Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3′UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization

Miniplating of metacarpal fractures: an outcome study

"n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 st1":*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Trauma to the hand is very common and consequently, metacarpal fractures are not rare entities. Some of these fractures need surgery. Considering the diversity of surgical methods available for these kinds of fractures and also the importance of achieving full function and speedy return to work for patients that are mainly young workers or athletes, this study was undertaken to investigate the outcome of treating these fractures by mini-plates."n"nMethods : Eighteen patients with open or comminuted fractures of metacarpal bones who were admitted to the emergency department of Sina Hospital between the years 2007 and 2010 underwent fixation surgery using mini-plates. Fourteen patients with 17 metacarpal fractures completed the study."n"nResults : Thirteen out of 14 patients had complete fracture union. The patient with non-union underwent revision surgery and bone graft. Four individuals developed an extensor lag of 15 degrees without functional impairment. Two patients had joint stiffness that was relieved after a period of physiotherapy and one developed wound dehiscence and discharge that improved with debridement and use of antibiotics without plate removal. Six patients had complaints regarding their hardware prominence and were satisfied after its removal. Overall, there was a 79% satisfaction rate upon the treatment."n"nConclusion: Despite the afore-mentioned complications, use of mini-plates seems to be a suitable treatment option for patients with comminuted metacarpal fractures. However, more studies with larger sample sizes are suggested to reach a firm conclusion."n"nKeywords: Fracture, metacarpal, mini-plates, complication

Risk of infection after open leg fractures: a survey in 66 patients

"n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi;} Background: Open fractures are associated with an increased risk of infection and healing complications. Management of open fractures is based on the following principles: assessment of the patient, classification of the injury, antibiotic therapy, debridement and wound management, Fracture stabilization, early bonegrafting, and supplemental procedures to achieve healing."n"nMethods: In a case- control retrospective study we evaluated 33 patients with open tibial fracture (type two gustillo) who were admitted in sina General hospital in Tehran, Iran during years 1999-2009 and were treated uniformly with external fixation as primary treatment in our center as case group and the other 33 patients with the same method and another 33 patients who had not been infected as control group. We compared the folders of case and control groups retrospectively. "n"nResults: There was no statisticant difference between two groups in mean age, gender, the mechanism of trauma and body mass index (p>0.05), while statistically significant difference between them in smoking habitus, blood transfusion, first debridment time, diabet mellitus, femoral shaft fracture (p<0.05). "n"nConclusions: Accompanying femoral fracture is the sign of high energy trauma and it is logical that it is an important risk factor for infection. In our study the time of the first debridment stablished as a significant factor influencing the infection rate in tibial open fracture. In some studies smoking had been recognized as a significant factor influencing in tibial bone open fracture our study reveals the same

Clinical Outcome Assessment of Medial Femoral Tunnel Placement in Anterior Cruciate Ligament Reconstruction

Introduction: Purpose of this study was to evaluate outcome of Anterior Cruciate Ligament (ACL) reconstruction surgery with a medial tibia tunnel entrance in patients with rupture of the ligament. Methods: This cross-sectional study was performed in patients admitted to Sina Hospital in Tehran from April 2009 to April 2011. ACL reconstruction was done by arthroscopic surgery and the patients were assessed six months after surgery. International Knee Documentation Committee (IKDC) as a standard questionnaire and arthrometer (model KT-1000) were used to measure patients' activity level and functional testing of the device, respectively. Final knee score was given to the patient based on the lowest score in each section which was presented in four groups: A, B, C and D. Results: one hundred seven patients with mean age of 29.61 ± 5.15 years (21-38 years) enrolled in this study among which 84 (78.5%) were males. Most common causes of knee trauma were sport (54.20%), road traffic accidents (19.62%), daily activities (16.82%) and work activity (9.3%). The mean femoral channel length was 44.75 ± 3.41mm. The mean of ROM of Knee after surgery was 143.21 ± 5.37 (133-150). The functional test was performed using an arthrometer and differences between two knees displacement were calculated six months after surgery which revealed that the difference between males and females was significant (p=0.03). Conclusion: The results showed the transtibial graft position is closer to the anatomical position in medial femoral tunnel placement

The Response of Chickpea Cultivars to Field Water Deficit

An experiment was carried out in 2006 to investigate the effects of different irrigation regimes (I1, I2, I3 and I4 for irrigation after 80, 110, 140 and 170 mm evaporation from class A pan, respectively) on ground cover, yield and yield components of four chickpea cultivars (Arman, ILC and Jam from kabuli type and Pirooz from desi type) in the field. In most stages of crop growth and development, the ground cover of ILC under different irrigation regimes was higher than that of the other cultivars. The ground cover of all chickpea cultivars was reduced, as water deficit severity increased. Grain yield and yield components were significantly affected by irrigation regimes. Mean grains per plant, 1000 grain weight and grain yield per unit area for I4 were significantly lower than those for other irrigation regimes, but these traits did not differ significantly among I1, I2 and I3. Thus, irrigation after 140 mm evaporation from class A pan could be a suitable irrigation regime for chickpea cultivars, when water resources are limited. Grains per plant did not differ significantly among chickpea cultivars. In comparison, the largest and the smallest grains were obtained from ILC and Pirooz, respectively. In general, mean 1000 grain weight of kabuli type cultivars was higher than that of desi type cultivar. The superiority of ILC in ground cover and 1000 grain weight resulted in higher grain yield, compared to other cultivars. However, no significant differences in grain yield of Arman, Jam and Pirooz were observed. Interaction of cultivar x irrigation for ground cover, grain weight and grain yield per unit area was not significant, indicating that ILC was a superior cultivar under both well and limited irrigation conditions

Effect of Water Deficit on Morphological Traits and Water Use Efficiency of Two Soybean (Glycine max L.) Cultivars

In order to investigate the effect of water limitation on morphological traits and water use efficiency in two soybean cultivars, a split-plot experiment was conducted in 2004 at the Research Farm of the Faculty of Agriculture, University of Tabriz, Iran. Irrigation treatments ( I1, I2, I3 and I4: irrigation after 60±3, 80±3, 100±3 and 120±3 mm evaporation from class A pan, respectively) were assigned to main plots, and two soybean cultivars (Zane and Huck) were allocated to the subplots. The results indicated that the Huck required less GDD (growing-degree days) to complete the growth and developmental stages, compared with Zane. Flowering and maturity for Huck occurred about 3 days earlier than those for Zane. The mean number of branches, plant height, biological and grain yields under well watering (I1) were higher than those under limited irrigations (I2, I3 and I4). All these traits were decreased with increasing water deficit. The highest harvest index was obtained from I1 treatment, however, this superiority was not significant statistically, when compared with other irrigation treatments. Therefore, it was concluded that water use efficiency (WUE) could be improved, with decreasing irrigation. However, the volume of water at each irrigation increased and grain yield decreased, as water deficit severed. Consequently, it seems that irrigation with low volume and short intervals might be more suitable for soybean production