Prediction of peptides binding to MHC class I and II alleles by temporal motif mining

Background: MHC (Major Histocompatibility Complex) is a key player in the immune response of most vertebrates. The computational prediction of whether a given antigenic peptide will bind to a specific MHC allele is important in the development of vaccines for emerging pathogens, the creation of possibilities for controlling immune response, and for the applications of immunotherapy. One of the problems that make this computational prediction difficult is the detection of the binding core region in peptides, coupled with the presence of bulges and loops causing variations in the total sequence length. Most machine learning methods require the sequences to be of the same length to successfully discover the binding motifs, ignoring the length variance in both motif mining and prediction steps. In order to overcome this limitation, we propose the use of time-based motif mining methods that work position-independently. Results: The prediction method was tested on a benchmark set of 28 different alleles for MHC class I and 27 different alleles for MHC class II. The obtained results are comparable to the state of the art methods for both MHC classes, surpassing the published results for some alleles. The average prediction AUC values are 0.897 for class I, and 0.858 for class II. Conclusions: Temporal motif mining using partial periodic patterns can capture information about the sequences well enough to predict the binding of the peptides and is comparable to state of the art methods in the literature. Unlike neural networks or matrix based predictors, our proposed method does not depend on peptide length and can work with both short and long fragments. This advantage allows better use of the available training data and the prediction of peptides of uncommon lengths

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining

Background: MHC (Major Histocompatibility Complex) is a key player in the immune response of most vertebrates. The computational prediction of whether a given antigenic peptide will bind to a specific MHC allele is important in the development of vaccines for emerging pathogens, the creation of possibilities for controlling immune response, and for the applications of immunotherapy. One of the problems that make this computational prediction difficult is the detection of the binding core region in peptides, coupled with the presence of bulges and loops causing variations in the total sequence length. Most machine learning methods require the sequences to be of the same length to successfully discover the binding motifs, ignoring the length variance in both motif mining and prediction steps. In order to overcome this limitation, we propose the use of time-based motif mining methods that work position-independently. Results: The prediction method was tested on a benchmark set of 28 different alleles for MHC class I and 27 different alleles for MHC class II. The obtained results are comparable to the state of the art methods for both MHC classes, surpassing the published results for some alleles. The average prediction AUC values are 0.897 for class I, and 0.858 for class II. Conclusions: Temporal motif mining using partial periodic patterns can capture information about the sequences well enough to predict the binding of the peptides and is comparable to state of the art methods in the literature. Unlike neural networks or matrix based predictors, our proposed method does not depend on peptide length and can work with both short and long fragments. This advantage allows better use of the available training data and the prediction of peptides of uncommon lengths

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure

Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. Conclusions: Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for \u3ci\u3eGalanthus\u3c/i\u3e L. Using the relative complexity measure

Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. Conclusions: Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters

Kişilerarası Çatışma Çözme Yaklaşımlarında Kontrol Odağının Rolü

Bu çalışmada, iletişim süreçlerine odaklanan kişilerarasıçatışma çözme yaklaşımlarıile kişisel bir değişken olan kontrol odağının bu yaklaşımların benimsenmesinde herhangi bir rolünün olup olmadığının araştırılmasıamaçlanmıştır. Araştırmanın örneklemini Ankara’da öğrenim gören ve yaşları18 ile 26 arasında değişen 307 üniversite öğrencisi oluşmaktadır. Araştırmada anket yöntemiyle veri toplanmışve ölçüm araçlarıolarak; ulusal kültüre uyarlama çalışmalarıyapılmışolan KişilerarasıÇatışma Çözme YaklaşımlarıÖlçeği ve Kontrol OdağıÖlçeği kullanılmıştır. Elde edilen bulgular; özellikle iç kontrol odaklıkişilerin yapıcıve olumlu çözüm süreçleri açısından yüzleşmeye daha çok önem verdiklerini, genel davranışsergilediklerini, çatışmaya yaklaştıklarını, kendilerini daha çok açtıklarınıve duygularınıdaha fazla sergilediklerini göstermektedir. Bununla birlikte demografik değişkenlerden cinsiyetin de çözüm yaklaşımlarının benimsenmesinde önemli rol oynadığıve kadınların çatışma süreçlerinde daha fazla yüzleştikleri, kendilerini daha çok açtıklarıve daha fazla duygusal ifadeler sergileyerek çözüme yönelik daha aktif ve etkili davranışlarda bulunduklarıortaya çıkmıştır. Tüm bu bulgular, kişilerarasıçatışma çözme süreçlerinde kişilik ve cinsiyet değişkenlerinin önemli rol oynadığınıgöstermektedir

Structural, surface morphology, dielectric and magnetic properties of holmium doped BiFeO3 thin films prepared by pulsed laser deposition

In this work, Bi1-xHoxFeO3 (with x = 0, 0.05, 0.10, 0.15 and 0.20) thin films were successfully grown on Si (100) substrates using pulsed laser deposition and the effect of Ho doping on the crystal structure, dielectric and magnetic properties were studied. X-ray diffraction studies on undoped BiFeO3 confirmed the presence of a rhombohedral phase with crystallite sizes in the 14–24 nm range. The surface morphology and microstructure of the thin films were analysed by field emission scanning electron microscopy and atomic force microscopy. The results reveal that the grain size decreases as the Ho doping concentration increases. X-ray photoemission spectroscopy was used to identify the chemical bonding, valance band and core levels of Ho doped BiFeO3 thin films. Dielectric constant and loss in Ho doped samples has been measured using a vector network analyzer and shows good dielectric behaviour compared to undoped BiFeO3. A vibrating sample magnetometer was used to investigate the magnetic properties for Ho doping with concentrations of x ≥ 0.15. In comparison to undoped BiFeO3, the doped films exhibited larger remanence and saturation magnetization. The enhancement of these properties due to Ho doping is discussed along with their relevance in designing multiferroic materials based on Bi1-xHoxFeO3 films for magnetic field sensors, multiple-state memories and spintronic elements

500,000 Years of Environmental History in Eastern Anatolia: The PALEOVAN Drilling Project

International Continental Scientific Drilling Program (ICDP) drilled a complete succession of the lacustrine sediment sequence deposited during the last ~500,000 years in Lake Van, Eastern Anatolia (Turkey). Based on a detailed seismic site survey, two sites at a water depth of up to 360 m were drilled in summer 2010, and cores were retrieved from sub-lake-floor depths of 140 m (Northern Basin) and 220 m (Ahlat Ridge). To obtain a complete sedimentary section, the two sites were multiple-cored in order to investigate the paleoclimate history of a sensitive semi-arid region between the Black, Caspian, and Mediterranean seas. Further scientific goals of the PALEOVAN project are the reconstruction of earthquake activity, as well as the temporal, spatial, and compositional evolution of volcanism as reflected in the deposition of tephra layers. The sediments host organic matter from different sources and hence composition, which will be unravelled using biomarkers. Pathways for migration of continental and mantle-derived noble gases will be analyzed in pore waters. Preliminary 40Ar/39Ar single crystal dating of tephra layers and pollen analyses suggest that the Ahlat Ridge record encompasses more than half a million years of paleoclimate and volcanic/geodynamic history, providing the longest continental record in the entire Near East to date

Evidence Map of Pancreatic Surgery–A living systematic review with meta-analyses by the International Study Group of Pancreatic Surgery (ISGPS)

Background: Pancreatic surgery is associated with considerable morbidity and, consequently, offers a large and complex field for research. To prioritize relevant future scientific projects, it is of utmost importance to identify existing evidence and uncover research gaps. Thus, the aim of this project was to create a systematic and living Evidence Map of Pancreatic Surgery. Methods: PubMed, the Cochrane Central Register of Controlled Trials, and Web of Science were systematically searched for all randomized controlled trials and systematic reviews on pancreatic surgery. Outcomes from every existing randomized controlled trial were extracted, and trial quality was assessed. Systematic reviews were used to identify an absence of randomized controlled trials. Randomized controlled trials and systematic reviews on identical subjects were grouped according to research topics. A web-based evidence map modeled after a mind map was created to visualize existing evidence. Meta-analyses of specific outcomes of pancreatic surgery were performed for all research topics with more than 3 randomized controlled trials. For partial pancreatoduodenectomy and distal pancreatectomy, pooled benchmarks for outcomes were calculated with a 99% confidence interval. The evidence map undergoes regular updates. Results: Out of 30, 860 articles reviewed, 328 randomized controlled trials on 35, 600 patients and 332 systematic reviews were included and grouped into 76 research topics. Most randomized controlled trials were from Europe (46%) and most systematic reviews were from Asia (51%). A living meta-analysis of 21 out of 76 research topics (28%) was performed and included in the web-based evidence map. Evidence gaps were identified in 11 out of 76 research topics (14%). The benchmark for mortality was 2% (99% confidence interval: 1%–2%) for partial pancreatoduodenectomy and <1% (99% confidence interval: 0%–1%) for distal pancreatectomy. The benchmark for overall complications was 53% (99%confidence interval: 46%–61%) for partial pancreatoduodenectomy and 59% (99% confidence interval: 44%–80%) for distal pancreatectomy. Conclusion: The International Study Group of Pancreatic Surgery Evidence Map of Pancreatic Surgery, which is freely accessible via www.evidencemap.surgery and as a mobile phone app, provides a regularly updated overview of the available literature displayed in an intuitive fashion. Clinical decision making and evidence-based patient information are supported by the primary data provided, as well as by living meta-analyses. Researchers can use the systematic literature search and processed data for their own projects, and funding bodies can base their research priorities on evidence gaps that the map uncovers. © 2021 The Author