A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins

<p>Abstract</p> <p>Background</p> <p>Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biological functions, scientists have been designing various types of predictors for identifying structurally flexible regions in proteins. In this respect, there are two major categories of predictors. One category of predictors attempts to identify conformationally flexible regions through analysis of protein tertiary structures. Another category of predictors works completely based on analysis of the polypeptide sequences. As the availability of protein tertiary structures is generally limited, the design of predictors that work completely based on sequence information is crucial for advances of molecular biology research.</p> <p>Results</p> <p>In this article, we propose a novel approach to design a sequence-based predictor for identifying conformationally ambivalent regions in proteins. The novelty in the design stems from incorporating two classifiers based on two distinctive supervised learning algorithms that provide complementary prediction powers. Experimental results show that the overall performance delivered by the hybrid predictor proposed in this article is superior to the performance delivered by the existing predictors. Furthermore, the case study presented in this article demonstrates that the proposed hybrid predictor is capable of providing the biologists with valuable clues about the functional sites in a protein chain. The proposed hybrid predictor provides the users with two optional modes, namely, the <it>high-sensitivity </it>mode and the <it>high-specificity </it>mode. The experimental results with an independent testing data set show that the proposed hybrid predictor is capable of delivering sensitivity of 0.710 and specificity of 0.608 under the <it>high-sensitivity </it>mode, while delivering sensitivity of 0.451 and specificity of 0.787 under the <it>high-specificity </it>mode.</p> <p>Conclusion</p> <p>Though experimental results show that the hybrid approach designed to exploit the complementary prediction powers of distinctive supervised learning algorithms works more effectively than conventional approaches, there exists a large room for further improvement with respect to the achieved performance. In this respect, it is of interest to investigate the effects of exploiting additional physiochemical properties that are related to conformational ambivalence. Furthermore, it is of interest to investigate the effects of incorporating lately-developed machine learning approaches, e.g. the random forest design and the multi-stage design. As conformational transition plays a key role in carrying out several essential types of biological functions, the design of more advanced predictors for identifying conformationally ambivalent regions in proteins deserves our continuous attention.</p

Morphology of Novel Chitosan Oligosaccharides Mod-ified Cross-linked Polyvinyl Alcohol Complex Foam (COS/cPVACF) Dressings with Fully Open-cell and Open-channel Microstructures via Active Molecules Cleaning Process for Wound Managements

The design of medical devices could be applied and developed for new treatment proce-dures instead of the traditional therapy procedures

Application and comparison of scoring indices to predict outcomes in patients with healthcare-associated pneumonia

Introduction: Healthcare-associated pneumonia HCAP is a relatively new category of pneumonia. It refers to infections that occur prior to hospital admission in patients with specific risk factors following contact or exposure to a healthcare environment. There is currently no scoring index to predict the outcomes of HCAP patients. We applied and compared different community acquired pneumonia CAP scoring indices to predict 30-day mortality and 3-day and 14-day intensive care unit ICU admission in patients with HCAP. Methods: We conducted a retrospective cohort study based on an inpatient database from six medical centers, recruiting a total of 444 patients with HCAP between 1 January 2007 and 31 December 2007. Pneumonia severity scoring indices including PSI pneumonia severity index, CURB 65 confusion, urea, respiratory rate, blood pressure , age 65, IDSA/ATS Infectious Diseases Society of America/American Thoracic Society, modified ATS rule, SCAP severe community acquired pneumonia, SMART-COP systolic blood pressure, multilobar involvement, albumin, respiratory rate, tachycardia, confusion, oxygenation, pH, SMRT- CO systolic blood pressure, multilobar involvement, respiratory rate, tachycardia, confusion, oxygenation, and SOAR systolic blood pressure, oxygenation, age, respiratory rate were calculated for each patient. Patient characteristics, co-morbidities, pneumonia pathogen culture results, length of hospital stay LOS, and length of ICU stay were also recorded. Results: PSI > 90 has the highest sensitivity in predicting mortality, followed by CURB-65 >= 2 and SCAP > 9 SCAP score area under the curve AUC: 0.71, PSI AUC: 0.70 and CURB-65 AUC: 0.66. Compared to PSI, modified ATS, IDSA/ATS, SCAP, and SMART-COP were easy to calculate. For predicting ICU admission Day 3 and Day 14, modified ATS AUC: 0.84, 0.82 , SMART-COP AUC: 0.84, 0.82, SCAP AUC: 0.82, 0.80 and IDSA/ ATS AUC: 0.80, 0 .79 performed better statistically significant difference than PSI, CURB- 65, SOAR and SMRT-CO. Conclusions: The utility of the scoring indices for risk assessment in patients with healthcare-associated pneumonia shows that the scoring indices originally designed for CAP can be applied to HCAP

Enteric bacterial loads are associated with interleukin-6 levels in systemic inflammatory response syndrome patients

AbstractBackgroundLoss of intestinal integrity is a critical contributor to excessive inflammation following severe trauma or major surgery. In the case of enterocyte damage, intestinal fatty acid-binding protein (IFABP) is released into the extracellular space. Excessive production of interleukin (IL)-6 can induce systemic inflammatory response syndrome (SIRS). However, the correlation of IL-6 with gut barrier failure and bacterial translocation in critically ill patients has not been well characterized.PurposesTo define the relationship between enteric bacterial loads and IL-6 levels in patients with SIRS.MethodsVariables related to prognosis and treatment were measured in 85 patients with SIRS upon admission to the emergency room. IL-6 and IFABP were measured using an enzyme-linked immunosorbent assay. Enteric bacterial loads in blood were measured through quantitative real-time polymerase chain reaction with primers specific for enteric bacteria.ResultsMultivariate analysis revealed a positive correlation between enteric bacterial loads and IL-6 levels in blood. Elevated IFABP concentration was associated with low blood pressure, high respiration rate, hyperglycemia, and high Sequential Organ Failure Assessment score. Elevated C-reactive protein concentrations were associated with higher soluble CD14 levels in blood.ConclusionEnterocyte damage is associated with hypotension and tachypnia in patients with SIRS. Gut function failure may permit enteric bacteria to enter the blood, thereby elevating IL-6 levels and inducing a systemic inflammatory response, resulting in multiple organ failure

Enterovirus type 71 2A protease functions as a transcriptional activator in yeast

Enterovirus type 71 (EV71) 2A protease exhibited strong transcriptional activity in yeast cells. The transcriptional activity of 2A protease was independent of its protease activity. EV71 2A protease retained its transcriptional activity after truncation of 40 amino acids at the N-terminus but lost this activity after truncation of 60 amino acids at the N-terminus or deletion of 20 amino acids at the C-terminus. Thus, the acidic domain at the C-terminus of this protein is essential for its transcriptional activity. Indeed, deletion of amino acids from 146 to 149 (EAME) in this acidic domain lost the transcriptional activity of EV71 2A protein though still retained its protease activity. EV71 2A protease was detected both in the cytoplasm and nucleus using confocal microscopy analysis. Coxsackie virus B3 2A protease also exhibited transcriptional activity in yeast cells. As expected, an acidic domain in the C-terminus of Coxsackie virus B3 2A protease was also identified. Truncation of this acidic domain resulted in the loss of transcriptional activity. Interestingly, this acidic region of poliovirus 2A protease is critical for viral RNA replication. The transcriptional activity of the EV71 or Coxsackie virus B3 2A protease should play a role in viral replication and/or pathogenesis

Recurrent disturbances and the degradation of hard coral communities in Taiwan

Recurrent disturbances can have a critical effect on the structure and function of coral reef communities. In this study, long-term changes were examined in the hard coral community at Wanlitung, in southern Taiwan, between 1985 and 2010. In this 26 year interval, the reef has experienced repeated disturbances that include six typhoons and two coral-bleaching events. The frequency of disturbance has meant that species susceptible to disturbance, such as those in the genus Acropora and Montipora have almost disappeared from the reef. Indeed, almost all hard coral species have declined in abundance, with the result that total hard coral cover in 2010 (17.7%) was less than half what it was in 1985 (47.5%). In addition, macro-algal cover has increased from 11.3% in 2003 to 28.5% in 2010. The frequency of disturbance combined with possible chronic influence of a growing human population mean that a diverse reef assemblage is unlikely to persist on this reef into the future

Increased functional connectivity of the posterior cingulate cortex with the lateral orbitofrontal cortex in depression

To analyze the functioning of the posterior cingulate cortex (PCC) in depression, we performed the first fully voxel-level resting state functional-connectivity neuroimaging analysis of depression of the PCC, with 336 patients with major depressive disorder and 350 controls. Voxels in the PCC had significantly increased functional connectivity with the lateral orbitofrontal cortex, a region implicated in non-reward and which is thereby implicated in depression. In patients receiving medication, the functional connectivity between the lateral orbitofrontal cortex and PCC was decreased back towards that in the controls. In the 350 controls, it was shown that the PCC has high functional connectivity with the parahippocampal regions which are involved in memory. The findings support the theory that the non-reward system in the lateral orbitofrontal cortex has increased effects on memory systems, which contribute to the rumination about sad memories and events in depression. These new findings provide evidence that a key target to ameliorate depression is the lateral orbitofrontal cortex

High levels of serum macrophage migration inhibitory factor and interleukin 10 are associated with a rapidly fatal outcome in patients with severe sepsis

SummaryObjectivesThe aim of this study was to delineate the association between high macrophage migration inhibitory factor (MIF) and interleukin 10 (IL-10) levels in the early phase of sepsis and rapidly fatal outcome.MethodsOne hundred and fifty-three adult subjects with the main diagnosis of severe sepsis (including septic shock) admitted directly from the emergency department of two tertiary medical centers and one regional teaching hospital between January 2009 and December 2011, were included prospectively. MIF and IL-10 levels were measured and outcomes were analyzed by Cox regression analysis according to the following outcomes: rapidly fatal outcome (RFO, death within 48h), late fatal outcome (LFO, death between 48h and 28 days), and survival at 28 days.ResultsAmong the three outcome groups, IL-10 levels were significantly higher in the RFO group (p < 0.001) and no significant differences were seen between the LFO and survivor groups. After Cox regression analysis, each incremental elevation of 1000 pg/ml in both IL-10 and MIF was independently associated with RFO in patients with severe sepsis. Each incremental elevation of 1000 pg/ml in IL-10 increased the RFO risk by a factor of 1.312 (95% confidence interval 1.094–1.575; p=0.003); this was the most significant factor leading to RFO in patients with severe sepsis.ConclusionsPatients with RFO exhibited simultaneously high MIF and IL-10 levels in the early phase of severe sepsis. Incremental increases in both IL-10 and MIF levels were associated with RFO in this patient group, and of the two, IL-10 was the most significant factor linked to RFO