  - Alzheimer’s disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics. © Copyright © 2020 Bajic, Essack, Zivkovic, Stewart, Zafirovic, Bajic, Gojobori, Isenovic and Spremo-Potparevic.
T2  - Frontiers in Genetics
T1  - The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”
VL  - 10
DO  - 10.3389/fgene.2019.01368
ER  - 

@article{
author = "Bajić, Vladan P. and Essack, Magbubah and Živković, Lada and Stewart, Alan J. and Zafirović, Sonja and Bajić, Vladimir B. and Gojobori, Takashi and Isenović, Esma R. and Spremo-Potparević, Biljana",
year = "2020",
abstract = "Alzheimer’s disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics. © Copyright © 2020 Bajic, Essack, Zivkovic, Stewart, Zafirovic, Bajic, Gojobori, Isenovic and Spremo-Potparevic.",
journal = "Frontiers in Genetics",
title = "The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”",
volume = "10",
doi = "10.3389/fgene.2019.01368"
}

Bajić, V. P., Essack, M., Živković, L., Stewart, A. J., Zafirović, S., Bajić, V. B., Gojobori, T., Isenović, E. R.,& Spremo-Potparević, B.. (2020). The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”. in Frontiers in Genetics, 10.
https://doi.org/10.3389/fgene.2019.01368

Bajić VP, Essack M, Živković L, Stewart AJ, Zafirović S, Bajić VB, Gojobori T, Isenović ER, Spremo-Potparević B. The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”. in Frontiers in Genetics. 2020;10.
doi:10.3389/fgene.2019.01368 .

Bajić, Vladan P., Essack, Magbubah, Živković, Lada, Stewart, Alan J., Zafirović, Sonja, Bajić, Vladimir B., Gojobori, Takashi, Isenović, Esma R., Spremo-Potparević, Biljana, "The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”" in Frontiers in Genetics, 10 (2020),
https://doi.org/10.3389/fgene.2019.01368 . .

TY  - JOUR
AU  - Essack, Magbubah
AU  - Salhi, Adil
AU  - Van Neste, Christophe
AU  - Raies, Arwa Bin
AU  - Tifratene, Faroug
AU  - Uludag, Mahmut
AU  - Hungler, Arnaud
AU  - Zarić, Božidarka
AU  - Zafirović, Sonja
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Bajić, Vladan P.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8945
AB  - Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.
T2  - Oxidative Medicine and Cellular Longevity
T1  - DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases
VL  - 2020
SP  - 5904315
DO  - 10.1155/2020/5904315
ER  - 

@article{
author = "Essack, Magbubah and Salhi, Adil and Van Neste, Christophe and Raies, Arwa Bin and Tifratene, Faroug and Uludag, Mahmut and Hungler, Arnaud and Zarić, Božidarka and Zafirović, Sonja and Gojobori, Takashi and Isenović, Esma R. and Bajić, Vladan P.",
year = "2020",
abstract = "Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.",
journal = "Oxidative Medicine and Cellular Longevity",
title = "DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases",
volume = "2020",
pages = "5904315",
doi = "10.1155/2020/5904315"
}

Essack, M., Salhi, A., Van Neste, C., Raies, A. B., Tifratene, F., Uludag, M., Hungler, A., Zarić, B., Zafirović, S., Gojobori, T., Isenović, E. R.,& Bajić, V. P.. (2020). DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. in Oxidative Medicine and Cellular Longevity, 2020, 5904315.
https://doi.org/10.1155/2020/5904315

Essack M, Salhi A, Van Neste C, Raies AB, Tifratene F, Uludag M, Hungler A, Zarić B, Zafirović S, Gojobori T, Isenović ER, Bajić VP. DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. in Oxidative Medicine and Cellular Longevity. 2020;2020:5904315.
doi:10.1155/2020/5904315 .

Essack, Magbubah, Salhi, Adil, Van Neste, Christophe, Raies, Arwa Bin, Tifratene, Faroug, Uludag, Mahmut, Hungler, Arnaud, Zarić, Božidarka, Zafirović, Sonja, Gojobori, Takashi, Isenović, Esma R., Bajić, Vladan P., "DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases" in Oxidative Medicine and Cellular Longevity, 2020 (2020):5904315,
https://doi.org/10.1155/2020/5904315 . .

TY  - JOUR
AU  - Gluvić, Zoran
AU  - Obradović, Milan M.
AU  - Lačković, Milena
AU  - Samardžić, Vladimir S.
AU  - Tica Jevtic, Jelena
AU  - Essack, Magbubah
AU  - Bajić, Vladimir B.
AU  - Isenović, Esma R.
PY  - 2019
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8484
AB  - What is known and objective: The HbA1C marker used in assessing diabetes control quality is not sufficient in diabetes patients with thalassaemia. Case description: A male diabetic patient with thalassaemia was hospitalized due to distal neuropathic pain, right toe trophic ulcer, unacceptable five-point glycaemic profile and recommended HbA1C value. After simultaneously initiated insulin therapy and management of ulcer by hyperbaric oxygen, the patient showed improved glycaemic control and ulcer healing, which led to the patient's discharge. What is new and conclusion: In thalassaemia and haemoglobinopathies, due to discrepancies in the five-point glycaemic profile and HbA1C values, it is necessary to measure HbA1C with a different method or to determine HbA1C and fructosamine simultaneously. © 2019 The Authors. Journal of Clinical Pharmacy and Therapeutics Published by John Wiley & Sons Ltd.
T2  - Journal of Clinical Pharmacy and Therapeutics
T1  - HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review
VL  - 45
IS  - 2
SP  - 379
EP  - 383
DO  - 10.1111/jcpt.13073
ER  - 

@article{
author = "Gluvić, Zoran and Obradović, Milan M. and Lačković, Milena and Samardžić, Vladimir S. and Tica Jevtic, Jelena and Essack, Magbubah and Bajić, Vladimir B. and Isenović, Esma R.",
year = "2019",
abstract = "What is known and objective: The HbA1C marker used in assessing diabetes control quality is not sufficient in diabetes patients with thalassaemia. Case description: A male diabetic patient with thalassaemia was hospitalized due to distal neuropathic pain, right toe trophic ulcer, unacceptable five-point glycaemic profile and recommended HbA1C value. After simultaneously initiated insulin therapy and management of ulcer by hyperbaric oxygen, the patient showed improved glycaemic control and ulcer healing, which led to the patient's discharge. What is new and conclusion: In thalassaemia and haemoglobinopathies, due to discrepancies in the five-point glycaemic profile and HbA1C values, it is necessary to measure HbA1C with a different method or to determine HbA1C and fructosamine simultaneously. © 2019 The Authors. Journal of Clinical Pharmacy and Therapeutics Published by John Wiley & Sons Ltd.",
journal = "Journal of Clinical Pharmacy and Therapeutics",
title = "HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review",
volume = "45",
number = "2",
pages = "379-383",
doi = "10.1111/jcpt.13073"
}

Gluvić, Z., Obradović, M. M., Lačković, M., Samardžić, V. S., Tica Jevtic, J., Essack, M., Bajić, V. B.,& Isenović, E. R.. (2019). HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review. in Journal of Clinical Pharmacy and Therapeutics, 45(2), 379-383.
https://doi.org/10.1111/jcpt.13073

Gluvić Z, Obradović MM, Lačković M, Samardžić VS, Tica Jevtic J, Essack M, Bajić VB, Isenović ER. HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review. in Journal of Clinical Pharmacy and Therapeutics. 2019;45(2):379-383.
doi:10.1111/jcpt.13073 .

Gluvić, Zoran, Obradović, Milan M., Lačković, Milena, Samardžić, Vladimir S., Tica Jevtic, Jelena, Essack, Magbubah, Bajić, Vladimir B., Isenović, Esma R., "HbA1C as a marker of retrograde glycaemic control in diabetes patient with co-existed beta-thalassaemia: A case report and a literature review" in Journal of Clinical Pharmacy and Therapeutics, 45, no. 2 (2019):379-383,
https://doi.org/10.1111/jcpt.13073 . .