[Study on the transfer mechanism and destructive law of the bacterial antibiotic resistance genes disinfected by chlorination]

Objective: To study the response of Escherichia coli (E. coli) HB101 (plasmid pUC19) and its carried antibiotic resistance genes to the process of cholorination under different environmental conditions. Methods: The E. coli strain was reacted with sodium hypochlorite at the concentration of 0.5, 0.75, 1.00, and 0.55 mg/L, then the residual chlorine and the colonies were detected at the 0.25, 1, 2, 5, 10, 20, and 30 min of the reaction, respectively. The first order disinfection kinetic model and EFH model were used to evaluate the inactivation effect of E. coli (plasmid pUC19) treated by sodium hypochlorite, while the plasmid pUC19 and antibiotic resistance gene amp(r) were detected by PCR method. Besides, the logarithm of Ct (residual chlorine in t) under different concentration were calculated. Results: The temperature and pH value played important roles on the inactivation of E. coli and elimination of plasmid pUC19 and amp(r) under the function of sodium hypochlorite. The Ct value needed for 5-log of E.coli HB101(pUC19) inactivation at 4, 20, 36 ℃ was 11.92, 10.28, 7.67, respectively, and when the pH was in 6.0, 7.0, 8.0, with chloride concentration were 0.75, 0.70, 0.55 mg/L, the Ct value needed for reached to 6.68, 10.28, 15.73 min·mg/L. At pH 7.2 condition, when the temperature was 4, 20, 36 ℃, and chloride concentration were 9, 5, 3 mg/L.The required Ct values to completely destroy the transformation function of free antibiotic resistant plasmids were 36.11, 34.17,16.09 min·mg/L. Sodium hypochlorite disinfection can release free ampr gene and even the transformed plasmid pUC19, and pollute the water body. Only when the Ct value reached 903.03 min·mg/L, the complete ampr gene can be destroyed which was far more exceed the bacterial lethal Ct value. Conclusion: Even if all the antibiotic resistant bacteria were inactivated, the antibiotic resistant plasmids or genes might still maintain complete with the transformable function, which may result in new potential risks of waterborne diseases.

Identification and Functional Studies of MYO1H for Mandibular Prognathism

Mandibular prognathism (MP) is regarded as a craniofacial deformity resulting from the combined effects of environmental and genetic factors, while the genetically predetermined component is considered to play an important role to develop MP. Although linkage and association studies for MP have identified multiple strongly associated regions and genes, the causal genes and variants responsible for the deformity remain largely undetermined. To address this, we performed targeted sequencing of 396 genes selected from previous studies as well as genes and pathways related with craniofacial development as primary candidates in 199 MP cases and 197 controls and carried out a series of statistical and functional analyses. A nonsynonymous common variant of MYO1H rs3825393, C>T, p.Pro1001Leu, was identified to be significantly associated with MP. During zebrafish embryologic development, expression of MYO1H orthologous genes were detected at mandibular jaw. Furthermore, jaw cartilage defects were observed in zebrafish knockdown models. Collectively, these data demonstrate that MYO1H is required for proper jaw growth and contributes to MP pathogenesis, expanding our knowledge of the genetic basis of MP.

[A customized method for information extraction from unstructured text data in the electronic medical records]

OBJECTIVE

There is a huge amount of diagnostic or treatment information in electronic medical record (EMR), which is a concrete manifestation of clinicians actual diagnosis and treatment details. Plenty of episodes in EMRs, such as complaints, present illness, past history, differential diagnosis, diagnostic imaging, surgical records, reflecting details of diagnosis and treatment in clinical process, adopt Chinese description of natural language. How to extract effective information from these Chinese narrative text data, and organize it into a form of tabular for analysis of medical research, for the practical utilization of clinical data in the real world, is a difficult problem in Chinese medical data processing.

METHODS

Based on the EMRs narrative text data in a tertiary hospital in China, a customized information extracting rules learning, and rule based information extraction methods is proposed. The overall method consists of three steps, which includes: (1) Step 1, a random sample of 600 copies (including the history of present illness, past history, personal history, family history, etc.) of the electronic medical record data, was extracted as raw corpora. With our developed Chinese clinical narrative text annotation platform, the trained clinician and nurses marked the tokens and phrases in the corpora which would be extracted (with a history of diabetes as an example). (2) Step 2, based on the annotated corpora clinical text data, some extraction templates were summarized and induced firstly. Then these templates were rewritten using regular expressions of Perl programming language, as extraction rules. Using these extraction rules as basic knowledge base, we developed extraction packages in Perl, for extracting data from the EMRs text data. In the end, the extracted data items were organized in tabular data format, for later usage in clinical research or hospital surveillance purposes. (3) As the final step of the method, the evaluation and validation of the proposed methods were implemented in the National Clinical Service Data Integration Platform, and we checked the extraction results using artificial verification and automated verification combined, proved the effectiveness of the method.

RESULTS

For all the patients with diabetes as diagnosed disease in the Department of Endocrine in the hospital, the medical history episode of these patients showed that, altogether 1 436 patients were dismissed in 2015, and a history of diabetes medical records extraction results showed that the recall rate was 87.6%, the accuracy rate was 99.5%, and F-Score was 0.93. For all the 10% patients (totally 1 223 patients) with diabetes by the dismissed dates of August 2017 in the same department, the extracted diabetes history extraction results showed that the recall rate was 89.2%, the accuracy rate was 99.2%, F-Score was 0.94.

CONCLUSION

This study mainly adopts the combination of natural language processing and rule-based information extraction, and designs and implements an algorithm for extracting customized information from unstructured Chinese electronic medical record text data. It has better results than existing work.

[Effect of Benzidine Test on DNA Analysis of Bloodstain]

OBJECTIVES

To explore the effect of benzidine test and related reagents on DNA analysis of bloodstain.

METHODS

A total of 970 bloodstain filter paper samples with 1 μL venous blood were collected, and 10 of them acted as control samples. After benzidine test and related reagent processing, DNA of 960 samples was extracted by Chelex-100 and silica bead methods and then multiplex amplified by AmpFℓSTR™ Identifiler™ Plus PCR kits. The results of STR typing were compared between different groups.

RESULTS

DNA were extracted immediately after benzidine test. Totally STR loci （3.80±1.34） were detected by silica bead method, while no STR loci were obtained by Chelex-100 method. Thirteen samples （21.7%） with whole STR typing results were obtained by drying after benzidine test, and the STR locus number （12.90±1.49） which obtained by silica bead method was much higher than by Chelex-100 method （4.70±1.96） （P<0.05）. When DNA was extracted immediately after the addition of glacial acetic acid, the STR locus number was （9.40±2.09） by silica bead method, but no STR typing result was obtained by Chelex-100 method. All 15 STR loci could be obtained by only adding glacial acetic acid after drying and only adding tetramethylbenzidine alcoholization liquid or 3% hydrogen peroxide liquid.

CONCLUSIONS

Benzidine test has significant influence on DNA analysis of bloodstain. The Chelex-100 method is not suitable for the DNA extraction of bloodstain after benzidine test. Drying after benzidine test and silica bead methods can effectively enhance the STR locus number of bloodstain.

Strategies to increase the efficacy of using gut microbiota for the modulation of obesity

Obesity is one of the most serious global public health challenges of the 21st century. The adjustment of gut microbiota is often recommended as an efficient strategy to treat obesity. This modulation of gut microbiota can be performed by many methods, including dietary intervention, antibiotic application, the use of prebiotics and probiotics, bariatric surgery and faecal microbiota transplantation. In most cases, positive effects have been observed in response to treatment, but invalid and even contrary effects have also been observed in some cases due to factors that are unrelated to intervention methods, such as genetic factors, patient age or gender, environmental microbiota, climate, geography and lifestyle. These factors can cause variation of gut microbial populations and thus should also be taken into consideration when selecting modulation strategies.

Ethnic disparities in progression to advanced liver disease and overall survival in patients with chronic hepatitis C: impact of a sustained virological response

BACKGROUND

Chronic hepatitis C (CHC) can lead to cirrhosis and hepatocellular carcinoma (HCC). A sustained virological response (SVR) is associated with improved outcomes, however, its impact on different ethnic groups is unknown.

AIM

To evaluate ethnic differences in the natural history of CHC and the impact of SVR.

METHODS

We conducted a cohort study of 8039 consecutive adult CHC patients seen at two medical centres in California between January 1997 and June 2016. Individual chart review confirmed CHC diagnosis.

RESULTS

Asian and Hispanic but not African American patients had significantly higher cirrhosis and HCC incidence than Caucasians. On multivariate analysis, Hispanic ethnicity was independently associated with increased cirrhosis (adjusted HR 1.37, CI, confidence interval 1.10-1.71, P=.006) and HCC risk (adjusted HR 1.47, CI 1.13-1.92, P=.004) compared to Caucasian. Asian ethnicity had a significant association with cirrhosis (adjusted HR 1.28, CI 1.02-1.61, P=.034) and HCC risk (adjusted HR 1.29, CI 0.94-1.77, P=.025). In patients who achieved SVR, Hispanic ethnicity was no longer independently associated with cirrhosis (adjusted HR 1.76, CI 0.66-4.71, P=.26) or HCC (adjusted HR 1.05, CI 0.27-4.08, P=.94); nor was Asian ethnicity (adjusted HR 0.62, CI 0.21-1.82, P=.38 for cirrhosis; 2.01, CI 0.63-6.36, P=.24 for HCC). Similar findings were observed with overall survival among the ethnicities by SVR status.

CONCLUSION

Hispanic and Asian ethnicity was independently associated with increased cirrhosis and HCC risk. Achieving an SVR eliminates the ethnic disparity in liver disease progression and overall survival between Hispanic and Asian vs Caucasian CHC patients.

Effect and mechanism of propofol in hepatic ischemia/reperfusion injury of rat

OBJECTIVE

Hepatic ischemia/reperfusion (I/R) injury remains to be one of the most common clinical diseases. This study aimed to explore the potential effect and mechanism of propofol in protecting rat liver from I/R injury.

MATERIALS AND METHODS

The hepatic I/R model was established in Sprague-Dawley (SD) rats by perfusing the liver with heparinized cold saline through the portal vein for 20 min. The rats were then received a 100 mg/kg/d propofol administration for the continuously 10 days. The hepatic function indexes of ALT, AST, and GGT were detected by ELISA. The apoptosis of hepatic cells was assessed by TUNEL analysis, and Bax and Bcl-2 expression changes were detected by qRT-PCR and Western blotting. In addition, serum pro-inflammatory factors and the signaling pathway-related protein expressions were detected.

RESULTS

Propofol markedly attenuated the increases of ALT, AST, and GGT induced by I/R. Propofol reduced I/R-induced apoptosis and pro-inflammatory factors secretion. Furthermore, propofol could promote the expression of phosphorylated (p)-AKT and inhibited the expression of p-mTOR.

CONCLUSIONS

Propofol protects hepatic I/R injury partly by reducing apoptosis and reducing the release of pro-inflammatory cytokines, which is possibly involved in the modulation of the PI3K/AKT/mTOR signaling pathway. All these data suggest that propofol may play certain positive roles in protecting the liver from I/R injury.

Dark Matter Search Results from the PICO-60 C_{3}F_{8} Bubble Chamber

New results are reported from the operation of the PICO-60 dark matter detector, a bubble chamber filled with 52 kg of C_{3}F_{8} located in the SNOLAB underground laboratory. As in previous PICO bubble chambers, PICO-60 C_{3}F_{8} exhibits excellent electron recoil and alpha decay rejection, and the observed multiple-scattering neutron rate indicates a single-scatter neutron background of less than one event per month. A blind analysis of an efficiency-corrected 1167-kg day exposure at a 3.3-keV thermodynamic threshold reveals no single-scattering nuclear recoil candidates, consistent with the predicted background. These results set the most stringent direct-detection constraint to date on the weakly interacting massive particle (WIMP)-proton spin-dependent cross section at 3.4×10^{-41}  cm^{2} for a 30-GeV c^{-2} WIMP, more than 1 order of magnitude improvement from previous PICO results.

Transcriptome analysis of potential simple sequence repeat markers in Ammopiptanthus mongolicus

Ammopiptanthus mongolicus, an evergreen broadleaf legume shrub, can survive under conditions of high and low temperature, extreme salinity, and drought. This attribute makes it an ideal model for studying mechanisms of stress tolerance in plants. However, simple sequence repeat (SSR) resources for this species are insufficient in public databases. In this study, a total of 44,959 unigenes identified from the A. mongolicus transcriptome were used for SSR analysis by MIcroSAtellite (MISA). A total of 13,859 SSRs were found to be distributed within 10,409 unigenes, with an average length of 15 bp and an average density of one SSR per 4.4 kb. There were 222 different motif types in the A. mongolicus transcriptome, and mononucleotide repeats represented the main type, accounting for 44.2% of all SSRs. The (A/T)n repeat was the most frequent motif, accounting for 42.37% of all SSRs. We also performed Gene Ontology functional analysis, Kyoto Encyclopedia of Genes and Genomes database pathway analysis, and eggNOG analysis, and identified 6157, 2301, and 9845 unigenes containing SSRs in these three databases, respectively. The functional categorization of A. mongolicus unigenes containing SSRs revealed that these unigenes represent many transcribed genes with different functions. These data provide sequence information that may be used to improve molecular-assisted markers for the study A. mongolicus genetic diversity.

Change in serum TSH levels within the reference range was associated with variation of future blood pressure: a 5-year follow-up study

Controversy exists on the relationship between serum thyrotropin (TSH) and blood pressure, and only a few prospective studies are available up to now. The study aimed to investigate the association between serum TSH within the reference range and blood pressure through a 5-year follow-up study. A total of 623 subjects with normal TSH were followed up for 5 years, including the measurement of demographic data, blood pressure, height, weight and serum TSH. Finally, 531 subjects were included in this prospective study. Body mass index (BMI), prevalence of hypertension, and systolic and diastolic blood pressure were all higher at follow-up than at baseline. Adjusted for age, gender, smoking status, BMI and homoeostasis model assessment of insulin resistance (HOMA-IR) at baseline, multiple linear regression analyses found no relationship between serum TSH at baseline and levels of blood pressure at follow-up, but the changes in serum TSH levels during follow-up was positively associated with the changes in systolic blood pressure (B=2.134, P<0.05), which became more significant in women but not significant in men. The change of systolic blood pressure in group of TSH increase >0.5 mIU l^-1 was significantly higher than in group of TSH decrease >0.5 mIU l^-1 within reference, after adjusting for age, gender, smoking status, BMI and HOMA-IR at baseline. This result became more significant in women, but no statistical significance was observed in men. Co-variation with serum TSH levels and blood pressure was observed during 5-year follow-up among people with normal TSH.

Rotavirus infection and histo-blood group antigens in the children hospitalized with diarrhoea in China

To explore the association between rotavirus (RV) infection and histo-blood group antigens (HBGAs), a cross-sectional study was conducted in children hospitalized with diarrhoea in China from November 2014 to February 2015. In total, 424 sets of stool, saliva and buccal cell samples were collected. For the 125 RV-negative samples, 92% (104/125) were secretors/partial secretors, 8% (10/125) were non-secretors. Among the 299 RV-positive samples, 277 were P[8] and 22 were P[4]. All P[4] and P[8] positive individuals were secretors/partial secretors except for one P[8] (0.3%, 1/299), which was a non-secretor. These findings indicate that P[8] and P[4] RVs preferably infect secretors/partial secretors (p <0.001).

[A long-term follow-up results of Enterprise stent in treatment of severe symptomatic basilar artery atherosclerotic stenosis]

OBJECTIVE

To evaluate the safety and efficacy of Enterprise stent in the treatment of severe symptomatic basilar artery atherosclerosis stenosis.

METHODS

All patients who underwent Enterprise stent for the treatment of symptomatic basilar artery atherosclerotic stenosis in our center from Nov. 2011 to Nov. 2014 were enrolled in the study. Preoperative and postoperative dual antiplatelet drugs and intensive lipid-lowering therapy were given to all the patients. Multi-modality imaging guiding for stent angioplasty was performed in all the patients, including head MRI or CT, CT or MRI perfusion, high resolution MRI for plaque analysis and angiography. Angiography after 6 months was recommended. The main outcome parameters were any stroke or death within 30 days, stroke recurrence in the basilar artery blood supply area during the follow-up period and in-stent restenosis.

RESULTS

A total of 35 cases were enrolled in the study with operation technical success rate of 100%. The average preoperative and postoperative stenosis rate was (83.0±10.1)% and (28.1±8.9)%. The main perioperative complication and mortality rate was 0. The average follow-up period was (10.6±7.9) months. During follow-up period, only 2 cases (5.7%) of TIA related to the stented artery were observed. In patients with follow-up period more than 6 months, 17 cases (56.7%) underwent cerebral angiography. Restenosis rate was 17.6%. One patient with in-stent restenosis suffered from transient cerebral ischemia and received another Enterprise stenting successfully.

CONCLUSION

Long term follow-up results show that Enterprise stent for the treatment of symptomatic basilar artery severe stenosis is safe and recurrence of stroke can be prevented effectively.

[Epidemiologic characteristics of noroviruses isolated in outpatients with acute gastroenteritis in Hangzhou area, from 2014 to 2015]

OBJECTIVE

To explore the epidemiologic characteristics of noroviruses isolated in patients with acute gastroenteritis in Hangzhou between March 2014 and April 2015.

METHODS

Stool specimens and clinical data were collected from 1 109 patients with acute gastroenteritis. Specimens were detected for noroviruses with GⅠand GⅡsubtypes by one-step double real-time RT-PCR. Some of the positive specimens were then randomly selected and amplified by multiplex RT-PCR. Those positive PCR products were sequenced and analyzed phylogenetically for testing the partial capsids of noroviruses.

RESULTS

Of the 1 109 stool specimens, positive rate of noroviruses was 26.87% (298/1 109). GⅡgenotype was the major viruses with the proportion as 25.52% (283/1 109), while 1.35% (15/1 109) belonged to GⅠgenotypes. There was no significant difference in the noroviruses detection rate of the different genders (P>0.05). However, in different age groups, GⅡgenotypes were predominant types of noroviruses, and the positive rates of GⅡgenotypes were 16.94% (<5 years-old), 19.45% (5-18 years-old) and 32.26% (≥18 years-old), respectively. In different seasons, noroviruses could be detected all year round, with positive rate as 29.67%-37.08% in the highly epidemic seasons (between December and March of the following year). The distribution trends were seen certain difference between noroviruses-GⅡand GⅠtypes. Additionally, results from the sequence analysis demonstrated that GⅡ-4 genotype was the prevalent strain of GⅡ genotypes, clustered into GⅡ-4/Sydney (46.43%, 13/28) and GⅡ-4/2006b (25.0%, 7/28), while GⅠstrains clustered into GⅠ-1.

CONCLUSION

Noroviruses appeared one of the major pathogens, leading to acute gastroenteritis. G Ⅱgenotypes of noroviruses, especially the G Ⅱ-4/Sydney variant strains and GⅡ-4/2006b variant strains, were considered to be the prevalent strains prevailed in Hangzhou areas from 2014 to 2015.

Bio-chemical characterization of a β-mannanase from Bacillus licheniformis HDYM-04 isolated from flax water-retting liquid and its decolorization ability of dyes

A β-mannanase was purified from the bacteria,Bacillus licheniformisHDYM-04, which was a high β-mannanase-producing strain (576.16 U mL⁻¹at 48 h during fermentation).