Recon3D enables a three-dimensional view of gene variation in human metabolism

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life

Multiscale community detection using markov dynamics

M.S. University of Hawaii at Manoa 2014.Includes bibliographical references.Complex networks is an interdisciplinary research area getting attention from a variety of disciplines including sociology, biology, and computer science. It studies the properties of complex systems that may have many functional or structural subunits. Community detection algorithms are one of the major approaches to analyse complex networks by finding these intermediate-level subunits called modules or communities. Furthermore, some networks may have multilevel or overlapping community structures. InfoMap is one of the best performing algorithms that finds the communities of a network by compressing the flow of information [25, 17]. In this work, we introduced Markov Dynamics to the InfoMap in order to detect communities at multiscales. Although Markov Dynamics have been applied to the InfoMap for undirected networks before [28], this was the first application of Markov Dynamics to the InfoMap for directed networks. Additionally, we added a feature to detect overlapping nodes using the compression of flow on the boundary nodes, similar to the approach described in [9] before. These two features were combined into the InfoMap for directed networks. We evaluated these two features on synthetic networks and benchmark graphs. We have comparable results with the Hierarchical InfoMap [26] for multilevel community detection, but improvement in runtime is needed. We evaluated the overlapping feature by its own ability, and found that it can detect overlapping nodes for networks with sparse overlaps

Perception of dyspnea during exacerbation and histamine-related bronchoconstriction in patients with asthma

WOS: 000237857400014PubMed: 16729784Background: Numerous studies have been performed concerning the perception of dyspnea during changes in airway caliber provoked in the laboratory setting, but studies of asthma exacerbation are scarce. Objective: To investigate whether the perception of dyspnea during histamine-induced bronchoconstriction might be used to identify patients with asthma who sense dyspnea poorly during exacerbation. Methods: The perception of dyspnea in 50 patients (45 female, 5 male) with asthma was evaluated at admission with exacerbation and during a stable period. Perceived intensity of dyspnea was estimated using a modified Borg scale. The perception of dyspnea in the stable period 4 to 6 weeks after exacerbation was measured with the histamine challenge test. Perception parameters were defined as the change in Borg score divided by the change in forced expiratory volume in 1 second (FEV1) as a percentage of the baseline FEV1 (Delta Borg/Delta FEV1) and as the Borg score at 20% decrease (PS20Histamine) or increase (PS20Exacerbation) in FEV1. Results: The perception of dyspnea during asthma exacerbation was unrelated to the perception of dyspnea during histamine-induced bronchoconstriction (for Delta Borg/Delta FEV1, beta = .08, P = .50; for PS20, beta = -.11, P = .40). The K value for the agreement of poor perceivers at exacerbation and during the stable period was -0.21 (P = .10). However, the intensity of dyspnea caused by histamine-induced bronchoconstriction was lower than that caused by asthma exacerbation (PS20: 1.6 +/- 1.1 vs 2.8 +/- 2.5. respectively. P = .004; Delta Borg/Delta FEV1: 0.08 +/- 0.05 vs 0.21 +/- 0.28, respectively, P = .001). Conclusion: The perception of dyspnea during asthma exacerbation is not correlated with the perception of dyspnea during histamine-induced bronchoconstriction. Therefore, the perception of dyspnea during histamine-induced bronchoconstriction cannot be used to identify the asthmatic patients who perceive dyspnea poorly

Giant chest wall tumour invading the abdominal cavity: simultaneous reconstruction of the chest wall and hemidiaphragm

WOS: 000254552400017PubMed: 1837773

Giant chest wall tumour invading the abdominal cavity: simultaneous reconstruction of the chest wall and hemidiaphragm

[No abstract available

Analysis of 282 patients with thoracic trauma

Amaç: Yaşamın ilk 30 yılında travmaya bağlı ölümlerin %20-25’ini göğüs travmaları oluşturmaktadır. Bu çalışmada, üç yıllık süre içinde merkezimizde izlenen toraks travmalı olgular değerlendirildi. Çalışma planı: Çalışmaya, 2003-2006 tarihleri arasında toraks travması nedeniyle merkezimizde tedavi edilen, 15 yaş üzerindeki 282 hasta (240 erkek, 42 kadın; ort. yaş 41±16; dağılım 16-98) alındı. Hastalar yaş, cinsiyet, travma etyolojisi, klinik bulgular, eşlik eden yaralanmalar, ameliyat endikasyonları, uygulanan cerrahi girişimler, gelişen komplikasyonlar ve mortalite açısından incelendi. Bulgular: Yaş ortalaması erkeklerde 43±17 (dağılım 16- 98), kadınlarda 33±10 (dağılım 16-61) bulundu (p<0.001). Travmaların erkeklerde görülmesi anlamlı derecede fazlaydı (p<0.001). Olguların 175’inde (%62.1) izole toraks travması, 107’sinde (%37.9) multipl travma vardı. Olguların 242’sinde (%85.8) künt, 40’ında (%14.2) penetran travma görüldü. Yaralanma nedeni 164 hastada (%58.2) trafik kazasıydı. Künt göğüs travması geçiren 101 olguda ek yaralanma görüldü. İki olguda büyükbaş hayvanların neden olduğu penetran yaralanma görüldü. Penetran travma geçiren sadece iki kadın hasta vardı. Tedavi sırasında künt toraks travması geçiren yedi hastada ventilatör desteği kullanıldı. Penetran göğüs travmalarının tümünde, künt göğüs travmalarının 150’sinde (%62) tüp torakostomi kullanıldı. Toplam 11 hastada torakotomi ve sternotomi uygulandı. Mortalite beş hastada görüldü; bunların hepsinde primer patoloji göğüs travması dışındaki nedenlerdi. Pnömotoraks ve akciğer kontüzyonları ulusal kaynaklarda bildirilen oranlardan daha yüksek bulundu. Hiçbir hastada kalp yaralanması gözlenmedi. Sonuç: Künt travma nedenleri arasında ilk sırayı motorlu taşıt kazaları almış olduğundan, ülkemiz genelinde olduğu gibi Zonguldak’ta da trafik kurallarına uyum konusunda halkın bilinçlendirilmesinin gerekli olduğu düşünüldü.Background: Thoracic trauma accounts for 20-25% of all deaths due to trauma during the first four decades of life. In this study, we reviewed patients who presented with thoracic trauma to our center during a three-year period. Methods: The study included 282 patients (240 males, 42 females; mean age 41±16 years; range 16 to 98 years) over 15 years of age, who were admitted to our emergency outpatient clinic with thoracic trauma between 2003 and 2006. The patients were evaluated with respect to age, gender, etiology, clinical findings, accompanying injuries, surgical indications, surgical interventions, complications, and mortality. Results: The mean age was 43±17 years (range 16 to 98 years) in men, and 33±10 years (range 16 to 61 years) in women (p<0.001). Men were involved in traumas significantly more than women (p<0.001). Isolated thoracic trauma was seen in 175 patients (62.1%) and multiple trauma in 107 patients (37.9%). Injuries were blunt in 242 patients (85.8) and penetrating in 40 patients (14.2%). Traffic accidents were the leading cause of traumas (n=164, 58.2%). Blunt thoracic injuries were accompanied by associated injuries in 101 patients. Two patients had penetrating thoracic injuries caused by animals. There were only two women with penetrating injuries. Seven patients with blunt thoracic injuries required ventilatory support. Tube thoracostomy was used in all penetrating thoracic injuries and in 150 patients (62%) with blunt trauma. Eleven patients underwent thoracotomy and sternotomy. Mortality occurred in five patients, all of whom had primary injuries other than thoracic trauma. The rates of pneumothorax and lung contusion were higher than those reported in domestic literature. None of the patients had cardiac injuries. Conclusion: Considering the high rate of traffic accidents in the etiology of blunt thoracic injuries, increasing public awareness for, and attitudes towards, safety driving measures is of special importance in Zonguldak and nationwid

Can Preoperative Parameters of Inflammation be Used to Predict Acute Kidney Injury in Pediatric Liver Transplant Recipients? A Single-Center Retrospective Study

Introduction: Inflammation is one of the factors involved in the occurrence and progression of acute kidney injury (AKI). We evaluated the relationship between preoperative systemic inflammatory markers and early postoperative AKI development in pediatric liver transplantation (LT) patients. Methods: Data from 190 pediatric patients were retrospectively analyzed. The preoperative neutrophil-to-lymphocyte ratio (NLR), systemic immune-inflammation index (SII), and pan-immune-inflammation value (PIV) levels were calculated. AKI was classified according to the Kidney Disease: Improving Global Outcomes staging. Patients who did not develop AKI in the early postoperative period were classified as group 0, patients with stage 1 AKI were classified as group 1, and patients with stage 2-3 AKI were classified as group 2. The relationship between the inflammatory parameters and AKI was evaluated. Results: AKI developed in 20% of patients, and 16.31% of these patients had severe AKI. The NLR, SII, and PIV values were significantly higher in patients with severe AKI (p<0.001). Preoperative high PIV values were found to be an independent predictor of AKI development. Conclusion: High preoperative PIV values may be used as a predictive factor for the development of early AKI in patients undergoing pediatric LT