Log-Poisson Hierarchical Clustering of Cosmic Neutral Hydrogen and Ly-alpha Transmitted Flux of QSO Absorption Spectrum

we study, in this paper, the non-Gaussian features of the mass density field of neutral hydrogen fluid and the Ly-alpha transmitted flux of QSO absorption spectrum from the point-of-view of self-similar log-Poisson hierarchy. It has been shown recently that, in the scale range from the onset of nonlinear evolution to dissipation, the velocity and mass density fields of cosmic baryon fluid are extremely well described by the She-Leveque's scaling formula, which is due to the log-Poisson hierarchical cascade. Since the mass density ratio between ionized hydrogen to total hydrogen is not uniform in space, the mass density field of neutral hydrogen component is not given by a similar mapping of total baryon fluid. Nevertheless, we show, with hydrodynamic simulation samples of the concordance $\Lambda$CDM universe, that the mass density field of neutral hydrogen, is also well described by the log-Poisson hierarchy. We then investigate the field of Ly$\alpha$ transmitted flux of QSO absorption spectrum. Due to redshift distortion, Ly$\alpha$ transmitted flux fluctuations are no longer to show all features of the log-Poisson hierarchy. However, some non-Gaussian features predicted by the log-Poisson hierarchy are not affected by the redshift distortion. We test these predictions with the high resolution and high S/N data of quasars Ly$\alpha$ absorption spectra. All results given by real data, including $\beta$-hierarchy, high order moments and scale-scale correlation, are found to be well consistent with the log-Poisson hierarchy. We compare the log-Poisson hierarchy with the popular log-normal model of the Ly$\alpha$ transmitted flux. The later is found to yield too strong non-Gaussianity at high orders, while the log-Poisson hierarchy is in agreement with observed data.Comment: 24 pages, 9 figures, accepted by Ap

Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis

BACKGROUND: The need for efficient algorithms to uncover biologically relevant phosphorylation motifs has become very important with rapid expansion of the proteomic sequence database along with a plethora of new information on phosphorylation sites. Here we present a novel unsupervised method, called Motif Finder (in short, F-Motif) for identification of phosphorylation motifs. F-Motif uses clustering of sequence information represented by numerical features that exploit the statistical information hidden in some foreground data. Furthermore, these identified motifs are then filtered to find "actual" motifs with statistically significant motif scores. RESULTS AND DISCUSSION: We have applied F-Motif to several new and existing data sets and compared its performance with two well known state-of-the-art methods. In almost all cases F-Motif could identify all statistically significant motifs extracted by the state-of-the-art methods. More importantly, in addition to this, F-Motif uncovers several novel motifs. We have demonstrated using clues from the literature that most of these new motifs discovered by F-Motif are indeed novel. We have also found some interesting phenomena. For example, for CK2 kinase, the conserved sites appear only on the right side of S. However, for CDK kinase, the adjacent site on the right of S is conserved with residue P. In addition, three different encoding methods, including a novel position contrast matrix (PCM) and the simplest binary coding, are used and the ability of F-motif to discover motifs remains quite robust with respect to encoding schemes. CONCLUSIONS: An iterative algorithm proposed here uses exploratory data analysis to discover motifs from phosphorylated data. The effectiveness of F-Motif has been demonstrated using several real data sets as well as using a synthetic data set. The method is quite general in nature and can be used to find other types of motifs also. We have also provided a server for F-Motif at http://f-motif.classcloud.org/, http://bio.classcloud.org/f-motif/ or http://ymu.classcloud.org/f-motif/

Potential protective role of hydrogen against cisplatininduced side effects during chemotherapy: A mini-review of a novel hypothesis for antagonism of hydrogen

Purpose: To review the potential protective role of hydrogen against cisplatin-induced side effects during chemotherapy.Methods: We searched PubMed and SCOPUS using the following keywords and combinations in titles, keywords, abstracts and full texts: cisplatin; side effects; chemotherapy; tumor; toxicity; hydrogen; reactive oxidative species; and ischemic reperfusion.Results: The pathogenesis of cisplatin-induced side effects is suggested based on the increased level of reactive oxidative species (ROS). Cisplatin induces ROS-dependent platelet apoptosis via the extracellular signal-regulated kinase (ERK) signaling pathway, which might have contributed to cisplatininduced hematotoxicity, and in particular, thrombocytopenia. Molecular hydrogen has been shown to have therapeutic effects against damage to various organs (especially kidney, brain and liver) caused by ischemic reperfusion (IR) through selective elimination of the most cytotoxic ROS hydrogen radicals without affecting other types of ROS involved in signal transduction in vitro and in vivo.Conclusion: Hydrogen may not only alleviate hematotoxicity in patients with hemorrhagic tendencies during cisplatin-based chemotherapy, but also has a potential protective effect against other side effects induced by cisplatin.Keywords: Reactive oxygen species, Hydrogen radicals, Cisplatin, Hepatotoxicity, Chemotherapy, Side effects, Antagonis

Square Key Matrix Management Scheme in Wireless Sensor Networks

In this paper we propose a symmetric cryptographic approach named Square Key Matrix Management Scheme (SKMaS) in which a sensor node named Key Distribution Server (KDS) is responsible for the security of key management. When the system starts up, the KDS sends its individual key and two sets of keys to sensor nodes. With the IDs, any two valid sensor nodes, e.g. i and j, can individually identify the corresponding communication keys (CKs) to derive a dynamic shared key (DSK) for encrypting/decrypting messages transmitted between them. When i leaves the underlying network, the CKs and the individually keys currently utilized by i can be reused by a newly joining sensor, e.g. h. However, when h joins the network, if no such previously-used IDs are available, h will be given a new ID, CKs and the individually key by the KDS. The KDS encrypts the CKs, with which an existing node q can communicate with h, with individual key so that only q rather than h can correctly decrypt the CKs. The lemmas and security analyses provided in this paper prove that the proposed system can protect at least three common attacks

Three-Dimensional Reconstruction of Thoracic Structures: Based on Chinese Visible Human

We managed to establish three-dimensional digitized visible model of human thoracic structures and to provide morphological data for imaging diagnosis and thoracic and cardiovascular surgery. With Photoshop software, the contour line of lungs and mediastinal structures including heart, aorta and its ramus, azygos vein, superior vena cava, inferior vena cava, thymus, esophagus, diaphragm, phrenic nerve, vagus nerve, sympathetic trunk, thoracic vertebrae, sternum, thoracic duct, and so forth were segmented from the Chinese Visible Human (CVH)-1 data set. The contour data set of segmented thoracic structures was imported to Amira software and 3D thorax models were reconstructed via surface rendering and volume rendering. With Amira software, surface rendering reconstructed model of thoracic organs and its volume rendering reconstructed model were 3D reconstructed and can be displayed together clearly and accurately. It provides a learning tool of interpreting human thoracic anatomy and virtual thoracic and cardiovascular surgery for medical students and junior surgeons

Serum total antioxidant capacity reflects severity of illness in patients with severe sepsis

INTRODUCTION: We conducted the present study to evaluate the changes in serum total antioxidant capacity (TAC) in patients with severe sepsis and to investigate the association between serum TAC and clinical severity. METHOD: This was a prospective observational study involving a sample of patients who met established criteria for severe sepsis and were admitted to the emergency department of a university teaching hospital. Serum TAC was determined using the total radical-trapping antioxidant parameter method. The levels of TAC, uric acid, albumin, and bilirubin in sera were obtained in the emergency department and evaluated to determine whether there were any correlations between the major antioxidant biomarkers and clinical severity of sepsis. The Acute Physiology and Chronic Health Evaluation (APACHE) II score was used for clinical evaluation of the severity of sepsis. RESULTS: A total of 73 patients with sepsis, with a mean (± standard deviation) APACHE II score of 23.2 ± 8.2 and a mortality rate of 26.0%, were included. Seventy-six healthy individuals served as control individuals. Among the patients, serum TAC levels correlated significantly with APACHE II scores. Patients who died also had higher TAC than did those who survived. Serum uric acid levels correlated significantly with serum TAC and APACHE II scores in patients with severe sepsis. CONCLUSION: Elevated serum TAC level may reflect clinical severity of sepsis. In addition, serum uric acid levels appear to contribute importantly to the higher TAC levels observed in patients with severe sepsis