A computational method to predict carbonylation sites in yeast proteins

Several post-translational modifications (PTM) have been discussed in literature. Among a variety of oxidative stress-induced PTM, protein carbonylation is considered a biomarker of oxidative stress. Only certain proteins can be carbonylated because only four amino acid residues, namely lysine (K), arginine (R), threonine (T) and proline (P), are susceptible to carbonylation. The yeast proteome is an excellent model to explore oxidative stress, especially protein carbonylation. Current experimental approaches in identifying carbonylation sites are expensive, time-consuming and limited in their abilities to process proteins. Furthermore, there is no bioinformational method to predict carbonylation sites in yeast proteins. Therefore, we propose a computational method to predict yeast carbonylation sites. This method has total accuracies of 86.32, 85.89, 84.80, and 86.80% in predicting the carbonylation sites of K, R, T, and P, respectively. These results were confirmed by 10-fold cross-validation. The ability to identify carbonylation sites in different kinds of features was analyzed and the position-specific composition of the modification site-flanking residues was discussed. Additionally, a software tool has been developed to help with the calculations in this method. Datasets and the software are available at https://sourceforge.net/projects/hqlstudio/ files/CarSpred.Y/.

[Clinical significance of the preoperative neutrophil lymphocyte ratio in the evaluation of the prognosis of laryngeal carcinoma]

OBJECTIVE

To explore the effect of preoperative neutrophil lymphocyte ratio (NLR) on the prognosis of patients with laryngeal carcinoma.

METHODS

Clinical data of 202 patients with laryngeal carcinoma treated from January 2004 to October 2009 were retrospective analyzed to determine the optimal critical value of NLR. To study whether NLR is an independent factor affecting the recurrence and 5-year survival rate of patients with laryngeal cancer after surgery, single factor and multivariate analyses were performed. The factors included age, gender, T stage, pathological differentiation, lymph node metastasis, primary tumor site and NLR value. The relationship between NLR and cervical lymph node metastasis was analyzed.

RESULTS

The optimal critical value of NLR was 2.85, by which cases were divided into high NLR group (NLR≥2.85) and low NLR group (NLR<2.85). Single factor and multivariate analyses indicated that T staging, lymph node metastasis, primary tumor location, and NLR were the independent factors affecting the recurrence of laryngeal carcinoma. T stage and lymph node metastasis were the independent factors affecting 5-year survival rate of laryngeal carcinoma. The increase of NLR value increased the rate of cervical lymph node metastasis.

CONCLUSION

Preoperative NLR level influences the recurrence and cervical lymph node metastasis of laryngeal carcinoma and can be considered a prognosis factor of laryngeal cancer.

The significance of fragile histidine triad protein as a molecular prognostic marker of bladder urothelial carcinoma

OBJECTIVES

The role and clinical significance of fragile histidine triad (FHIT) gene in the pathogenesis of bladder urothelial carcinoma (UC) and the potential of Fhit protein as a prognostic biomarker for UC were investigated.

METHODS

FHIT expression was determined according to semiquantitative immunohistochemical staining for Fhit protein levels in normal bladder and bladder UC tissues. Associations between FHIT expression, clinicopathological features and survival were evaluated.

RESULTS

This study evaluated 42 cases of normal bladder and 125 cases of bladder UC; bladder UC cases had a median follow-up of 53.5 months. Immuno histochemistry showed that 95.2% of normal cases and 47.2% of bladder UC cases, respectively, were positive for Fhit protein; this difference was statistically significant. There was a significant association between negative FHIT expression in bladder UC and advanced tumour stage, high pathological grade, large tumour size, tumour recurrence and reduced survival time, but no association with age, gender, tumour number or tumour shape.

CONCLUSIONS

The FHIT gene may have an important role in the pathogenesis of bladder UC and was expressed at lower levels in bladder UC compared with normal bladder tissue. Using Fhit protein as a biomarker could provide important information about patient prognosis.

Moxifloxacin monotherapy for treatment of complicated intra-abdominal infections: a meta-analysis of randomised controlled trials

To evaluate the efficacy and safety of moxifloxacin monotherapy for treatment of complicated intra-abdominal infections. PubMed, EMBASE, Science Direct, ClinicalTrials.gov and Cochrane Central Register of Controlled Trials were searched to retrieve randomised controlled trials (RCTs) compared moxifloxacin monotherapy with other antibiotics in the treatment of complicated intra-abdominal infections from January 1999 to July 2011. A meta-analysis of all included randomised controlled trials was performed. Four randomised controlled trials including a total of 2444 patients with complicated intra-abdominal infections were included for meta-analysis. The results of the meta-analysis indicated that the moxifloxacin was associated with similar clinical cure rate (four RCTs, 1934 patients, OR = 0.80, 95% CI: 0.61, 1.04, p = 0.09), bacteriological success rates (four RCTs, 1484 patients, OR = 0.79, 95% CI: 0.59, 1.05, p = 0.11) and mortality (four RCTs, 2227 patients, OR = 0.91, 95% CI: 0.45, 1.83, p = 0.79) compared with the control group. The overall incidence of adverse events of moxifloxacin was significantly higher than that in the control group (three RCTs, 1367 patients, OR = 1.33, 95% CI: 1.07, 1.63, p = 0.008), although the incidence of drug-related adverse events (three RCTs, 1601 patients, OR = 1.13, 95% CI: 0.69, 1.85, p = 0.63) and serious adverse events (three RCTs, 1815 patients, OR = 1.23, 95% CI: 0.59, 2.60, p = 0.58) were similar between the compared treatment groups. Moxifloxacin is an effective and relatively safe option for the treatment of patients with intra-abdominal infections. Moxifloxacin monotherapy has similar efficacy to combination therapy.

A cross-sectional study on levels of second-hand smoke in restaurants and bars in five cities in China

OBJECTIVES

To assess indoor second-hand smoke (SHS) exposure in restaurants and bars via PM(2.5) (fine particles 2.5 μm in diameter and smaller) level measurements in five cities in China.

METHODS

The study was conducted from July to September in 2007 in Beijing, Xi'an, Wuhan, Kunming and Guiyang. Portable aerosol monitors were used to measure PM(2.5) concentrations in 404 restaurants and bars. The occupant density and the active smoker density were calculated for each venue sampled.

RESULTS

Among the 404 surveyed venues, 23 had complete smoking bans, 9 had partial smoking bans and 313 (77.5%) were observed to have allowed smoking during sampling. The geometric mean of indoor PM(2.5) levels in venues with smoking observed was 208 μg/m(3) and 99 μg/m(3) in venues without observed smoking. When outdoor PM(2.5) levels were adjusted, indoor PM(2.5) levels in venues with smoking observed were consistently significantly higher than in venues without smoking observed (F=80.49, p<0.001). Indoor PM(2.5) levels were positively correlated with outdoor PM(2.5) levels (partial rho=0.37 p<0.001) and active smoker density (partial rho=0.34, p<0.001).

CONCLUSIONS

Consistent with findings in other countries, PM(2.5) levels in smoking places are significantly higher than those in smoke-free places and are strongly related to the number and density of active smokers. These findings document the high levels of SHS in hospitality venues in China and point to the urgent need for comprehensive smoke-free laws in China to protect the public from SHS hazards, as called for in Article 8 of the Framework Convention on Tobacco Control, which was ratified by China in 2005.

A cross-sectional study on levels of secondhand smoke in restaurants and bars in five cities in China

OBJECTIVES

To assess indoor secondhand smoke (SHS) exposure in restaurants and bars via PM(2.5) level measurements in five cities in China.

METHODS

The study was conducted from July to September in 2007 in Beijing, Xi'an, Wuhan, Kunming and Guiyang. PM(2.5) concentrations were measured in 404 restaurants and bars using portable aerosol monitors. The occupant density and the active smoker density were calculated for each venue sampled.

RESULTS

Among the 404 surveyed venues, 23 had complete smoking bans, nine had partial smoking bans and 313 (77.5%) had smoking observed during sampling. The geometric mean of indoor PM(2.5) levels in venues with smoking observed was 208 μg/m(3) and 99 μg/m(3) in venues without smoking observed. When outdoor PM(2.5) levels were adjusted, indoor PM(2.5) levels in venues with smoking observed were consistently significantly higher than those in venues without smoking observed (F=80.49, p<0.001). Indoor PM(2.5) levels were positively correlated with outdoor PM(2.5) levels (partial ρ=0.37 p<0.001) and active smoker density (partial ρ=0.34, p<0.001).

CONCLUSIONS

Consistent with findings in other countries, PM(2.5) levels in smoking places are significantly higher than those in smoke-free places and are strongly related to the number and density of active smokers. These findings document the high levels of SHS in hospitality venues in China and point to the urgent need for comprehensive smoke-free laws in China to protect the public from SHS hazards, as called for in Article 8 of the Framework Convention on Tobacco Control, which was ratified by China in 2005.

The pulmonary toxicity of multi-wall carbon nanotubes in mice 30 and 60 days after inhalation exposure

The pulmonary toxicity, induced by multi-wall carbon nanotubes in mice, was studied after 30-day and 60-day inhalation exposure. The mice were exposed to multi-wall carbon nanotubes aerosol with weighted mean concentration of 32.61 mg/m3, once in very two days, 6 hours in an exposure day. After 30-day and 60-day inhalation exposure, the pulmonary toxicity of multi-wall carbon nanotubes was assessed using biochemical indices in bronchoalveolar lavage fluid and pathological examination. It was found that the aerosolized multi-wall carbon nanotubes did not induce obvious pulmonary toxicity in 30-day exposure group, but induced severe pulmonary toxicity in 60-day exposure group.

Gene profiling after knocking-down expression of nucleostemin in Hela cells using oligonucleotide DNA microarray

Nucleostemin (NS) is preferentially and exclusively expressed in the stem cells and cancer cells, but not in differentiated adult tissues and cells. NS is likely to take part in controlling the proliferation and differentiation switch in stem cells and progenitor cells. Its deregulation in cancer also contributes to the elevated proliferation and undifferentiation of cancer cells. However, the mechanisms by which NS helps to maintain both cancer and stem cells in undifferentiated state remain unclear. In this study, we carried out gene profilings using oligonucleotide DNA microarray after knocking down the expression of NS in Hela cells. Of the 21,329 genes, 200 genes were found differentially expressed in NS silenced Hela cells with > 2 fold ratio (either > 2 or < 0.5). Category analysis indicated these differential genes were mainly related with cancer pathogenesis, cell death, cell growth and proliferation. NS related gene pathway analysis suggested NS was mostly involved in the networks of cell cycle and differentiation controls. p53 may not be the only partner of NS in its regulated pathways. c-Myc may directly or indirectly interact with it to control the proliferation and differentiation switch in cancer cells. Our study provides a general view of the NS-target genes, and indicates the possible pathways in which NS plays its role in proliferation control.

Renal replacement lipomatosis

We report a relatively rare case of renal replacement lipomatosis presenting as a renal mass. Computed tomography revealed a predominantly low-density and roundish mass, with an irregular renal parenchyma, high-density calcification, and abundant low-density fat. The differential diagnosis before surgery was squamous cell carcinoma, teratoma, or angiomyolipoma of the kidney. The case was initially misdiagnosed, because we had no experience with this disease. After mass exploration, histological examination confirmed the diagnosis of renal replacement lipomatosis. The patient was free from signs of recurrence 10 months after the operation.

[Study on the relationship between allergic rhinitis and airway hyperresponsiveness]

OBJECTIVE

In order to study the relationship between allergic rhinitis and airway hyperresponsiveness.

METHOD

Each of them were separately engaged skin test with antigen. All 50 patients had intense positive reaction to artemisia pollen (++-+++), but all controls were negative. We conducted bronchial provocation test (BPT) with 1:100 (w/v) artemisia pollen. Before and after BPT, we separately tested the forced expiratory volume in first second (FEV1) which represented ventilative function and eosinophil cationic protein (ECP) in their serum.

RESULT

Before BPT, 50 patients and 20 normal controls had no trachea symptoms. FEV1 of 50 patients is (70 +/- 20)%, that normal controls is (85.6 +/- 8.9)% (P < 0.001). After BPT, in 50 patients, 23 cases felt constriction in the chest, 10 cases had wheezes, 5 cases had asthma, 12 cases had no symptoms. At the same time, all of normal controls had no symptoms. After BPT, FEV1 of 50 patients is (60 +/- 20)%, that of normal controls was (85.6 +/- 8.9)% (P < 0.05), ECP of patients was (30.37 +/- 18.92) micrograms/L, that of controls was (5.245 +/- 3.228) micrograms/L (P < 0.05).

CONCLUSION

Patients with allergic rhinitis not only have chronic inflammation in their nose mucosa that results from allergic react, but also have chronic inflammation in bronchus which leads to AHR. The results reveal that most patients with allergic rhinitis have AHR (76%).

Three new taxane diterpenoids from the seeds of the Chinese yew, Taxus chinensis var mairei

Three new taxoids were isolated from the seeds of the Chinese yew, Taxus chinesis var mairei, their structures were established as 9alpha, 13alpha-diacetoxy-5alpha-cinnamoyloxy-11(15-->1)-abeo-taxa-4(20),11-diene-10beta, 15-diol, 2alpha,9alpha,10beta-triacetoxy-taxa-4(20),11-diene-5alpha,13alpha-diol and 2alpha,7beta,10beta-triacetoxy-5alpha-cinnamyloxy-9alpha-hydroxy-taxa-4(20),11-diene-13-one on the basis of 1D, 2D NMR, and MS spectral analyses.

Growth of Qinghai Tibetans living at three different high altitudes

This study compares the stature, weight, skinfolds, upper arm muscle area, and chest dimensions of Tibetan children, adolescents, and young adults who were born and raised, or who had lived from infancy, at 3,200 m, 3,800 m, and 4,300 m in Qinghai Province, People's Republic of China. While the individuals measured in Qinghai are among the tallest and heaviest Tibetans reported in the literature, they are nevertheless smaller and lighter than well-off children living at low altitude. The pattern of size variation among Tibetan males and females measured at the three high altitudes, along with evidence of a secular trend at 4,300 m, suggests that nutrition may significantly effect growth at high altitude. Only minor differences in thorax dimensions exist between Tibetan males and females measured at 3,200 m and 3,800 m. However, Tibetan males at 4,300 m possess slightly narrower and deeper chests (during and after adolescence) than males at 3,200 m and 3,800 m. Since individuals from 3,800 m and 4,300 m belong to the same local populations, this characteristic is unlikely to be genetically determined. However, it may be related to differences in the degree of hypoxia or to the influences of other environmental conditions.

[Effects of poria cocos on ototoxicity induced by kanamycin in guinea-pigs]

In order to prevent the ototoxicity of kanamycin (KM), the effects of Poria Cocos (PC) on the ototoxicity induced by KM in guinea-pigs was observed by infusing the PC decoction into the guinea-pigs with comparing the difference in the general intoxicating symptom, prayer's reflex (PR) threshold, brainstem auditory evoked potentials (BAEPs) and the absence rate of outer hair cells in the first turn of cochlea. The results suggested that the ototoxicity of KM was retarded by giving the PC decoction. On 7th day after given KM, PR threshold of 4,6,8 kHz in the medicated group and control group were 4.7 +/- 1.5 dB, 5.7 +/- 2.4 dB, 2.7 +/- 1.2 dB and 10.5 +/- 3.2 dB, 12.1 +/- 3.7 dB, 8.5 +/- 2.7 dB respectively. BAEPs threshold on 13th day given KM raised 22.7 +/- 9.7 dB in the medicated group and 51.3 +/- 14.4 dB in control group. The absence rate of outer hair cells in first turn of cochlea were 39.4% and 67.4% respectively. The results suggested that PC might be antagonistic to the ototoxicity of KM in guinea-pigs.

[Measurement of the single muscle fiber action potentials and jitter value in tibialis anterior muscles of rabbits in situ]

With a home-made jitter data processing board and microcomputer for recording extracellular single fiber action potential (SF-AP), variations of the time intervals of the SF-AP pairs, or the jitters, from two adjacent muscle fibers in the unique motor unit in tibialis' anterior in response to repeated stimuli were measured. The jitter distribution of 936 recorded from 7 rabbits was positively showed with a percentile value of P75-P25 of 54.99-14.61 microseconds. The data suggested that the lower limit was smaller than that of skeletal muscles in normal human and that there exists also some differences in the jitter values of SFEMG between human and rabbit muscles.

Hyperreiterated DNA regions are conserved among Bradyrhizobium japonicum serocluster 123 strains

We have identified and cloned two DNA regions which are highly reiterated in Bradyrhizobium japonicum serocluster 123 strains. While one of the reiterated DNA regions, pFR2503, is closely linked to the B. japonicum common and genotype-specific nodulation genes in strain USDA 424, the other, pMAP9, is located next to a Tn5 insertion site in a host-range extension mutant of B. japonicum USDA 438. The DNA cloned in pFR2503 and pMAP9 are reiterated 18 to 21 times, respectively, in the genomes of B. japonicum serocluster 123 strains. Gene probes from the reiterated regions share sequence homology, failed to hybridize (or hybridized poorly) to genomic DNA from other B. japonicum and Bradyrhizobium spp. strains, and did not hybridize to DNA from Rhizobium meliloti, Rhizobium fredii, Rhizobium leguminosarum biovars trifolii, phaseoli, and viceae, or Agrobacterium tumefacians. The restriction fragment length polymorphism hybridization profiles obtained by using these gene probes are useful for discriminating among serologically related B. japonicum serocluster 123 strains.

Heating pattern of helical microwave intracavitary oesophageal applicator

Helical microwave intracavitary oesophageal (HMIO) applicators were designed to operate at frequencies of 433 MHz and 915 MHz. Heating patterns were studied within muscle-equivalent phantom by thermographic camera and fibreoptic thermometers. The results showed that frequency significantly influenced the microwave heating pattern. The 433 MHz applicator had a single power deposition region, the longitudinal specific absorption rate (SAR) distribution appeared to be nearly even, and the maximum SAR value occurred close to the centre of the active length of the applicator. The 915 MHz applicator had two power deposition regions, the peak SAR values occurred at about 1/4 and 3/4 of the active length respectively. The radial SAR distribution suggested that there is no obvious difference between the 433 MHz and 915 MHz applicators in that the average radial penetration of 50% surface SAR (RP50) was about 0.65 cm. It was also shown that power deposition was axially symmetric for both 433 MHz and 915 MHz HMIO applicators. It is shown that better impedance matching is more important for intracavitary hyperthermia than for external hyperthermia. Choosing HMIO applicators in clinical practice is also discussed.

Experimental assessment of phased-array heating of neck tumours

An investigation of phased-array microwave systems (PAMS) for non-invasively inducing hyperthermia, primarily in neck lesions, has been done with implications for applications at other sites such as lung and pelvis. Our general approach was to combine numerical and analytical approaches with parallel experimental studies. In this paper we will concentrate only on the experimental aspects. The object, such as a homogeneous cylindrical phantom or a neck phantom, was encircled with several standard applicators driven by a single source, but with relative phase and amplitude control over each applicator. The relative phases of the applicators were adjusted by using an implanted monopole antenna connected to an HP network analyser. Power was applied and the specific absorption rate (SAR) was determined by using split phantoms and thermography or by measuring temperature transients dT/dt, recorded by implanted thermometer probes. We found that at 915 MHz for our applicators (SMA Co.) the centre of an 11 cm diameter muscle-like phantom heated to about 33% of the value at the surface in front of the applicator. Similarly, we were able to show significant SAR at the centre of realistically sized neck phantoms using four phased apertures of 915 MHz. Furthermore, substantial improvement was observed if the frequency was lowered to about 400 MHz.

Application of biotin-avidin system, determination of circulating immune complexes, and evaluation of antibody response in different hydatidosis patients

The avidin-biotin-peroxidase complex enzyme-linked immunosorbent assay (ABC-ELISA) and standard ELISA were used for the detection of Echinococcus granulosus antibody in sera of 101 patients operated on for hydatid disease, 40 patients with miscellaneous nonhydatid diseases, and 61 normal subjects. Sensitivity and specificity of the two procedures were comparable and the geometric mean antibody titer detected with ABC-ELISA was higher than with standard ELISA. The ABC-ELISA is a sensitive, specific, simple, and convenient method for diagnosing hydatidosis.

Changes in myocardial oxygen demand and instantaneous ventricular vascular volume during prolonged cross-clamping and reperfusion of the abdominal aorta

In 47 animals (rats, rabbits) the cardiac side effects of prolonged (3 to 6 hours) abdominal aortic cross-clamping and unclamping (3 to 6 hours) were investigated. The relative instantaneous ventricular vascular volume (IVVV), a factor reflecting myocardial blood supply and the rate pressure product (RPP) representing myocardial oxygen demand were used as parameters. Following cross-clamping the IVVV showed an initial decrease while the myocardial oxygen demand revealed a sudden increase. After unclamping, the myocardial oxygen demand decreased and IVVV improved. Minimal levels of both IVVV and RPP occurred at 6 hours following unclamping. This may be an effect of a myocardial inhibiting substance, released by ischemia and necrosis of the lower extremity.