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The Effects of COVID-19 Measures on Air Pollutant Concentrations at Urban and Traffic Sites in Istanbul
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
AEROSOL AND AIR QUALITY RESEARCH
Yazar(lar) :
Ulku Alver Sahin
Yıl :
2020
The Effects of COVID-19 Measures on Air Pollutant Concentrations at Urban and Traffic Sites in Istanbul Since December 2019, most countries have been working to stop the spread of SARS-CoV-2, the virus responsible for COVID- 19. This study assessed the impact of COVID- 19 measures on air pollutant concentrations measured in urban areas and traffic stations on both the European and The average concentrations of NO2, PM2.5, PM10 and CO during peak traffic hours were significantly (p < 0.01) decreased under COVID- 19 measures.
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Since December 2019, most countries have been working to stop the spread of SARS-CoV-2, the virus responsible for COVID-19. These measures, which include restricting movement, have environmental consequences. This study assessed the impact of COVID-19 measures on air pollutant concentrations measured in urban areas and traffic stations on both the European and Asian sides of Istanbul during March 2020. Significant reductions in pollutants: 32-43% (PM10), 19-47% (PM2.5), 29-44% (NO2), 40-58% (CO) and 34-69% (SO2) were calculated. The clearest reductions at the traffic stations were in NO2 which originates primarily from vehicle exhaust. The reduction of NO2 at the traffic station on the European side was found higher comparing the Asian side. The average concentrations of NO2, PM2.5, PM10 and CO during peak traffic hours were significantly (p < 0.01) decreased under COVID-19 measures. The results indicate that due to the measures taken in Istanbul and across Turkey and to control the spread of the virus, anthropogenic activities such as industry, vehicle traffic and sea transport have decreased, and consequently, air pollution has been significantly reduced. These pollutant levels demonstrate the anthropogenic contribution to air pollution and can inform clean air actions in Istanbul and in others cities throughout the world.
DOI : 10.4209/aaqr.2020.05.0239
Sayi :20
issue :9
Sayfa :1874-1885
Sınıflandırma :
2
Development of a Multi-Dimensional Parametric Model With Non-Pharmacological Policies for Predicting the COVID-19 Pandemic Casualties
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
IEEE ACCESS
Yazar(lar) :
Kemal Balikci , Sule Colak , Adem Polat , Onder Tutsoy
Yıl :
2020
Development of a Multi-Dimensional Parametric Model With Non-Pharmacological Policies for Predicting the COVID-19 Pandemic Casualties Coronavirus Disease 2019 ( COVID- 19) has spread the world resulting in detrimental effects on human health, lives, societies, and economies. In this paper, we developed Suspicious-Infected-Death with Non-Pharmacological policies (SpID-N) model to analyze the properties of the COVID- 19 casualties
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Coronavirus Disease 2019 (COVID-19) has spread the world resulting in detrimental effects on human health, lives, societies, and economies. The state authorities mostly take non-pharmacological actions against the outbreak since there are no confirmed vaccines or treatments yet. In this paper, we developed Suspicious-Infected-Death with Non-Pharmacological policies (SpID-N) model to analyze the properties of the COVID-19 casualties and also estimate the future behavior of the outbreak. We can state the key contributions of the paper with three folds. Firstly, we propose the SpID-N model covering the higher-order internal dynamics which cause the peaks in the casualties. Secondly, we parametrize the non-pharmacological policies such as the curfews on people with chronic disease, people age over 65, people age under 20, restrictions on the weekends and holidays, and closure of the schools and universities. Thirdly, we explicitly incorporate the internal and coupled dynamics of the model with these multi-dimensional non-pharmacological policies. The corresponding higher-order and strongly coupled model has utterly unknown parameters and we construct a batch type Least Square (LS) based optimization algorithm to learn these unknown parameters from the available data. The parametric model and the predicted future casualties are analyzed extensively.
DOI : 10.1109/ACCESS.2020.3044929
Sayi :8
Sayfa :225272-225283
Sınıflandırma :
3
Modeling and analysis of COVID-19 epidemics with treatment in fractional derivatives using real data from Pakistan
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
EUROPEAN PHYSICAL JOURNAL PLUS
Yazar(lar) :
Stuart Townley , Jian Zu , Sania Qureshi , Mehmet Yavuz , Parvaiz Ahmad Naik
Yıl :
2020
Modeling and analysis of COVID-19 epidemics with treatment in fractional derivatives using real data from Pakistan Novel coronavirus called COVID- 19 is a newly emerged virus that appeared in many countries of the world, but the actual source of the virus is not yet Moreover, the fitting of parameters through least squares curve fitting technique is performed, and the average absolute relative error between COVID- 19 The numerical solution of the proposed COVID- 19 fractional-order model under the Caputo operator is obtained by using generalized AdamsBashforth-Moulton
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Coronaviruses are a large family of viruses that cause different symptoms, from mild cold to severe respiratory distress, and they can be seen in different types of animals such as camels, cattle, cats and bats. Novel coronavirus called COVID-19 is a newly emerged virus that appeared in many countries of the world, but the actual source of the virus is not yet known. The outbreak has caused pandemic with 26,622,706 confirmed infections and 874,708 reported deaths worldwide till August 31, 2020, with 17,717,911 recovered cases. Currently, there exist no vaccines officially approved for the prevention or management of the disease, but alternative drugs meant for HIV, HBV, malaria and some other flus are used to treat this virus. In the present paper, a fractional-order epidemic model with two different operators called the classical Caputo operator and the Atangana-Baleanu-Caputo operator for the transmission of COVID-19 epidemic is proposed and analyzed. The reproduction number R-0 is obtained for the prediction and persistence of the disease. The dynamic behavior of the equilibria is studied by using fractional Routh-Hurwitz stability criterion and fractional La Salle invariant principle. Special attention is given to the global dynamics of the equilibria. Moreover, the fitting of parameters through least squares curve fitting technique is performed, and the average absolute relative error between COVID-19 actual cases and the model's solution for the infectious class is tried to be reduced and the best fitted values of the relevant parameters are achieved. The numerical solution of the proposed COVID-19 fractional-order model under the Caputo operator is obtained by using generalized AdamsBashforth-Moulton method, whereas for the Atangana-Baleanu-Caputo operator, we have used a new numerical scheme. Also, the treatment compartment is included in the population which determines the impact of alternative drugs applied for treating the infected individuals. Furthermore, numerical simulations of the model and their graphical presentations are performed to visualize the effectiveness of our theoretical results and to monitor the effect of arbitrary-order derivative.
DOI : 10.1140/epjp/s13360-020-00819-5
Sayi :135
issue :10
Sınıflandırma :
4
Mobilizing the research ecosystem for scientific advances towards positive impact in the context of the COVID-19 Pandemic
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
TURKISH JOURNAL OF MEDICAL SCIENCES
Yazar(lar) :
Hasan Mandal
Yıl :
2020
Mobilizing the research ecosystem for scientific advances towards positive impact in the context of the COVID-19 Pandemic - 19 infection. - 19 pandemic. - 19.
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This special issue of the Turkish Journal of Medical Sciences is dedicated to providing scientific advances in the process of better understanding the SARS-CoV-2 virus that causes the COVID-19 infection. The special issue is published in a special time in which science-based approaches, cocreation-based collaboration, and the effective utilization and integration of competences have a crucial role during the race against time while combating the COVID-19 pandemic. In this process, the Scientific and Technological Research Council of Turkey (TUBITAK), which publishes academic journals including the Turkish Journal of Medical Sciences, has taken rapid action to mobilize the research community. This includes forming new scientific coalitions in record time, the opening of new calls across the research ecosystem, the organization of a virtual scientific conference, and the launch of a new portal in support of cocreation processes and open science. In addition, various teleconferences that bring together various disciplines at the national and international level have taken place. All of these efforts provide multiple venues to support the common effort of combating the COVID-19 pandemic with R&D and development as a common objective. The sharing of evidence-based knowledge and scientific progress is an effective approach towards providing important contributions for combating the COVID-19 pandemic. The research articles that are contained in this special issue of the Turkish Journal of Medical Sciences involves a special collection dedicated to COVID-19. This short communication aims to provide an introduction of the major initiatives that have been taken in the scientific landscape with a focus on Turkey.
DOI : 10.3906/sag-2004-180
Sayi :50
Sayfa :485-488
Sınıflandırma :
5
Special Report on the Impact of the COVID-19 Pandemic on Clinical EEG and Research and Consensus Recommendations for the Safe Use of EEG
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
CLINICAL EEG AND NEUROSCIENCE
Yazar(lar) :
Hendrik Kajosch , Hendrik Kajosch , Ryouhei Ishii , Claudio Imperatori , Bahar Guntekin , Giulia Maria Giordano , Derek Fisher , Andreas Fallgatter , Carles Escera , Daniel Dumalin , Giorgio Di Lorenzo , Silvia Comani , Carla Buttinelli , Martin Brunovsky , Luigi Bianchi , Viviana Betti , Maurizio Bertollo , Michela Balconi , Claudio Babiloni , Kemal Arikan , Salvatore Campanella
Yıl :
2021
Special Report on the Impact of the COVID-19 Pandemic on Clinical EEG and Research and Consensus Recommendations for the Safe Use of EEG The global COVID- 19 pandemic has affected the economy, daily life, and mental/physical health. We report a survey of the impact of COVID- 19 on the use of clinical EEG in practice and research in several countries, and the recommendations of an international
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Introduction. The global COVID-19 pandemic has affected the economy, daily life, and mental/physical health. The latter includes the use of electroencephalography (EEG) in clinical practice and research. We report a survey of the impact of COVID-19 on the use of clinical EEG in practice and research in several countries, and the recommendations of an international panel of experts for the safe application of EEG during and after this pandemic.
DOI : 10.1177/1550059420954054
Sayi :52
issue :1
Sayfa :3-28
Sınıflandırma :
6
SARS-CoV-2 neutralizing antibody development strategies
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
TURKISH JOURNAL OF BIOLOGY
Yazar(lar) :
Aylin Ozdemir Bahadir , Saban Tekin , Hivda Ulbegi Polat , Muge Serhatli , Filiz Kaya , Fatima Yucel , Hasan Umit Ozturk , Melis Denizci Oncu , Bertan Koray Balcioglu
Yıl :
2020
The virus spread triggered a health crisis (the COVID- 19 disease) within three months, with socioeconomic implications. No approved targeted-therapies are available for COVID- 19, yet.
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In December 2019 a novel coronavirus was detected in Wuhan City of Hubei Province-China. Owing to a high rate of transmission from human to human, the new virus called SARS-CoV-2 differed from others by its unexpectedly rapid spread. The World Health Organization (WHO) described the most recent coronavirus epidemic as a global pandemic in March 2020. The virus spread triggered a health crisis (the COVID-19 disease) within three months, with socioeconomic implications. No approved targeted-therapies are available for COVID-19, yet. However, it is foreseen that antibody-based treatments may provide an immediate cure for patients. Current neutralizing antibody development studies primarily target the S protein among the structural elements of SARS-CoV-2, which mediates the cell entry of the virus through the angiotensin converting enzyme 2 (ACE2) receptor of host cells. This review aims to provide some of the neutralizing antibody development strategies for SARS-CoV-2 and in vitro and in vivo neutralization assays.
DOI : 10.3906/biy-2005-91
Sayi :44
issue :3
Sayfa :203-214
Sınıflandırma :
Biyotıp %100
Viroloji %100
7
Design tactics for enhancing the adaptability of primary and middle schools to the new needs of postpandemic reuse
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
ARCHNET-IJAR INTERNATIONAL JOURNAL OF ARCHITECTURAL RESEARCH
Yazar(lar) :
Inanc Sencan , Elif Isik Akkuyu , Handan Guzelci , Sema Alacam , Asena Kumsal Sen Bayram , Orkan Zeynel Guzelci
Yıl :
2020
design tactics (DTs) for supporting the adaptability of existing primary and middle school buildings into the emerging needs of coronavirus disease 2019 ( COVID - 19).
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Purpose - The aim of this study is to present design tactics (DTs) for supporting the adaptability of existing primary and middle school buildings into the emerging needs of coronavirus disease 2019 (COVID-19). The study introduces a novel algorithmic model for postoccupancy evaluation of the existing school buildings and provides solutions to enhance the adaptability of these buildings.
DOI : 10.1108/ARCH-10-2020-0237
Sınıflandırma :
8
Computational drug repurposing study of the RNA binding domain of SARS-CoV-2 nucleocapsid protein with antiviral agents
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
BIOTECHNOLOGY PROGRESS
Yazar(lar) :
Kemal Turhan , Ezgi Ozyurt , Gizem Tatar
Yıl :
2020
The recent outbreak of coronavirus disease ( COVID- 19) in China caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to worldwide the development of novel compounds for further in vitro and in vivo studies of SARS-CoV-2, as well as possible new drug repurposing strategies to treat COVID - 19 disease.
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The recent outbreak of coronavirus disease (COVID-19) in China caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to worldwide human infections and deaths. The nucleocapsid (N) protein of coronaviruses (CoVs) is a multifunctional RNA binding protein necessary for viral RNA replication and transcription. Therefore, it is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. This study addresses the potential to repurpose antiviral compounds approved or in development for treating human CoV induced infections against SARS-CoV-2 N. For this purpose, we used the docking methodology to better understand the inhibitory mechanism of this protein with the existing 34 antiviral compounds. The results of this analysis indicate that rapamycin, saracatinib, camostat, trametinib, and nafamostat were the top hit compounds with binding energy (-11.87, -10.40, -9.85, -9.45, -9.35 kcal/mol, respectively). This analysis also showed that the most common residues that interact with the compounds are Phe66, Arg68, Gly69, Tyr123, Ile131, Trp132, Val133, and Ala134. Subsequently, protein-ligand complex stability was examined with molecular dynamics simulations for these five compounds, which showed the best binding affinity. According to the results of this study, the interaction between these compounds and crucial residues of the target protein were maintained. These results suggest that these residues are potential drug targeting sites for the SARS-CoV-2 N protein. This study information will contribute to the development of novel compounds for further in vitro and in vivo studies of SARS-CoV-2, as well as possible new drug repurposing strategies to treat COVID-19 disease.
DOI : 10.1002/btpr.3110
Sınıflandırma :
Viroloji %99
9
Biotin Functionalized Self-Assembled Peptide Nanofiber as an Adjuvant for Immunomodulatory Response
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
BIOTECHNOLOGY JOURNAL
Yazar(lar) :
Ayse B Tekinay , Mustafa O Guler , Turgay Tekinay , Mohammad Aref Khalily , Nuray Gunduz , Sehmus Tohumeken , Muhammed Burak Demircan
Yıl :
2020
immunoengineering applications as a biomaterial for the delivery of a diverse set of antigens derived from intracellular pathogens, emerging viral diseases such as COVID - 19, or cancer cells to induce humoral and cellular immune responses against the antigens.
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Biotinylated peptide amphiphile (Biotin-PA) nanofibers, are designed as a noncovalent binding location for antigens, which are adjuvants to enhance, accelerate, and prolong the immune response triggered by antigens. Presenting antigens on synthetic Biotin-PA nanofibers generated a higher immune response than the free antigens delivered with a cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODN) (TLR9 agonist) adjuvant. Antigen attached Biotin-PA nanofibers trigger splenocytes to produce high levels of cytokines (IFN-gamma, IL-12, TNF-alpha, and IL-6) and to exhibit a superior cross-presentation of the antigen. Both Biotin-PA nanofibers and CpG ODN induce a Th-1-biased IgG subclass response; however, delivering the antigen with Biotin-PA nanofibers induce significantly greater production of total IgG and subclasses of IgG compared to delivering the antigen with CpG ODN. Contrary to CpG ODN, Biotin-PA nanofibers also enhance antigen-specific splenocyte proliferation and increase the proportion of the antigen-specific CD8(+) T cells. Given their biodegradability and biocompatibility, Biotin-PA nanofibers have a significant potential in immunoengineering applications as a biomaterial for the delivery of a diverse set of antigens derived from intracellular pathogens, emerging viral diseases such as COVID-19, or cancer cells to induce humoral and cellular immune responses against the antigens.
DOI : 10.1002/biot.202000100
Sayi :15
issue :12
Sınıflandırma :
Biyotıp %100
Antikorlar %92
10
Phylogenetic analysis of SARS-CoV-2 genomes in Turkey
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak 1:
Aperta - TÜBİTAK Açık Arşivi
Dergi:
Turkish Journal of Biology
Yazar(lar) :
Berk Turhan , Berkay Selçuk , Zeynep Kılınç , Burak İşlek , Defne Çirci , Aylin Bircan , Ogün Edebali
Yıl :
2020
COVID- 19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. COVID-19
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COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first 30 SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find 2 of the seventeen subclusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.
DOI : 10.3906/biy-2005-35-sup
Anahtar Kelimeler : genome sequence, evolution, phylogenetics, COVID-19, SARS-CoV-2
issue :44
Sayfa :146-156
Sınıflandırma :
11
iBioProVis: interactive visualization and analysis of compound bioactivity space
Araştırma Makalesi

Araştırma Makalesi
Open Access
Kaynak :
Aperta - TÜBİTAK Açık Arşivi
Dergi:
BIOINFORMATICS
Yazar(lar) :
Volkan Atalay , Rengul Cetin-Atalay , Tunca Dogan , Aybar Acar , Ahmet Sureyya Rifaioglu , Ataberk Donmez
Yıl :
2020
ACE2 binding compounds and seven antiviral drugs were closely embedded in which two of them have been under clinical trial for Coronavirus disease 19 ( COVID- 19).
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iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and in the context of compounds' cognate targets. Similar compounds, which are embedded to proximate points on the 2D map, may bind the same or similar target proteins. Thus, iBioProVis can be used to easily observe the structural distribution of one or two target proteins' known ligands on the 2D compound space, and to infer new binders to the same protein, or to infer new potential target(s) for a compound of interest, based on this distribution. Principal component analysis (PCA) projection of the input compounds is also provided, Hence the user can interactively observe the same compound or a group of selected compounds which is projected by both PCA and embedded by t-SNE. iBioProVis also provides detailed information about drugs and drug candidate compounds through cross-references to widely used and well-known databases, in the form of linked table views. Two use-case studies were demonstrated, one being on angiotensin-converting enzyme 2 (ACE2) protein which is Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein receptor. ACE2 binding compounds and seven antiviral drugs were closely embedded in which two of them have been under clinical trial for Coronavirus disease 19 (COVID-19).
DOI : 10.1093/bioinformatics/btaa496
Sayi :36
issue :14
Sayfa :4227-4230
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