PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Letter Citation - WoS: 18Yemen's Triple Emergency: Food Crisis Amid a Civil War and COVID-19 Pandemic(Elsevier, 2021-11) Hashim, Hashim Talib; Miranda, Adriana Viola; Babar, Maryam Salma; Essar, Mohammad Yasir; Hussain, Hasham; Ahmad, Shoaib; Basalilah, Ashraf Fhed MohammedYemen has been termed as the world's worst humanitarian crisis by the United Nations. About 20.1 million (more than 50% of population) Yemenis are facing hunger and 10 million are severely food insecure according to reports by the World Food Programme. With the spread of COVID-19, the situation in Yemen has worsened and humanitarian aid from other countries has become the basis of life for hundreds of thousands of Yemenis after the threat of famine. Yemen is practically one of the poorest countries in the world. It has structural vulnerabilities that have developed over a protracted period of conflict and poor governance and more than 50% live in starving, they suffer for getting one meal a day. To prevent a total collapse of Yemen's food crises, the government and the international community should act now more decisively.Article Citation - WoS: 16Citation - Scopus: 22Ultrasonic-Assisted Production of Precipitated Calcium Carbonate Particles From Desulfurization Gypsum(Elsevier, 2021-04) Altiner, Mahmut; Top, Soner; Kaymakoglu, BurcinThis study aimed to investigate the effect of ultrasonic application on the production of precipitated calcium carbonate (PCC) particles from desulfurization gypsum via direct mineral carbonation method using conventional and venturi tube reactors in the presence of different alkali sources (NaOH, KOH and NH4OH). The venturi tube was designed to determine the effect of ultrasonication on PCC production. Ultrasonic application was performed three times (before, during, and after PCC production) to evaluate its exact effect on the properties of the PCC particles. Scanning electron microscope (SEM), X-ray diffraction (XRD), Atomic force microscope (AFM), specific surface area (SSA), Fourier transform infrared spectrometry (FTIR), and particle size analyses were performed. Results revealed the strong influence of the reactor types on the nucleation rate of PCC particles. The presence of Na+ or K+ ions in the production resulted in producing PCC particles containing only calcite crystals, while a mixture of vaterite and calcite crystals was observed if NH4+ ions were present. The use of ultrasonic power during PCC production resulted in producing cubic calcite rather than vaterite crystals in the presence of all ions. It was determined that ultrasonic power should be conducted in the venturi tube before PCC production to obtain PCC particles with superior properties (uniform particle size, nanosized crystals, and high SSA value). The resulting PCC particles in this study can be suitably used in paint, paper, and plastic industries according to the ASTM standards.Article Citation - WoS: 1Citation - Scopus: 2Protocol for Determining the Average Speed and Frequency of Kinesin and Dynein-Driven Intraflagellar Transport (IFT) in C. Elegans(Elsevier, 2022-09) Turan, Merve G.; Kantarci, Hanife; Temtek, Sadiye D.; Cakici, Onur; Cevik, Sebiha; Kaplan, Oktay, IHere, we present a protocol to image a fluorescent-labeled intraflagellar trans-port (IFT) component in Caenorhabditis elegans with fluorescence microscopy, including steps of sample preparations, in vivo live-cell imaging, and post -micro-scopy analysis with kymographs. This protocol breaks down all processes into three categories: (1) pre-imaging preparations, (2) preparations for the time of image acquisition, and (3) post-imaging analyses. The protocol can be applied to determine the speed and frequency of moving particles. For complete details on the use and execution of this protocol, please refer to Cevik et al. (2021).Article Citation - WoS: 4Citation - Scopus: 4Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells(Elsevier, 2022-12) Ayaz-Guner, Serife; Acar, Mustafa Burak; Boyvat, Dudu; Guner, Huseyin; Bozalan, Habibe; Guzel, Melis; Ozcan, ServetAnalysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnet-ically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, fol-lowed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.Article Citation - WoS: 3Citation - Scopus: 4Prediction of Biomechanical Properties of Ex Vivo Human Femoral Cortical Bone Using Raman Spectroscopy and Machine Learning Algorithms(Elsevier, 2025-09) Unal, Mustafa; Unlu, Ramazan; Uppuganti, Sasidhar; Nyman, Jeffry S.This study applied Raman spectroscopy (RS) to ex vivo human cadaveric femoral mid-diaphysis cortical bone specimens (n = 118 donors; age range 21-101 years) to predict fracture toughness properties via machine learning (ML) models. Spectral features, together with demographic variables (age, sex) and structural parameters (cortical porosity, volumetric bone mineral density), were fed into support vector regression (SVR), extreme tree regression (ETR), extreme gradient boosting (XGB), and ensemble models to predict fracture-toughness metrics such as crack-initiation toughness (Kinit) and energy-to-fracture (J-integral). Feature selection was based on Raman-derived mineral and organic matrix parameters, such as nu 1Phosphate (PO4)/CH2-wag, nu 1PO4/ Amide I, and others, to capture the complex composition of bone. Our results indicate that ensemble models consistently outperformed individual models, with the best performance for crack initiation toughness (Kinit) prediction being achieved using the ensemble approach. This yielded a coefficient of determination (R2) of 0.623, root-mean squared error (RMSE) of 1.320, mean absolute error (MAE) of 1.015, and mean percentage absolute error (MAPE) of 0.134. For prediction of the overall energy to propagate a crack (J-integral), the XGB model achieved an R2 of 0.737, RMSE of 2.634, MAE of 2.283, and MAPE of 0.240. This study highlights the importance of incorporating mineral quality properties (MP) and organic matrix properties (OMP) for enhanced prediction accuracy. This work represents the first-ever study combining Raman spectroscopy with other clinical and structural features to predict fracture toughness of human cortical bone, demonstrating the potential of artificial intelligence (AI) and ML in advancing bone research. Future studies could focus on larger datasets and more advanced modeling techniques to further improve predictive capabilities.Article Citation - WoS: 2Citation - Scopus: 2Membrane Binding and Lipid-Protein Interaction of the C2 Domain From Coagulation Factor V(Elsevier, 2024) Ohkubo, Y. Zenmei; Radulovic, Peter W.; Kahira, Albert N.; Madsen, Jesper J.Anchoring of coagulation factors to anionic regions of the membrane involves the C2 domain as a key player. The rate of enzymatic reactions of the coagulation factors is increased by several orders of magnitude upon membrane binding. However, the precise mechanisms behind the rate acceleration remain unclear, primarily because of a lack of understanding of the conformational dynamics of the C2-containing factors and corresponding complexes. We elucidate the membrane-bound form of the C2 domain from human coagulation factor V (FV-C2) by characterizing its membrane binding the specific lipid -protein interactions. Employing all-atom molecular dynamics simulations and leveraging the highly mobile membrane-mimetic (HMMM) model, we observed spontaneous binding of FV-C2 to a phosphatidylserine (PS)-containing membrane within 2-25 ns across twelve independent simulations. FV-C2 interacted with the membrane through three loops (spikes 1-3), achieving a converged, stable orientation. Multiple HMMM trajectories of the spontaneous membrane binding provided extensive sampling and ample data to examine the membrane-induced effects on the conformational dynamics of C2 as well as specific lipid -protein interactions. Despite existing crystal structures representing presumed "open" and "closed" states of FV-C2, our results revealed a continuous distribution of structures between these states, with the most populated structures differing from both "open" and "closed" states observed in crystal environments. Lastly, we characterized a putative PS-specific binding site formed by K23, Q48, and S78 located in the groove enclosed by spikes 1-3 (PS-specificity pocket), suggesting a different orientation of a bound headgroup moiety compared to previous proposals based upon analysis of static crystal structures.Article Citation - WoS: 20Citation - Scopus: 28Leisure Mobility Changes During the COVID-19 Pandemic- An Analysis of Survey and Mobile Phone Data in Sweden(Elsevier, 2023-06) Osth, John; Toger, Marina; Turk, Umut; Kourtit, Karima; Nijkamp, PeterThe COVID-19 pandemic affected travelling in general, and the leisure mobility and the spatial distribution of travellers in particular. In most parts of the world, both domestic and international travel has been replaced by restrictive policies and recommendations on mobility. A modal shift from public transport towards private cars and micro-mobility was also observed. This study seeks to trace the implications of the COVID-19 pandemic for leisure mobility. We use a unique Swedish database containing daily mobility patterns of pseudonymised mobile phone users, combined with a survey on vacation transport behaviour. By contrasting mobility patterns for selected holiday days during the unaffected summer of 2019 with corresponding dates in 2020 and 2021, we are able to model and detect the pandemic effects on tourism and recreational mobility. Moreover, by identifying the general mobility patterns, we analyse whether and how the transport mode has changed. Using data on the spatial distribution of recreational amenities, we identify locations that were favoured during the pandemic. In Sweden, even though the pandemic decreased in spread and severity during the summers, most travel restrictions were still enforced, international vacations uncommon, and larger vacation spots, such as amusement parks and cultural institutions, were closed down. Swedish vacation homes in remote or rural areas were quickly booked. This change in recreational behaviour, where less populated areas, open air and nature recreation were favoured over indoor or crowded urban cultural activities, was more substantial in 2021 than in 2020. This result shows how policies can effectively be developed, so that Swedes respond properly to recommendations and adjust their vacation plans.Article Citation - WoS: 8Citation - Scopus: 8Comparative Genomics of Loigolactobacillus Coryniformis With an Emphasis on L. Coryniformis Strain FOL-19 Isolated From Cheese(Elsevier, 2023) Gumustop, Ismail; Ortakci, FatihLoigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome sequencing for FOL-19. Then, genomic characterization of FOL-19 against ten available whole genome sequences of the same species isolated from kimchi, silage, fermented meat, air of cowshed, dairy, and pheasant chyme was performed to uncover the genetic diversity and biotechnological potential of overall species. The average genome size of 2.93 +/- 0.1 Mb, GC content of 42.96% +/- 0.002, number of CDS of 2905 +/- 165, number of tRNA of 56 +/- 10, and number of CRISPR elements of 6.55 +/- 1.83 was found. Both Type I and II Cas clusters were observed in L. coryniformis. No bacteriocin biosynthesis gene clusters were found. All strains harbored at least one plasmid except KCTC 3167. All strains were predicted to carry multiple IS elements. The most common origin of the IS elements was belong to Lactiplantibacillus plantarum. Comparative genomic analysis of L. coryniformis revealed hypervariability at the strain level and the presence of CRISPR/Cas suggests that L. coryniformis holds a promising potential for being a reservoir for new CRISPR-based tools. All L. coryniformis strains except PH-1 were predicted to harbor pdu and cbi-cob-hem gene clusters encoding industrially relevant traits of reuterin and cobalamin biosynthesis, respectively. These findings put a step forward for the genomic characterization of L. coryniformis strains for biotechnological applications via genome-guided strain selection to identify industrially relevant traits.Data Paper Citation - WoS: 34Citation - Scopus: 41Big Data Acquired by Internet of Things-Enabled Industrial Multichannel Wireless Sensors Networks for Active Monitoring and Control in the Smart Grid Industry 4.0(Elsevier, 2021-04) Faheem, Muhammad; Fizza, Ghulam; Ashraf, Muhammad Waqar; Butt, Rizwan Aslam; Ngadi, Md. Asri; Gungor, Vehbi CagriSmart Grid Industry 4.0 (SGI4.0) defines a new paradigm to provide high-quality electricity at a low cost by reacting quickly and effectively to changing energy demands in the highly volatile global markets. However, in SGI4.0, the reliable and efficient gathering and transmission of the observed information from the Internet of Things (IoT)-enabled Cyberphysical systems, such as sensors located in remote places to the control center is the biggest challenge for the Industrial Multichannel Wireless Sensors Networks (IMWSNs). This is due to the harsh nature of the smart grid environment that causes high noise, signal fading, multipath effects, heat, and electromagnetic interference, which reduces the transmission quality and trigger errors in the IMWSNs. Thus, an efficient monitoring and real-time control of unexpected changes in the power generation and distribution processes is essential to guarantee the quality of service (QoS) re-quirements in the smart grid. In this context, this paper de-scribes the dataset contains measurements acquired by the IMWSNs during events monitoring and control in the smart grid. This work provides an updated detail comparison of our proposed work, including channel detection, channel assign-ment, and packets forwarding algorithms, collectively called CARP [1] with existing G-RPL [2] and EQSHC [3] schemes in the smart grid. The experimental outcomes show that the dataset and is useful for the design, development, testing, and validation of algorithms for real-time events monitoring and control applications in the smart grid. (C) 2021 The Authors. Published by Elsevier Inc.Data Paper Citation - WoS: 26Citation - Scopus: 33Big Datasets of Optical-Wireless Cyber-Physical Systems for Optimizing Manufacturing Services in the Internet of Things-Enabled Industry 4.0(Elsevier, 2022-06) Faheem, Muhammad; Butt, Rizwan AslamThe Industry 4.0 revolution is aimed to optimize the product design according to the customers' demand, quality requirements and economic feasibility. Industry 4.0 employs advanced two-way communication technologies for optimizing the manufacturing process to increase the sales of the products and revenues to cope the existing global economy issues. In Industry 4.0, big data obtained from the Internet of Things (IoT)-enabled industrial Cyber-Physical Systems (CPS) plays an important role in enhancing the system service performance to boost the productivity with enhanced quality of customer experience. This paper presents the big datasets obtained from the Internet of things (IoT)-enabled Optical Wireless Sensor Networks (OWSNs) for optimizing service systems' performance in the electronics manufacturing Industry 4.0. The updated raw and analyzed big datasets of our published work [3] contain five values namely, data delivery, latency, congestion, throughput, and packet error rate in OWSNs. The obtained dataset are useful for optimizing the service system performance in the electronics manufacturing Industry 4.0. (c) 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)