Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.Comment: 21 pages, 7 figures, 1 tabl

Stakeholders’ Perspectives on Utilization of Logging Residues for Bioenergy in Turkey

Although using logging residues for bioenergy is not a new issue for countries such as Sweden, Finland, Austria, Germany, etc. that are developed in terms of forestry, it is a new issue that requires studying for countries such as Turkey. This study investigates the views of forest engineers working in forest enterprises, researchers working in forestry research institutes and academicians working at universities concerning the use of logging residues for bioenergy that are not currently used in energy production. Within the framework of the study, a questionnaire was sent out to 181 forest engineers, 77 academic staff members and 29 research institute employees, a total of 287 respondents. According to the results of the study, logging residues that are either left in the forest floor or collected by forest villagers for the purpose of fire wood have a favorable potential for energy and forestry if they are used in bioenergy production. Thus, the issue is substantial and of primary importance for Turkey. On the other hand, there are barriers in developing bioenergy sector and using logging residues for this purpose. In order to remove these barriers, first of all, forestry administration should clarify its strategies and policies related to the issue

Information content capabilities of very high resolution optical space imagery for updating GIS database

Nowadays, the number and capacity of very high resolution optical satellites grows permanently, so the access to very high resolution space images is not any more a problem. The use of Geographic Information Systems (GISs) together with Remote Sensing became important. With the increased ground resolution a competition to aerial images exist. For the generation of topographic maps, today available as GIS, the accuracy and the information content - what elements can be identified in the image - are important. Both may limit the presentation scale of topographic maps. As horizontal accuracy 0.25mm up to 0.3mm in the map scale are accepted. The required information content is more complicate. The object details to be presented in topographic maps vary from area to area which is based on the planned and unplanned areas. In this study, images from IRS-1C, Kompsat-1, SPOT 5, OrbView-3, IKONOS, QuickBird and WorldView-1 have been used for topographic mapping. For this reason, Zonguldak test fields are an important area for applications of the high resolution imageries. The details which can be identified in the space images dominantly depends upon the ground resolution, available as ground sampling distance (GSD). In this study, high resolution imageries have been tested depending on the GSD and corresponding to the map scales for updating GIS database. © 2015 SPIE

Osculating mate of a Frenet curve in the Euclidean 3-space

A new kind of partner curves called osculating mate of a Frenet curve is introduced. Some characterizations for osculating mate are obtained and using the obtained results some special curves such as slant helix, spherical helix, C-slant helix and rectifying curve are constructed

Slant helices and Darboux helices in Myller Configuration

In this paper, we study slant helix (or $\overset{\_}{\xi}_{2}$-helix) and Darboux helix in Myller configuration $M$. We show that a curve in $M$ is a slant helix if and only if it is a Darboux helix. We give the alternative frame of a curve in $M$. Furthermore, we obtain the differential equations characterizing the curves in $M$ by means of both Frenet type frame and alternative frame.Comment: arXiv admin note: text overlap with arXiv:2305.0754

The Evaluation of Clinicopathological and Immunohistochemical Findings of Cervical Clear Cell Carcinoma in a Bitch

Background: Clear cell carcinoma (CCC) of the cervix is a rarely seen malignant tumor which is classified in adenocarcinomas of the endometrium. It is responsible for 2.15-3.0% of endometrial tumors. The diagnosis is difficult and is still controversial in uterine carcinomas. Macroscopically, masses were protruding to endometrial surface. However, the definitive diagnosis was carried by microscopical evaluation. The cells contain clear cytoplasm. The cells are seen in this pattern because there is either glycogenation or secretoric activity in the cells.Case: In the present case, clinicopathologic and immunohistochemical findings of clear cell carcinoma of the cervix were defined in a 3 year-old spayed Golden retriever bitch. Previously spayed bitch, which had vaginal discharge for the last month-long, was submitted to the Department of Obstetrics and Gynecology, Ankara University, Faculty of VeterinaryMedicine. In the general clinical examination, vaginoscopy was performed and vaginal cytology was obtained from smear. The source of discharge was detected as cervix uteri. In vaginal cytologic examination, erythrocyte, neutrophile and superficial cells were observed. In abdominal ultrasonography, a hypoechoic mass was detected at cranial part of the urinary bladder. To evaluate the general health condition of the dog, total blood counting and serum biochemistry were analyzed in addition to assessing its hormone prophlye. Estrogen and progesterone levels were evaluated. Estradiol (E2) level was measured as 23 pg/mL and progesterone level was measured as 1.96 ng/mL from collected serum. The cervical mass in diameters of 3x4x2.5 cm was removed in operation. In macroscopical examination, it had spherical and regularly shape.After the macroscopical examination, tissue samples were fixed in 10% buffered formalin. Then, the samples stained with Haematoxylin-Eosin (H&E), Masson’s trichrome and PAS stainings, respectively. At the macroscopic and histological examinations, the mass was diagnosed as clear cell carcinoma. Immunohistochemically, the tumor was stained with CK19 α-SMA, vimentin, desmin, TGF-β, VEGF, CEA, ER and PR markers. Other markers gave moderate to severe reactions in exception for no or weak ER and PR positivities. In direction of these results, clear cell carcinoma of cervix had been found remarkably due to first description in a spayed bitch on the basis of knowledge.Discussion: Clear cell carcinoma (CCC) is one type of the endometrial carcinomas. It is frequently known to have aggressive behavior and unfavorable prognosis. In human counterparts, clear cell carcinoma is frequently reoccurred in caudoabdominal and pelvic region even after being removed. The occurrence of clear cell carcinoma has highly increasedwith diethylstilbestrol usage during pregnancy. The situation on uterine carcinoma is nearly same in domestic animals. It is related to prolonged estrogenism. In this case, the bitch has been under prolong exposure to estrogenic effect. Indeed the estradiol level was high when compared to spayed female. Also, it is thought that the reason of high estradiol leveldoes not depend on the ovarian remnant. It is believed this situation may be relevant to exogen hormone usage. Vaginal smear confirmed erythrocyte (due to bleeding), predominantly superficial cells to it’s under estrogenic effect even despite being spayed.Keywords: clear cell carcinoma, cervix, clinicopathology, marker, bitch

DESIGN AND DEVELOPMENT OF AN LADM-BASED EXTERNAL DATA MODEL FOR LAND REGISTRY AND CADASTRE TRANSACTIONS IN TURKEY: A CASE STUDY OF TREASURY REAL PROPERTIES

The processes starting with the identification and registration of treasury properties have an essential place in the cadastral systems. Spatial data modelling studies were conducted in 2002 to establish a common standard structure on the fundamental similarities of land management systems. These studies were stated as a beginning named Core Cadastral Domain Model (CCDM), since 2006, it has been started to be made under the name of LADM. This model was accepted in 2012 as a standard model in the field of land administration by the International Organization for Standardization (ISO). In this study, an external model class is proposed for LADM’s transactions related to Treasury’s real estates properties which are related National Property Automation Project (MEOP). In order to determine the deficiency of this current external model, databases containing records related to spatial data and property rights were examined, and the deficiencies related to transactions on treasury properties were determined. The created external class is associated with the LADM’s LA_Party, LA_RRR, LA_SpatialUnit and LA_BAUnit master classes. Herewith the standardization of the external data model is ensured. If the external model is implemented by the responsible standardization of the archiving processes will be more comfortable and faster to registe

Alemdar Mustafa Paşa’nın devlet hayatı

06.03.2018 tarihli ve 30352 sayılı Resmi Gazetede yayımlanan “Yükseköğretim Kanunu İle Bazı Kanun Ve Kanun Hükmünde Kararnamelerde Değişiklik Yapılması Hakkında Kanun” ile 18.06.2018 tarihli “Lisansüstü Tezlerin Elektronik Ortamda Toplanması, Düzenlenmesi ve Erişime Açılmasına İlişkin Yönerge” gereğince tam metin erişime açılmıştır.Alemdar Mustafa Paşa 1765 yılında Hotin'de doğdu. Hacı Hasan Ağa'nın oğludur. Babası gibi Yeniçeri Ocağı'na girmiştir. Daha sonra Tirsinikli İsmail Ağa'nın hizmetine girmiştir. Kısa sürede Efendisinin güvenini kazanıp, kabiliyeti sayesinde hızla yükselmiştir. Alemdar Mustafa'nın lakabı İsmail Efendisine bayraktarlık yapmasından ileri gelir.Alemdar Mustafa kazandığı başarılarla önce Hassa Silahşörü rütbesi (1799) daha sonra Kapıcıbaşılık rütbesini (1803) bir müddet sonra da Hezargrad âyanlığına tayin edilmiştir. Alemdar Mustafa, Tirsinikli İsmail'in ölümü üzerine onun yerine Ruscuk âyanı oldu (1806). Bu sırada başlayan Rusya savaşı sırasında Rumeli'de oluşan zafiyet dolayısıyla III. Selim tarafından Alemdar Mustafa'ya önce vezirlik rütbesi ve Silistre valiliği daha sonra Tuna Seraskerliği verilmiştir (Şubat 1807)Bu savaş sırasında tertiplenen Kabakçı Mustafa isyanı neticesinde III. Selim tahttan indirilip, Nizam-ı Cedit'e son verilip IV. Mustafa tahta çıkarılmıştır. Bu sırada İstanbul'da ve orduda Nizam-ı Cedit ricali avı başlamıştır. Bunun üzerine Ruscuk Yaranı denilen kişiler Alemdar Mustafa Paşa'ya sığınmışlardır. Daha sonra Alemdar Mustafa'yla anlaşan Ruscuk Yaranı III. Selim'i tekrar tahta çıkarmak için İstanbul'a gelmeyi başarmışlardır. Alemdar Mustafa İstanbul'a varmadan önce adamını gönderip Kabakçı Mustafa'yı öldürtmüştür.Kendisinin yerine Alemdar Mustafa'nın III. Selim'i tahta çıkaracağını anlayan IV. Mustafa, III. Selim ve II. Mahmud'un öldürülmeleri için emir vermiştir. III. Selim'i öldürtmüş ama II: Mahmud kurtulmayı başarmıştır. Padişah olan II. Mahmud, Alemdar'ı sadrazam yapmıştır. Sadrazam olan Alemdar Mustafa Paşa âyanları toplayarak Sened-i İttifak denen belgeyi oluşturmuş ve Sekban-ı Cedid denen orduyu kurmuştur. Daha sonra Yeniçeriler tarafından tertiplenen bir isyan sırasında kendi konağında sıkışan Alemdar Mustafa Paşa intihar ederek kendisiyle beraber 300-400 Yeniçeriyi de öldürmüştür.Anahtar Kelimeler: Alemdar Mustafa Paşa, III. Selim, IV. Mustafa, Kabakçı Mustafa, Sened-i İttifakAlemdar Mustafa Pasha was born in 1765 in Hotin. He was the son of Hacı Hasan Aga. Like his dad, He enrolled the janissaries, then entered the service of Tirsinikli İsmail Aga. In a short time, due to the confidence of his master, he increased his popularity rapidly. His Monikers (onun lakabı İsmail Efendisine bayraktarlık yapmasından ileri gelir)With his rank of successes, he was appointed Hassa Silahşörü (1799) then Kapıcıbaşılık rütbesi (1803) and then Hezargrad âyanlığı. Because of the death of Tirsinikli İsmail, Alemdar Mustafa became the Ruscuk âyanı instead of him (1806).Due to beginning of Russian war at this time, which had cawsed vulnerability in Rumeli, He gained the Grand vizier rütbesi, then was given the governship of Silistre, then was given Tuna Seraskerliği (February 1807).During this war, as a result of Kabakçı Mustafa Rebellion, III. Selim was downloaded from the throne and IV. Mustafa was ascended to the throne. For this time It had begun hunting both in İstanbul and army to Nizam-ı Cedid.As a resut, Ruscuk Yaranı achieved to come back İstanbul fort o ascend him (III. Selim) to the throne back. Alemdar Mustafa was killed Kabakçı Mustafa on his way. As IV. Mustafa understood, who would ascend the throne, III. Selim was killed by IV. Mustafa; but II. Mahmud was succeded to get rid of from him.The Sultan II. Mahmud made Grand vizier to him. The Grand Vizier Alemdar collected Âyans and created the document which was called Sened-i İttifak and and set up the Sekban-ı Cedid Army.Later, during a riot organized by janissaries, he committed suicide in his own mansionKeywords: Alemdar Mustafa Pasha, III. Selim, IV. Mustafa, Kabakçı Mustafa, Sened-i İttifa

Clinicopathological Evaluation of Disseminated Metastases of Transmissible Venereal Tumor in a Spayed Bitch

Background: Although transmissible venereal tumor (TVT, transmissible venereal sarcoma, Sticker’s sarcoma) that affects dogs and other canids can be seen in many countries, it especially emerges in the countries which homeless dog population is very high. Female dogs are more susceptible than males. Transmissible venereal tumor is usually transmitted to genital organs during coitus and occasionally by social behavior such as sniffing and licking. The tumor is generally observed in the posterior part of the vagina. The tumor usually appears in various sizes, in the appearance of cauliflower, red and fragile. Metastases are rarely reported in cases with TVT. Metastases have been detected in lung, liver, tonsils, skin, lymph nodes, muscles, spleen. The diagnosis of transmissible venereal tumor is achived by considering the history of the animal, gross lesions, cytological examination and histopathology. Chemotherapy is frequently used in the treatment of TVT. In addition, radiotherapy, cryosurgery, surgical incision and immunotherapy are rarely applied for treatment. Chemical agents such as doxorubicin, vincristine sulfate, cyclophosphamide, methotrexate are preferred for chemotherapy.Case: Metastases to all mammary lobes, cervix uteri, neck, skin, gluteal muscles, the oropharyngeal region, and primary vaginal mass were described in spayed bitch, a 10-year old and mixed breed. The clinical examination manifested, fragile and hemorrhagic masses which resemble cauliflower in the vagina, neck, and inguinal region. Furthermore firm and multilobular masses in all mammary lobes, oropharyngeal region, and gluteal muscles of right leg were detected. Firstly, vaginal cytology was performed in order to confirm. In vaginal cytology, round to polyhedral shaped transmissible venereal tumor cells including cytoplasmic vacuoles and polychromatic nuclei were identified. Histopathologically, solid areas included oval- to round-shaped cells with prominent, hyperchromatic nuclei in all masses. Also, some of them comprised mitotic figures in their nuclei. In general, the tumor cells were separated by thin fibrous septa. Additionally, the cells were completely infiltrated to the mammary gland. In contrast, oropharyngeal and subdermal region of neck consisted more solid areas under the epidermis. There was lymphocyte infiltration at the periphery of the cells. For gluteal mass, TVT cells were confined in muscle bundles. Transmissible venereal tumor cases are often located in genital organs and their metastases are rarely encountered in comparison with other tumors. In this case report, metastases to cervical tissue, neck skin, oropharyngeal mucosa and gluteal muscles, mammary lobes are found.Discussion: When the sexual activity is high, the incidence of TVT increases. It especially develops in bitches in estrus. Breed, sex and age are not a cause of predisposition for TVT. Transmissible venereal tumors’ malignancy can increase in some cases, although TVT is known as a benign tumor. Prevalence of metastases was found fairly low in the studies. Metastases to mammary region, to subcutaneous region, to brain, to eye, to lung, to uterus, to ovary, to liver, to spleen have been reported. In conclusion, even if a bitch is acyclic, transmissible venereal tumor can be developed and thus the risk of its disseminated metastasis must be considered. Moreover, since the masses have not regresed for a long time, this situation may be related to severe immunosupression in the bitch

CXC chemokine ligand 12 and g protein-coupled receptor 30 expressions in canine mammary tumors of mixed origin

Köpek meme tümörleri etiyopatogenezinde karmaşık bir seri etkileşimleri içerir. Dişi köpeklerde en yaygın karşılaşılan problemdir. Bu çalışmada, köpek meme tümörlerinde yangısal süreç ve tümör gelişimde bir çeşit chemokin olan chemokine CXC Ligand 12 (CXCL12) ile G protein coupled receptor 30 (GPCR30) ekspresyonlarının rollerini ortaya koymak amaçlandı. Bu amaçla, klinik ve patomorfolojik değerlendirmeden sonra, malignant formda mikst orjinli 18 olgu (mixed-type carcinoma-n=6, complex-type carcinoma-n=3, carcinosarcoma-n=7, carcinoma and malignant myoepithelioma-n=2) çalışmaya dahil edildi. Neoplazik değişikliklere eşlik eden yangısal hücreler ağırlıklı olarak nötrofil lökosit ve sırasıyla lenfosit, plazma hücresi ile makrofajlardan oluşuyordu. İmmunohistokimyasal olarak CXCL12 ve GPCR30 ekpsresyonları skorlandı. Her iki belirteçte ekspresyonların çoğu meme bezleri, duktal epitel hücreler, miyoepitel hücreleri ile yangısal hücrelerde orta şiddetteydi. Ancak, fibrosit ve fibroblastlarda genelde hafif şiddetteydi. Mikst orjinli köpek meme tümörleri ile subakut yangı arasında yakın bir ilişki olduğu düşünüldü. Ayrıca, yangısal hücrelerin meme bezlerinin farklılaşmasını içeren hücresel çevrenin bu mikst neoplazik dönüşümünü tetikleyebileceği veya başlatabileceği sonucuna varıldı.Canine mammary tumors (CMT) included complex interactions in the etiopathogenesis. It is the most common problem of neoplasia in female dogs. The aim of this study was to reveal the roles of chemokine CXC Ligand 12 (CXCL12) and G protein coupled receptor 30 (GPCR30) expressions in the inflammatory process and neoplastic development in canine mammary glands. Therefore, after clinical and pathomorphological evaluation, 18 cases of mixed origin malignant forms (mixed-type carcinoma-n=6, complex-type carcinoma-n=3, carcinosarcoma-n=7, carcinoma and malignant myoepithelioma-n=2)] were examined in the study. Inflammatory cells accompanying neoplastic changes, were determined to consist of predominantly neutrophils and leukocytes, followed by lymphocytes, plasma cells and macrophages. The CXCL12 and GPCR30 expressions were scored. immunohistochemically. Most of the expressions for both markers were moderate in the mammary gland and duct epithelial cells, myoepithelial cells and inflammatory cells. Fibrocytes and fibroblasts gave a mild reaction in general, and no reaction was found in the myxoid, chondroid and osteoid matrix. There was considered to be a close relationship between mixed composition CMT and subacute inflammation, and thus it was concluded that inflammtory cells may trigger or initiate neoplastic transformation in the cellular environment including differentiated cells of the mammary gland