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Publication Metadata only A Bayesian generalized linear model for Crimean–Congo hemorrhagic fever incidents(Springer, 2018) Ryu, Duchwan; Bilgili, Devrim; Liang, Faming; Ebrahimi, Nader; Ergönül, Önder; Faculty Member; School of Medicine; 110398Global spread of the Crimean-Congo hemorrhagic fever (CCHF) is a fatal viral infection disease found in parts of Africa, Asia, Eastern Europe and Middle East, with a fatality rate of up to 30%. A timely prediction of the prevalence of CCHF incidents is highly desirable, while CCHF incidents often exhibit nonlinearity in both temporal and spatial features. However, the modeling of discrete incidents is not trivial. Moreover, the CCHF incidents are monthly observed in a long period and take a nonlinear pattern over a region at each time point. Hence, the estimation and the data assimilation for incidents require extensive computations. In this paper, using the data augmentation with latent variables, we propose to utilize a dynamically weighted particle filter to take advantage of its population controlling feature in data assimilation. We apply our approach in an analysis of monthly CCHF incidents data collected in Turkey between 2004 and 2012. The results indicate that CCHF incidents are higher at Northern Central Turkey during summer and that some beforehand interventions to stop the propagation are recommendable. Supplementary materials accompanying this paper appear on-line.Publication Open Access A disconnect between upslope shifts and climate change in an Afrotropical bird community(Wiley, 2020) Neate-Clegg, Montague H. C.; O'Brien, Timothy G.; Mulindahabi, Felix; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 327589Climate change threatens to push species to higher elevations and eventual extinction. Birds, in particular, are shown to be shifting upslope in the Neotropics and Southeast Asia. Yet previous studies have lacked the temporal resolution to investigate distributional dynamics over time in relation to climatic fluctuations, especially in the understudied Afrotropics. Here, we used 15 years of point-count data from across an elevational gradient (1,767-2,940 m) in Rwanda, to assess elevational shift rates and dynamics in a community of Afrotropical birds. In general, species shifted their elevations upslope by 1.9 m/year, especially at their lower elevational limits which shifted by 4.4 m/year. Importantly, these shifts occurred despite the fact that local temperature and precipitation showed little trend over the study period. Moreover, the interannual distributions of few species were associated with temperature, suggesting that temperature played little direct role in determining elevational distributions of birds. Instead, upslope shifts may be more related to incremental shifts in habitat and resources which lag behind decades of increased temperature in the region. Precipitation appeared to have more of an effect than temperature in determining interannual elevational changes, allowing species to expand their ranges in years of higher rainfall. Our results highlight the need to understand the mechanisms driving upslope shifts as they occur throughout the tropics. It will be critical for montane regions of the tropics to preserve contiguous blocks of forest across elevational gradients to allow wildlife to shift unimpeded.Publication Metadata only A survey of women who cryopreserved oocytes for non-medical indications (social fertility preservation)(Springer, 2021) Akin, Öznur Dündar; Ertaş, Sinem; N/A; N/A; N/A; N/A; Ata, Ayşe Seyhan; Ata, Mustafa Barış; Yakın, Kayhan; Urman, Cumhur Bülent; Doctor; Faculty Member; Faculty Member; Faculty Member; N/A; School of Medicine; School of Medicine; School of Medicine; American Hospital; School of Medicine; N/A; N/A; N/A; 182910; 106822; 12147To evaluate the expectations, experiences, and fertility awareness status of women who underwent social oocyte cryopreservation. Cohort survey study was conducted at an academic medical center. All women who underwent social oocyte cryopreservation between January 2015 and June 2016 were recruited. One hundred thirty-three women were contacted by phone to participate in a survey. The questionnaire investigated the initial motivation towards freezing, intentions to use cryopreserved oocytes, treatment experience, awareness of fertility and knowledge about chances of having a live birth with their frozen oocytes. The mean age at the time of oocyte freezing was 38.5 +/- 2.68 years. The average number of mature oocytes cryopreserved was 5.48 +/- 6.6 (1-16). Two major motivations were absence of a male partner (40%) and an anticipated age-related fertility decline (42%). Almost 60% overestimated the chances of natural conception, as well as the success of IVF at the age of 40 years. Half of the oocyte bankers reported that fertility declined between ages 35 and 39, but only 28% of patients estimated the live birth rate per cryopreserved oocyte correctly. Overall 98.8% stated that they would recommend oocyte cryopresevation to a friend, and 72% felt more secure in terms of reproductive potential. Despite comprehensive personalized counseling prior to the start of ovarian stimulation, many women do not seem to have a realistic understanding of reproductive aging. Even though gamete cryopreservation provides some insurance, overestimating the effectiveness of oocyte cryopreservation can also lead to a false sense of security.Publication Metadata only Bayesian framework for parametric bivariate accelerated lifetime modeling and its application to hospital acquired infections(Wiley, 2016) Bilgili, D.; Ryu, D.; Ebrahimi, N; Ergönül, Önder; Faculty Member; School of Medicine; 110398Infectious diseases that can be spread directly or indirectly from one person to another are caused by pathogenic microorganisms such as bacteria, viruses, parasites, or fungi. Infectious diseases remain one of the greatest threats to human health and the analysis of infectious disease data is among the most important application of statistics. In this article, we develop Bayesian methodology using parametric bivariate accelerated lifetime model to study dependency between the colonization and infection times for Acinetobacter baumannii bacteria which is leading cause of infection among the hospital infection agents. We also study their associations with covariates such as age, gender, apache score, antibiotics use 3 months before admission and invasive mechanical ventilation use. To account for singularity, we use Singular Bivariate Extreme Value distribution to model residuals in Bivariate Accelerated lifetime model under the fully Bayesian framework. We analyze a censored data related to the colonization and infection collected in five major hospitals in Turkey using our methodology. The data analysis done in this article is for illustration of our proposed method and can be applied to any situation that our model can be used.Publication Metadata only Dealing with repetitions in sequencing by hybridization(Elsevier, 2006) Blazewicz, Jacek; Glover, Fred; Kasprzak, Marta; Markiewicz, Wojciech T.; Rebholz-Schuhmann, Dietrich; Swiercz, Aleksandra; Department of Industrial Engineering; Oğuz, Ceyda; Faculty Member; Department of Industrial Engineering; College of Engineering; 6033DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divided into two groups. The first group consisted of sequences containing positive and negative errors in the spectrum, at a rate of up to 20%, excluding errors coming from repetitions. The second group consisted of sequences containing repeated oligonucleotides, and containing additional errors up to 5% added into the spectra. Our new method outperforms the best alternative procedures for both data sets. Moreover, the method produces solutions exhibiting extremely high degree of similarity to the target sequences in the cases without repetitions, which is an important outcome for biologists.Publication Open Access Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific(Canadian Science Publishing, 2021) Hobbs, James; Baxter, Randall; Lewis, Levi S.; Benjamin, Alyssa; Finger, Amanda J.; Department of Molecular Biology and Genetics; Sağlam, İsmail Kudret; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 168783The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations.Publication Metadata only How to tackle natural focal infections: from risk assessment to vaccination strategies(Springer International Publishing Ag, 2017) Busani, Luca; Platonov, Alexander E.; Rezza, Giovanni; Ergönül, Önder; Faculty Member; School of Medicine; 110398Natural focal diseases are caused by biological agents associated with specific landscapes. The natural focus of such diseases is defined as any natural ecosystem containing the pathogen's population as an essential component. In such context, the agent circulates independently on human presence, and humans may become accidentally infected through contact with vectors or reservoirs. Some viruses (i.e., tick-borne encephalitis and Congo-Crimean hemorrhagic fever virus) are paradigmatic examples of natural focal diseases. When environmental changes, increase of reservoir/vector populations, demographic pressure, and/or changes in human behavior occur, increased risk of exposure to the pathogen may lead to clusters of cases or even to larger outbreaks. Intervention is often not highly cost-effective, thus only a few examples of large-scale or even targeted vaccination campaigns are reported in the international literature. To develop intervention models, risk assessment through disease mapping is an essential component of the response against these neglected threats and key to the design of prevention strategies, especially when effective vaccines against the disease are available.Publication Metadata only Microrna analysis of human decidua mesenchymal stromal cells from preeclampsia patients(W B Saunders Co Ltd, 2021) Kamali Simsek, Nilüfer; Benian, Ali; Çelik, Hale Göksever; Günel, Tuba; N/A; N/A; N/A; Şevgin, Kübra; Ergün, Yağmur; Karahüseyinoğlu, Serçin; N/A; Master Student; Faculty Member; N/A; Graduate School of Health Sciences; School of Medicine; N/A; N/A; 110772Introduction: In preeclampsia (PE), human decidua mesenchymal stromal cells (hDMSCs) are exposed to abnormally high levels of oxidative stress and inflammatory factors circulating in the maternal blood. MicroRNAs (miRNAs) have been shown to have a significant impact on the differentiation, maturation and function of mesenchymal stromal cells (MSCs). Our aim in the present study is firstly to investigate differentially expressed miRNA levels to be used as a biomarker in the early detection of PE and secondly to investigate whether those differentially expressed miRNAs in hDMSCs have an effect on the pathogenesis of PE. Methods: This study covers miRNA expression analysis of hDMSCs from 7 PE patient and 7 healthy pregnant women and is a preliminary study to investigate putative biomarkers. After cell culture and cell sorting, total RNA including miRNAs were isolated from hDMSCs. Let 7b 3p, let 7f 1 3p, miR-191-3p, miR-550a-5p, miR-33b-3p and miR-425-3p were used for miRNA analysis and U6 snRNA was used for normalization of the samples. MiRNA analysis was performed by droplet digital polymerase chain reaction (ddPCR) method and obtained results were evaluated statistically. Results: As a result of the analysis, it was observed that the levels of hsa-miR-33b-3p significantly (AUC: 0.93, p = 0.04, fold change: 4.5) increased in hDMSC of PE patients compared to healthy controls. However, let-7b-3p, let7f-1-3p, miR-191-3p, miR-550a-5p, and miR-425-3p were not considered as significant because they did not meet the p < 0,05 requirement. Discussion: Within the scope of the study, it is predicted that miR-33b-3p (p = 0.004, AUC = 0.93) can be used as a biomarker in detecting PE.Publication Metadata only Modeling reflex asymmetries with implicit delay differential equations(Elsevier, 1998) Mallet-Paret, J; Department of Mathematics; Atay, Fatihcan; Faculty Member; Department of Mathematics; College of Sciences; 253074Neuromuscular reflexes with time-delayed negative feedback, such as the pupil light reflex, have different rates depending on the direction of movement. This asymmetry is modeled by an implicit first-order delay differential equation in which the value of the rate constant depends on the direction of movement. Stability analyses are presented for the cases when the rate is: (1) an increasing and (2) a decreasing function of the direction of movement. It is shown that the stability of equilibria in these dynamical systems depends on whether the rate constant is a decreasing or increasing function. In particular, when the asymmetry has the shape of an increasing step function, it is possible to have stability which is independent of the value of the time delay or the steepness (i.e., gain) of the negative feedback. (C) 1998 Society for Mathematical Biology.Publication Open Access Multi-modal communication: song sparrows increase signal redundancy in noise(The Royal Society, 2019) Beecher, Michael D.; Department of Psychology; Akçay, Çağlar; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 272053Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has focused on signals in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poorly understood. Here, we ask whether song sparrows (Melospiza melodia) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.