Urban ecological characteristics and vascular wall flora on the Anatolian side of Istanbul, Turkey

The aim of this study is to specify the urban ecologic characteristics of Istanbul and to show their reflection to the vascular wall flora of the Anatolian side, which is a distinctive wall habitat. Plants samples of the urban habitat were collected from the top and vertical surfaces of walls during 2005-2007. A total of 101 taxa (81 species, 13 subspecies and 7 varieties) belonging to 74 genera and 33 families were recorded. It was determined that 80 species were Dicotyledones while 1 was Monocotyledone. The families with the largest number of taxa were Asteraceae (18 species, 22.22%), Poaceae (8 species, 9.87%), Lamiaceae and Brassicaceae (5 species, 6.17%), and Polygonaceae and Scrophulariaceae (4 species, 4.93%). The most common plant species on walls were Parietaria judaica L. (Urticaceae), Stellaria media (L.) Vill. subsp. media (Caryophyllaceae), and Mercurialis annua L. (Euphorbiaceae). The percentage of phytogeographical elements among the recorded taxa varied as follows: Euro-Siberian (6 taxa, 7.41%), Mediterranean (11 taxa, 13.58%), E. Mediterranian (2 taxa, 2.47%), Irano-Turanian (1 taxon, 1.23%) and unknown (61 taxa, 75.31%). It was found that 6 taxa (7.41%) were cosmopolitan, 12 (14.82%) were widespread while 1 (1.23%) was endemic. The results were compared with some other European wall floras and some similarities and dissimilarities were noted

Ethnopharmacological study of medicinal plants from Khoy city of West Azerbaijan- Iran

251-267The main objective of this study was to gather information on the use of plants by native people along with therapies suggested by the conventional healers of Khoy. It was analyzed and some important indices including, frequency of citation (FC), cultural importance index (IC), use report (UR) and informants consensus factor (ICF) were calculated. A total of 123 plant taxa belonging to 46 families used for cure of various ailments are reported in this investigation. Among the plants evaluated Apiaceae, Lamiaceae and Asteraceae were the dominant families. The most repeatedly utilized parts are aerial parts (23.2%), followed by leaves (18%). Most frequently used method for consumption has been raw (19.7%), followed by infusion (16.5%). Maximum value of ICF was obtained in digestive system category (with 0.81), followed by respiratory and blood use categories (each with 0.80). Malva neglecta Wallr. was the most cited plant, followed by Mentha longifolia (L.) L. and Plantago major L., Cichorium intybus L. and Salix aegyptiaca L. seem to be the most culturally important plants. The indices like IC and FC could be helpful in selecting important medicinal plant species for further pharmacological investigations in order to find new biologically active compounds

Evaluation of oxidative stress in degenerative rotator cuff tears

Background: Oxidative stress occurs as a result of the disruption of the balance between the formations of reactive oxygen species and antioxidant defense mechanisms during the conversion of nutrients into energy. Increased body oxidative stress has been reported to be involved in the etiology of several degenerative and chronic diseases. We hypothesized that the body oxidative stress level is higher in patients with atraumatic degenerative rotator cuff tear than that in healthy individuals. Methods: The patients who underwent arthroscopic repair for atraumatic, degenerative rotator cuff tear were prospectively evaluated. A total of 30 patients (group 1, 19 females and 11 males; mean age: 57.33 ± 6.96 years; range: 50-77 years) and 30 healthy individuals (group 2, 18 females and 12 males; mean age: 56.77 ± 6 years; range: 51-72 years) were included in the study. The Constant and American Shoulder and Elbow Surgeons scoring systems were used to evaluate the clinical outcomes. Serum oxidative stress parameters of the patients and the control group were biochemically evaluated. Accordingly, thiol/disulfide (DS) balance (DS/native thiol [NT], DS/total thiol [TT]), Total Oxidant Status (TOS), oxidative stress index, and nuclear factor erythroid-2–associated factor-2 values were used as the biochemical parameters indicating an increase in the serum oxidative stress level. Total antioxidant status and NT/TT values served as the biochemical parameters indicating a decrease in the serum oxidative stress level. Results: The study follow-up duration was 12 months. A statistically significant increase was observed in American Shoulder and Elbow Surgeons and Constant scores of patients who underwent arthroscopic rotator cuff repair relative to that during the preoperative period (P = .01). The values of biochemical parameters (DS/NT, DS/TT, TOS, oxidative stress index, and nuclear factor erythroid-2–associated factor-2), which indicated an increase in the serum oxidative stress, were significantly higher in preoperative patients than those in postoperative patients, albeit the control group values were significantly lower than those of the postoperative patients. The biochemical parameters (NT/TT and total antioxidant status) indicating a decrease in the serum oxidative stress levels were significantly higher in the postoperative patients than those in the preoperative patients and significantly lower than those in the control group. Conclusion: High levels of markers indicating an increase in the serum oxidative stress in patients with degenerative rotator cuff rupture suggested that TOS may be involved in the etiopathogenesis of rotator cuff degeneration. Although the oxidative load decreases during the postoperative period, the fact that it is still higher than that in healthy individuals supports this claim. © 2022 Journal of Shoulder and Elbow Surgery Board of Trustee

GOPred: GO Molecular Function Prediction by Combined Classifiers

Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred)

The frequency of Duchenne muscular dystrophy/Becker muscular dystrophy and Pompe disease in children with isolated transaminase elevation: results from the observational VICTORIA study

IntroductionElevated transaminases and/or creatine phosphokinase can indicate underlying muscle disease. Therefore, this study aims to determine the frequency of Duchenne muscular dystrophy/Becker muscular dystrophy (DMD/BMD) in male children and Pompe disease (PD) in male and female children with isolated hypertransaminasemia.MethodsThis multi-center, prospective study enrolled patients aged 3–216 months with serum alanine transaminase (ALT) and/or aspartate transaminase (AST) levels >2× the upper limit of normal (ULN) for ≥3 months. Patients with a known history of liver or muscle disease or physical examination findings suggestive of liver disease were excluded. Patients were screened for creatinine phosphokinase (CPK) levels, and molecular genetic tests for DMD/BMD in male patients and enzyme analysis for PD in male and female patients with elevated CPK levels were performed. Genetic analyses confirmed PD. Demographic, clinical, and laboratory characteristics of the patients were analyzed.ResultsOverall, 589 patients [66.8% male, mean age of 63.4 months (standard deviation: 60.5)] were included. In total, 251 patients (188 male and 63 female) had CPK levels above the ULN. Of the patients assessed, 47% (85/182) of male patients were diagnosed with DMD/BMD and 1% (3/228) of male and female patients were diagnosed with PD. The median ALT, AST, and CPK levels were statistically significantly higher, and the questioned neurological symptoms and previously unnoticed examination findings were more common in DMD/BMD patients than those without DMD/BMD or PD (p < 0.001).DiscussionQuestioning neurological symptoms, conducting a complete physical examination, and testing for CPK levels in patients with isolated hypertransaminasemia will prevent costly and time-consuming investigations for liver diseases and will lead to the diagnosis of occult neuromuscular diseases. Trial RegistrationClinicaltrials.gov NCT04120168

Kartal İlçesi (İstanbul)’ nin kentsel ekolojisi

KARTAL İLÇESİ'NİN (İSTANBUL) KENTSEL EKOLOJİK ÖZELLİKLERİCanlıların birbirleriyle ve çevreleriyle ilişkilerini anlamaya çalışan ekolojistler, yıllarca çalışmalarını, insan uygarlıklarından çok uzaklarda, kimi zaman ıssız bir adada, kimi zaman da tropik yağmur ormanlarında yapmıştır. Halbuki kentler, ekolojik çeşitlilik açısından, eş büyüklükteki bir kırsal alan kadar zengin olabilmektedir. Günümüzde dünya nüfusunun hemen hemen yarısı kentlerde yaşamaktadır. Böylece çevre sorunlarının büyük bir kısmı kentlere taşınmıştır.Bununla birlikte kentlerde, doğal yaşam ortamlarının korunması ve sürdürülmesi, kentliye yaşanılabilir olmasının yanında dinlenip zevk alabileceği bir ortam oluşturulması, ancak kentsel ekolojinin ilke ve değerlerinin planlamaya girmesiyle mümkün olabilmektedir. "Kartal İlçesi'nin (İstanbul) Kentsel Ekolojik Özellikleri" adlı çalışmada, İstanbul'un yeşil bölgelerinden biri olan Kartal İlçesinin, plansız kentleşme sonuçları ve alınabilecek önlemleri ortaya konmuştur. Ayrıca Kartal İlçesi'nin dahilinde bulunan kentsel habitat çeşitleri belirlenmiş, bu habitatlarda yaşayan yerli ve yabancı bitki türlerinin bir envanteri çıkarılmıştır. Kartal İlçesi'nin bitki türlerinin envanteri çıkarılırken, öncelikle vejetasyon mevsimlerinde, ilçedeki değişik habitatlarda dolaşılarak bitki örnekleri toplanmış, toplanan örnekler herbaryum tekniklerine uygun olarak kurutulmuş ve teşhis edilmiştir. Çalışmada Kartal İlçesi'nde toplam 455 bitki taksonu saptanmıştır. Bunların 356'sı doğal, 99'u ise exotik bitkilerdir. En çok doğal bitki taksonu bulunan familya Asteraceae'dir. En çok exotik bitki türü bulunan familya ise Rosaceae'dir. Ayrıca çalışmada, öncelikle İstanbul'da daha sonra da bütün kentlerde kentsel ekolojik çalışmaların yaygınlaştırılmasının gerekliliği vurgulanmıştır. Haziran 2004 Volkan ALTAYABSTRACTTHE URBAN ECOLOGICAL CHARACTERISTICS OF KARTAL TOWN (ISTANBUL)For years, the ecologists who have been trying to understand the relationship of the organisms with each others and their environments have done research far away from civilization, sometimes on a desolate island or sometimes in tropical rainforests. On the other hand, from the point of ecological diversity, an urban area can be as rich as a rural area in the same size. Today, about half of the world's population live in urban areas. Therefore, most of the ecological problems have been brought to the cities. Nevertheless, in cities, preserving and maintaining natural habitats, providing a place not only to live but also to enjoy and to relax is only possible by applying the principles and concepts of urban ecology in planning. The research study titled the urban ecological characterıstic of Kartal Town presents the outcomes of unplanned urbanization and possible preventive measures to be taken. Moreover, different kinds of urban habitat within the frontiers of Kartal have been described and an inventorial study containing native and exotic plant taxa has been realized. For this plant inventory of Kartal Town, all the greenery in the area has been explored especially in the vegetation seasons and plant samples have been collected and later, these samples have been dried and labelled according to herbarium procedure. Then they have been determined. In this study, within the frontiers of Kartal Town, a total of 455 taxa of plants have been determined, where as 356 of them are natural whilst 99 are exotic. The most native taxa are in the family of Asteraceae, where as the most found kind of exotic plant family is Rosaceae. .Moreover, the necessity of having ecological studies become widespread in urban areas, initrally in İstanbul and later in other places has been emphasized in the study.June 2004Volkan ALTA

Proteom analizi ile fare karaciğer dokusu proteinlerinde 7,8 - dihidroksi - 3- (4-metilfenil) kumarinin neden olabileceği değişikliklerin saptanması

PROTEOM ANALİZİ İLE FARE KARACİĞER DOKUSU PROTEİNLERİNDE 7,8-DİHİDROKSİ-3-(4-METİLFENİL) KUMARİNİN NEDEN OLABİLECEĞİ DEĞİŞİKLİKLERİN SAPTANMASI Flavonoid sınıfı bileşiklerden olan kumarinler, antikoagülan etkilerinin yanısıra bilinen kolesterol düşürücü özellikleri nedeni ile de önemlidir. Bu çalışmada, Bölümümüz Organik Kimya Anabilimdalınca sentezlenen ve kolesterol düşürücü etkisi olduğu daha önceki çalışmalarımızda saptanan 7,8-dihidroksi-3-(4-metilfenil) kumarinin, hiperlipidemi oluşturulmuş serum kolesterol düzeyi yüksek sıçan karaciğer proteinleri üzerindeki etkisi, proteom tekniği kullanılarak araştırılmıştır. Hiperlipidemi oluşturulmuş Sprague-Dawley türü sıçana 7,8-dihidroksi-3-(4-metilfenil) kumarin uygulanmış ve karaciğer dokusu çıkarılmıştır. Kontrol olarak, ilaç uygulanmamış hiperlipidemik serum kolesterol düzeyi yüksek aynı tür sıçan karaciğer dokusu kullanılmıştır. İki boyutlu elektroforez işlemi sonucunda sıçan karaciğer protein profilinin pI: 5,5-9 aralığında yoğunlaştığı belirlenmiştir. Molekül ağırlığı olarak da en büyük yoğunluğun 25-30 kDa bölgesinde olduğu saptanmıştır. Kullandığımız PDQuest görüntüleme sistemi yardımı ile 1358 spot belirlenmiştir. Bunların içinde farklılık gösteren 14 tanesinin MALDI-Tof analizi yapılarak Matrix-Science protein veri tabanı ile karşılaştırılmış, molekül ağırlıkları ve pI değerleri saptanmıştır. Proteomik analizlerle elde edilen bu bilgiler kolesterol düşürücü ilaçların etkisinin anlaşılmasında yararlı olabilecektir. ABSTRACT DETERMINATION OF POSSIBLE CHANGES IN THE PROTEINS OF RAT LIVER TISSUE INDUCED WITH 7,8-DIHYDROXY-3-(4-METHYLPHENIL) COUMARIN BY PROTEOM ANALYSIS Coumarins, are a class of compounds called flavonoids, which are significant not only for their anticoagulant effect but also for their cholesterol lowering effect. In this study, the effect of 7,8-dihydroxy-3-(4-methylphenil) coumarin, which was synthesized by Organic Chemistry Division of our department and its cholesterol lowering effect was proven in our previous studies, on the liver proteins of hyperlipidemic Sprague-Dawley rat by proteom analysis. We investigated the effect of 7,8-dihydroxy-3-(4-methylphenil) coumarin on the protein profiles of the liver tissues of hyperlipidemic Sprague-Dawley rat by proteom analysis. 7,8-dihydroxy-3-(4-methylphenil) coumarin was administrated orally to hyperlipidemic induced Sprague-Dawley rat with high serum cholesterol level. As control hyperlipidemia induced with high serum cholesterol level same strain rat liver was used. The 2D PAGE revealed that the liver protein profile was intensified in the range pI: 5,5-9, on the other hand the heavies molecular weight occured in the range 25-30 kDa. The PDQuest scanning and projection program displayed 1358 spots. After analysis the credible proteins number is 14. These proteins were excised and identified by MALDI-Tof analysis and compared to Matrix-Science protein data base. Their molecular weights and pI values are determined. These collected data will be of assistance in understanding the mechanismes of cholesterol lowering effect of 7,8-dihydroxy-3-(4-methylphenil) coumarin

Kartal İlçesi (İstanbul)’ nin kentsel ekolojisi

KARTAL İLÇESİ'NİN (İSTANBUL) KENTSEL EKOLOJİK ÖZELLİKLERİ Canlıların birbirleriyle ve çevreleriyle ilişkilerini anlamaya çalışan ekolojistler, yıllarca çalışmalarını, insan uygarlıklarından çok uzaklarda, kimi zaman ıssız bir adada, kimi zaman da tropik yağmur ormanlarında yapmıştır. Halbuki kentler, ekolojik çeşitlilik açısından, eş büyüklükteki bir kırsal alan kadar zengin olabilmektedir. Günümüzde dünya nüfusunun hemen hemen yarısı kentlerde yaşamaktadır. Böylece çevre sorunlarının büyük bir kısmı kentlere taşınmıştır.Bununla birlikte kentlerde, doğal yaşam ortamlarının korunması ve sürdürülmesi, kentliye yaşanılabilir olmasının yanında dinlenip zevk alabileceği bir ortam oluşturulması, ancak kentsel ekolojinin ilke ve değerlerinin planlamaya girmesiyle mümkün olabilmektedir. "Kartal İlçesi'nin (İstanbul) Kentsel Ekolojik Özellikleri" adlı çalışmada, İstanbul'un yeşil bölgelerinden biri olan Kartal İlçesinin, plansız kentleşme sonuçları ve alınabilecek önlemleri ortaya konmuştur. Ayrıca Kartal İlçesi'nin dahilinde bulunan kentsel habitat çeşitleri belirlenmiş, bu habitatlarda yaşayan yerli ve yabancı bitki türlerinin bir envanteri çıkarılmıştır. Kartal İlçesi'nin bitki türlerinin envanteri çıkarılırken, öncelikle vejetasyon mevsimlerinde, ilçedeki değişik habitatlarda dolaşılarak bitki örnekleri toplanmış, toplanan örnekler herbaryum tekniklerine uygun olarak kurutulmuş ve teşhis edilmiştir. Çalışmada Kartal İlçesi'nde toplam 455 bitki taksonu saptanmıştır. Bunların 356'sı doğal, 99'u ise exotik bitkilerdir. En çok doğal bitki taksonu bulunan familya Asteraceae'dir. En çok exotik bitki türü bulunan familya ise Rosaceae'dir. Ayrıca çalışmada, öncelikle İstanbul'da daha sonra da bütün kentlerde kentsel ekolojik çalışmaların yaygınlaştırılmasının gerekliliği vurgulanmıştır. Haziran 2004 Volkan ALTAY ABSTRACT THE URBAN ECOLOGICAL CHARACTERISTICS OF KARTAL TOWN (ISTANBUL) For years, the ecologists who have been trying to understand the relationship of the organisms with each others and their environments have done research far away from civilization, sometimes on a desolate island or sometimes in tropical rainforests. On the other hand, from the point of ecological diversity, an urban area can be as rich as a rural area in the same size. Today, about half of the world's population live in urban areas. Therefore, most of the ecological problems have been brought to the cities. Nevertheless, in cities, preserving and maintaining natural habitats, providing a place not only to live but also to enjoy and to relax is only possible by applying the principles and concepts of urban ecology in planning. The research study titled the urban ecological characterıstic of Kartal Town presents the outcomes of unplanned urbanization and possible preventive measures to be taken. Moreover, different kinds of urban habitat within the frontiers of Kartal have been described and an inventorial study containing native and exotic plant taxa has been realized. For this plant inventory of Kartal Town, all the greenery in the area has been explored especially in the vegetation seasons and plant samples have been collected and later, these samples have been dried and labelled according to herbarium procedure. Then they have been determined. In this study, within the frontiers of Kartal Town, a total of 455 taxa of plants have been determined, where as 356 of them are natural whilst 99 are exotic. The most native taxa are in the family of Asteraceae, where as the most found kind of exotic plant family is Rosaceae. . Moreover, the necessity of having ecological studies become widespread in urban areas, initrally in İstanbul and later in other places has been emphasized in the study. June 2004 Volkan ALTA

İstanbul’un Anadolu Yakası’ının kentsel vejetasyonu

İSTANBUL’UN ANADOLU YAKASI’NIN KENTSEL VEJETASYONU İstanbul’un Anadolu Yakası’nın kent vejetasyonunu analiz etmek ve birlikler halinde sınıflandırmak amacı ile yapılan bu çalışma, Braun-Blanquet metodu ile gerçekleştirilmiştir. Çalışma sonucunda, araştırma alanında dağılım gösteren toplam olarak oniki adet birlik ve onüç adet bitki grubu tesbit edilmiştir. Birliklerden altısı ilk defa tarafımızdan tanımlanmış olup, bilim dünyası için yenidir. Tesbit edilmiş bulunan birlik ve bitki grupları şunlardır: Lamio purpurei – Calenduletum arvensis Ass. Nova Birliği Erodio malacoidis – Asphodeletum fistulosi Ass. Nova Birliği Lathyro digitati – Asphodeletum aestivi Ass. Nova Birliği Dauco guttati – Centauretum diffusae Ass. Nova Birliği Lepidio graminifolii - Diplotaxetum tenuifoliae Ass. Nova Birliği Cirsio polycephali – Inuletum viscosae Ass. Nova Birliği Silybo – Urticetum Br.-Bl. (1931) 1936 em. Br.-Bl. & al. 1951 Birliği Cardario drabae – Agropyretum repentis Müler & Görs 1969 Birliği Galio – Conietum maculati Riv.- Mart. ex G. Löpez 1978 Birliği Chenopodio albi – Amaranthetum blitoidis Carretero, 1995 Birliği Phillyrea latifola – Laurus nobilis Quezel, Barbero & Akman, 1980 Birliği Querceto – Pistacietum lentisci Schwarz, 1936 Birliği Sarcopoterium spinosum Bitki Grubu Erica manipuliflora Bitki Grubu Tordylium apulum Bitki Grubu Sinapis arvensis Bitki Grubu Rapistrum rugosum Bitki Grubu Carduus pycnocephalus subsp. albidus Bitki Grubu Carduus nutans Bitki Grubu Centaurea iberica Bitki Grubu Centaurea solstitialis subsp. solstitialis Bitki Grubu Rumex crispus Bitki Grubu Ammi visnaga Bitki Grubu Cichorium intybus Bitki Grubu Parietaria judaica Bitki Grubu Bu birliklerin floristik, ekolojik ve sintaksonomik analizleri yapılmış, araştırma alanında, sinkorolojik dağılımları verilmiştir. Maruz kaldıkları antropojenik tahribatın derecesi, Hemerobi Skalası ile açıklanmıştır. Birliklerin oluşum ve gelişim koşulları ortaya konmuş ve irdelenmiştir. Bu vejetasyonun tahribatının önlenmesi, ya da en azından, mevcut durumunun korunması için alınması gereken tedbirler, öneriler şeklinde sunulmuştur. ABSTRACT THE URBAN VEGETATION OF ISTANBUL-ANATOLIAN SIDE This study aims to analyse and classify the urban vegetation distribution as associations in the Anatolian Side of İstanbul. Braun-Blanquet method was used for classification. As a result of the study, a total of 25 associations and plant groups (twelwe associations and thirteen plant groups) distributing in the study area was found. Six of these associations have been idendified for the first time and they are new for the scientific world. These associations and plant groups are as follows: Lamio purpurei – Calenduletum arvensis Ass. Nova Erodio malacoidis – Asphodeletum fistulosi Ass. Nova Lathyro digitati – Asphodeletum aestivi Ass. Nova Dauco guttati – Centauretum diffusae Ass. Nova Lepidio graminifolii - Diplotaxetum tenuifoliae Ass. Nova Cirsio polycephali – Inuletum viscosae Ass. Nova Silybo – Urticetum Br.-Bl. (1931) 1936 em. Br.-Bl. & al. 1951 Ass. Cardario drabae – Agropyretum repentis Müler & Görs 1969 Ass. Galio – Conietum maculati Riv.- Mart. ex G. Löpez 1978 Ass. Chenopodio albi – Amaranthetum blitoidis Carretero, 1995 Ass. Phillyrea latifola – Laurus nobilis Quezel, Barbero & Akman, 1980 Ass. Querceto – Pistacietum lentisci Schwarz, 1936 Ass. Sarcopoterium spinosum Plant Group Erica manipuliflora Plant Group Tordylium apulum Plant Group Sinapis arvensis Plant Group Rapistrum rugosum Plant Group Carduus pycnocephalus subsp. albidus Plant Group Carduus nutans Plant Group Centaurea iberica Plant Group Centaurea solstitialis subsp. solstitialis Plant Group Rumex crispus Plant Group Ammi visnaga Plant Group Cichorium intybus Plant Group Parietaria judaica Plant Group The floristical, ecological and syntaxonomical analyses of these associations were realized and their distributions in the study area were given. The degree of the anthropogenic damage on them was explained by the Hemerobie Scale. The formation and development conditions of the associations were described and discussed. Protection aganist damage of this vegetation or at least protection of the existent situation were presented as suggestions