Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7-18 years old children from the American Gut Project

BACKGROUND

The association between the gut microbiota and obesity in young children and adolescents is not fully studied.

OBJECTIVES

This study investigated the associations between the gut microbiota and body mass index (BMI) level (underweight, normal, overweight, obese) and lifestyles (diet type and exercise frequency), controlling for demographic and clinical factors among children aged 7-18 years.

METHODS

A cohort study was conducted on 267 children aged 7-18 years from the American Gut Project. 16S rRNA sequences were analysed by QIIME 2™. Composition of gut microbiota and its associations with BMI level, weight change and lifestyles were analysed using linear decomposition model.

RESULTS

Significant factors affecting the gut microbiota were BMI level (p = 0.009), exercise frequency (p = 0.003) and diet type (p = 0.01), controlling for age, sex and use of antibiotics and probiotics. More bacterial operational taxonomic units (OTUs) were associated with BMI level (120 OTUs) and diet type (122 OTUs) than exercise frequency (67 OTUs). Actinobacteria phylum had significantly depleted OTUs for BMI level, diet type and exercise frequency; Proteobacteria phylum had significantly enriched OTUs for higher BMI level and Firmicutes phylum had significantly enriched OTUs for more frequent exercise.

CONCLUSIONS

Significant associations were found between the gut microbiota composition and BMI level and lifestyles controlling for demographic and clinical factors in children aged 7-18 years.

A multiplex real-time PCR assay for the detection and differentiation of five bovine pinkeye pathogens

Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is one of the most common eye diseases in cattle. Several pathogens have been associated with IBK cases, however, Moraxella bovis, Moraxella bovoculi, Mycoplasma bovis, Mycoplasma bovoculi and bovine herpesvirus type 1 (BHV-1) are most frequently observed. A multiplex real-time PCR assay using two reactions was developed for the detection and differentiation of these five pathogens. Detection sensitivities of the multiplex assays were compared to singleplex reactions testing for the same targets. Correlation coefficients (R²) of >0.99, and PCR efficiencies between 92 and 106% were demonstrated in all singleplex and multiplex real-time PCR reactions. The limits of detection (LOD) of multiplex assays for Moraxella bovis, Moraxella bovoculi, Mycoplasma bovis, Mycoplasma bovoculi and BHV-1 were 19, 23, 25, 24 and 26 copies per reaction, respectively. No cross amplification was observed for specificity testing of 179 IBK positive clinical samples and 55 non-target clinical samples. Percentage of clinical samples positive for Mycoplasma bovoculi, Moraxella bovoculi, Moraxella bovis, BHV-1 and Mycoplasma bovis were 88.8% (159/179), 75.9% (136/179), 60.3% (108/179), 11.7% (21/179) and 10.0% (18/179), respectively. Moraxella bovis, Moraxella bovoculi and Mycoplasma bovoculi were more prevalent than Mycoplasma bovis and BHV-1 in IBK samples collected from animals in this study population. Our data indicates that the multiplex real-time PCR panel assay is highly sensitive and highly specific for the detection and differentiation of the five major pathogens associated with bovine pinkeye.

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A multiplex real-time PCR is developed for the detection of five major IBK pathogens.

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Correlation coefficients of all standard curves were >0.99.

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PCR amplification efficiencies for the five pathogens were between 92% and 106%.

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Limits of detection were between 19 and 26 copies per reaction for the five pathogens.

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Moraxella bovoculi, Mycoplasma bovoculi, and Moraxella bovis were more prevalent IBK pathogens.

Pathological Changes of Petechial Hemorrhage after High Temperature Treatment

OBJECTIVES

To study the main features of mechanical asphyxia--the pathological characteristics of petechial hemorrhage after high temperature effect （roasted, boiled） and its changing rules.

METHODS

Rabbit model of mechanical asphyxia death with choking neck and death from anteposition hanging was established. The experimental rabbits were randomly divided into roasted group and boiled group （n=4, in each group）. The laryngeal ventricles and cardiopulmonary tissues in the roasted group were roasted for 3, 6 and 10 min, and the positions of petechial hemorrhage were observed and photographed. The same organs and tissues in the boiled group were heated in boiling water （100 ℃）, and were observed and photographed at 30 and 60 s. Then histopathological examination was performed on all the laryngeal ventricles and cardiopulmonary tissues.

RESULTS

The petechial hemorrhage originating from laryngeal ventricle, trachea and lung did not disappear after high temperature treatment in the eight rabbits. The deepened color was visible to naked eyes and distinct from the surrounding normal tissues, with bleeding under the microscope.

CONCLUSIONS

Petechial hemorrhage caused by mechanical asphyxia would not disappear under high temperature, which might be related to the manner of death, the intensity and time of action, and the individual differences.

A multiplex real-time PCR assay for the detection and differentiation of the newly emerged porcine circovirus type 3 and continuously evolving type 2 strains in the United States

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A multiplex real-time PCR assay was developed for PCV2 and PCV3 detection and differentiation.

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Sensitivity was determined by standard curves with viral isolates and positive diagnostic samples.

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Specificity was determined by testing common swine viruses.

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The assay was validated on 336 swine diagnostic samples.

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Limited data indicated that PCV3 has higher prevalence than PCV2 in the US.

A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for the detection and differentiation of porcine circovirus type 3 (PCV3) and type 2 (PCV2) strains. The assay coverage was 97.9% (184/188) for PCV3 and 99.1% (1889/1907) for PCV2 sequences that were available from the current GenBank database. The PCR amplification efficiencies were 98–99% for plasmids, and 92–96% for diagnostic samples, with correlation coefficients all greater than 0.99. The limit of detection (LOD) determined as plasmid copies per reaction was 17 for PCV3 and 14 for PCV2. The assay specifically detected the targeted viruses without cross reacting to each other or to other common porcine viruses. Among 336 swine clinical samples collected in 2018, 101 (30.1%) were PCV3 positive, 56 (16.7%) were PCV2 positive and 18 (5.4%) were co-positives. Sixty selected PCV3 positives were confirmed by Sanger sequencing, and 53 of the 56 PCV2 positive samples were tested positive by another validated PCR assay.

[Contamination and pathogenicity analysis of listeria monocytogenes in restaurant in Heilongjiang Province]

Objective: To study the contamination, serotype, pulsed field gel electrophoresis (PFGE) and drug resistance of listeria monocytogenes (L.monocytogenes) in the process of restaurant kitchens in Heilongjiang Province. Methods: Seventeen typical restaurants were selected from three cities in Heilongjiang Province in 2016, and 590 kitchen samples were collected and tested according to the national standard method. The serotype, pulsed field gel electrophoresis (PFGE) and drug resistance of isolated strains were analyzed. Results: L. monocytogenes was found in 104 of 590 of the samples analysed (17.63%). The isolates belong to six serotypes (1/2 a, 1/2 b, 1/2c, 3a, 3 b, 4 b) and self-condensing bacteria, and 57.38% (70 strains) of the strains belong to serotype 1/2b. Two highly pathogenic serotype 4b was detected for human listeria disease. The results of PFGE analysis show that the bacteria have cross-contamination in the environment, tools, equipment, food and personnel. The drug resistance results showed that 2 strains were resistant to tetracycline, 1 strain was resistant to erythromycin, 13 strains were intermediate to tetracycline, and 2 strains were resistant to tetracycline and erythromycin. Conclusion: There is a certain degree of L. monocytogenes cross-contamination in the catering kitchen in Heilongjiang Province. And an important serotype 4b that can cause human Listeria disease was detected.

DNA Microarray-Based Genomic Characterization of the Pathotypes of Escherichia coli O26, O45, O103, O111, and O145 Isolated from Feces of Feedlot Cattle †

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, referred to as the top six non-O157 serogroups, are responsible for more than 70% of human non-O157 STEC infections in North America. Cattle harbor non-O157 strains in the hindgut and shed them in the feces. The objective of this study was to use the U.S. Food and Drug Administration (FDA) E. coli identification (ECID) DNA microarray to identify the serotype, assess the virulence potential of each, and determine the phylogenetic relationships among five of the six non-O157 E. coli serogroups isolated from feedlot cattle feces. Forty-four strains of STEC, enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), or putative nonpathotype E. coli (NPEC) of cattle origin and five human clinical strains of EHEC were assayed with the FDA-ECID DNA microarray. The cattle strains harbored diverse flagellar genes. The bovine and human strains belonging to serogroups O26, O45, and O103 carried stx₁ only, O111 carried both stx₁ and stx₂, and O145 carried either stx₁ or stx₂. The strains were also positive for various subtypes of intimin and other adhesins (IrgA homologue adhesin, long polar fimbriae, mannose-specific adhesin, and curli). Both human and cattle strains were positive for LEE-encoded type III secretory system genes and non-LEE-encoded effector genes. SplitsTree4, a program used to determine the phylogenetic relationship among the strains, revealed that the strains within each serogroup clustered according to their pathotype. In addition to genes encoding Shiga toxins, bovine non-O157 E. coli strains possessed other major virulence genes, including those for adhesins, type III secretory system proteins, and plasmid-borne virulence genes, similar to human clinical strains. Because virulence factors encoded by these genes are involved in the pathogenesis of various pathotypes of E. coli, the bovine non-O157 strains could cause human illness. The FDA-ECID DNA microarray assay rapidly provided a profile of the virulence genes for assessment of the virulence potential of each strain.

Feed batch sequencing to decrease the risk of porcine epidemic diarrhea virus (PEDV) cross-contamination during feed manufacturing

Feed has been identified as a vector of transmission for porcine epidemic diarrhea virus (PEDV). The objective of this study was to determine if feed batch sequencing methods could minimize PEDV cross-contamination. Porcine epidemic diarrhea virus-free swine feed was manufactured to represent the negative control. A 50 kg feed batch was mixed in a pilot scale feed mill for 5 min, sampled, then discharged for 10 min into a bucket elevator and sampled again upon exit. Next, a pathogenic PEDV isolate was used to inoculate 49.5 kg of PEDV-free feed to form the positive control. The positive control was mixed, conveyed and sampled similar to the negative control. Subsequently, 4 sequence batches (sequence 1 to 4) were formed by adding a 50 kg batch of PEDV-negative feed to the mixer after the prior batch was mixed and conveyed; all sequences were mixed, conveyed, and sampled similar to the negative and positive control batches. None of the equipment was cleaned between batches within a replicate. This entire process was replicated 3 times with cleaning the feed mill between replicates. Feed was then analyzed for PEDV RNA by real-time reverse transcriptase semiquantitative polymerase chain reaction (rRT-PCR) as measured by cycle threshold (Ct) and for infectivity by bioassay. Sequence 1 feed had higher (P ˂ 0.05) rRT-PCR Ct values than the positive batch and sequence 2 feed had higher (P ˂ 0.05) Ct values than sequence 1, regardless of sampled location. Feed sampled from the mixer from sequence 2, 3, and 4 was rRT-PCR negative whereas feed sampled from the bucket elevator was rRT-PCR negative from sequence 3 and 4. Bioassay was conducted using 66 mixed sex 10-d-old pigs confirmed negative for PEDV allocated to 22 different rooms. Pigs were initially 10-d old. Control pigs remained PEDV negative for the study. All pigs from the mixer positive batch (9/9) and bucket elevator positive batch (3/3) were rRT-PCR positive on fecal swabs by the end of the study. One replicate of pigs from mixer sequence 1 was rRT-PCR positive (3/3) by 7 dpi. One replicate of mixer pigs from sequence 2 was rRT-PCR positive (3/3) by 7 dpi although no detectable PEDV RNA was found in the feed. The results demonstrate sequenced batches had reduced quantities of PEDV RNA although sequenced feed without detectible PEDV RNA by rRT-PCR can be infectious. Therefore, a sequencing protocol can reduce but not eliminate the risk of producing infectious PEDV carryover from the first sequenced batch of feed.

Monolithic multiple colour emission from InGaN grown on patterned non-polar GaN

A novel overgrowth approach has been developed in order to create a multiple-facet structure consisting of only non-polar and semi-polar GaN facets without involving any c-plane facets, allowing the major drawbacks of utilising c-plane GaN for the growth of III-nitride optoelectronics to be eliminated. Such a multiple-facet structure can be achieved by means of overgrowth on non-polar GaN micro-rod arrays on r-plane sapphire. InGaN multiple quantum wells (MQWs) are then grown on the multiple-facet templates. Due to the different efficiencies of indium incorporation on non-polar and semi-polar GaN facets, multiple-colour InGaN/GaN MQWs have been obtained. Photoluminescence (PL) measurements have demonstrated that the multiple-colour emissions with a tunable intensity ratio of different wavelength emissions can be achieved simply through controlling the overgrowth conditions. Detailed cathodoluminescence measurements and excitation-power dependent PL measurements have been performed, further validating the approach of employing the multiple facet templates for the growth of multiple colour InGaN/GaN MQWs. It is worth highlighting that the approach potentially paves the way for the growth of monolithic phosphor-free white emitters in the future.

Determining the impact of commercial feed additives as potential porcine epidemic diarrhea virus mitigation strategies as determined by polymerase chain reaction analysis and bioassay

Mitigation of porcine epidemic diarrhea virus (PEDV) was assessed using two feed additives (0.5% inclusion of a benzoic acid [BA] product and 0.02% inclusion of an essential oil [EO] product; DSM Nutritional Products Inc., Parsippany, NJ), and combination of both products (0.5% BA and 0.02% EO) in spray-dried porcine plasma (SDPP) and a swine gestation diet (FEED) as determined by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and bioassay. Viral RNA quantification was performed at 7 sampling days post-laboratory inoculation (d 0, 1, 3, 7, 14, 21, and 42) and infectivity was assessed via bioassay with 10-d-old pigs. There was a tendency for treatment × feed matrix × day interaction (P = 0.094), in which the cycle threshold (Ct) value increased over time in FEED when treated with both feed additives, whereas there was no increase over time observed in SDPP treated with both feed additives. There was a feed matrix × day interaction (P < 0.001) in which Ct increased over time in FEED, whereas very little increase over time was observed in SDPP. A tendency for a treatment × feed matrix effect (P = 0.085) was observed where FEED treated with the combination of EO and BA had a greater (P < 0.05) PEDV Ct value than other FEED treatments, and all SDPP treatments had the lower PEDV Ct values compared to FEED treatments (P < 0.05). Overall, the combination of both feed additives was most effective at reducing the quantity of genetic material as detected by qRT-PCR (P < 0.001) compared to either additive alone or no feed additive. Virus shedding was observed in the d 7 postinoculation SDPP treatment that was treated with both feed additives, as well as d 0 untreated FEED and d 0 FEED treated with both feed additives. No other treatment bioassay room had detectible RNA shed and detected in fecal swabs or cecal contents. In summary, the combination of EO and BA enhanced the degradation of PEDV RNA in feed but had little impact on RNA degradation in SDPP. Both untreated feed and feed treated with the combination of EO and BA resulted in infection at d 0 post-laboratory inoculation; however, neither set of samples was infective at d 1 postinoculation. In addition, SDPP harbored greater levels of quantifiable RNA for a longer duration of time compared to FEED, and these viral particles remained viable for a longer duration of time indicating differences in viral stability exist between different feed matrices.

Evaluation of the effects of flushing feed manufacturing equipment with chemically treated rice hulls on porcine epidemic diarrhea virus cross-contamination during feed manufacturing

Various strategies have been proposed to mitigate potential risk of porcine epidemic diarrhea virus (PEDV) transmission via feed and feed ingredients. Wet disinfection has been found to be the most effective decontamination of feed mill surfaces; however, this is not practical on a commercial feed production scale. Another potential mitigation strategy would be using chemically treated rice hulls flushed through the feed manufacturing equipment. Therefore, the objective of this study was to determine the effects of medium-chain fatty acids (MCFA) or formaldehyde-treated rice hull flush batches as potential chemical mitigation strategies for PEDV during feed manufacturing. Feed without evidence of PEDV RNA contamination was inoculated with PEDV. Based on polymerase chain reaction analysis, this feed had a cycle threshold (Ct) = 30.2 and was confirmed infective in bioassay. After manufacturing the PEDV-positive feed, untreated rice hulls, formaldehyde-treated rice hulls, 2% MCFA- (a 1:1:1 blend of hexanoic, octanoic, and decanoic acid) treated rice hulls, or 10% MCFA-treated rice hulls were flushed through laboratory scale mixers. For the untreated rice hulls, 3 of 6 samples had detectable PEDV RNA, whereas 1 of 6 formaldehyde-treated rice hull flush samples and 2 of 6 of the 2% MCFA rice hull flush samples had detectable PEDV RNA. However, PEDV RNA was not detected in any of the 10% MCFA rice hull flush samples. Then, rice hulls treated with 10% MCFA were mixed and discharged through a production scale mixer and bucket elevator following PEDV-positive feed. No rice hull flush or feed samples from the mixer following chemically treated rice hull flush had detectible PEDV RNA. However, one 10% MCFA rice hull sample collected from the bucket elevator discharge spout had detectible PEDV RNA. Dust collected following mixing of PEDV contaminated feed had detectable PEDV RNA (Ct = 29.4) and was infectious. However, dust collected immediately after the 10% MCFA rice hull flush batch had a reduced quantity of PEDV RNA (Ct = 33.7) and did not cause infection. Overall, the use of rice hull flushes effectively reduced the quantity of detectible RNA present after mixing a batch of PEDV-positive feed. Chemical treatment of rice hulls with formaldehyde or 10% MCFA provided additional reduction in detectible RNA. Finally, dust collected after manufacturing PEDV-inoculated feed has the potential to serve as a vector for PEDV transmission.

Closed-incision negative-pressure therapy decreases complications in ventral hernia repair with concurrent panniculectomy

PURPOSE

Ventral hernia repair with concurrent panniculectomy (VHR-PAN) is associated with high wound complication rates despite reported increased patient satisfaction. Some surgeons believe negative-pressure therapy after primary closure of the surgical incision (ciNPT) may lower wound complications in high-risk abdominal wounds. This study aims to evaluate if ciNPT improves outcomes in patients undergoing VHR-PAN.

METHODS

An 8-year retrospective cohort study was performed on patients who underwent VHR-PAN. Patients were divided into two groups: those who received closed-incision negative-pressure therapy ("ciNPT") and those who received standard sterile dressings ("SSD"). The primary outcome of interest was the rate of postoperative complications between these groups. Complications were subdivided into surgical site occurrences (which included surgical site occurrences that required an intervention), return to the operating room, and hernia recurrence.

RESULTS

A total of 104 patients were analyzed: 62 in the ciNPT group and 42 in the SSD group. Median follow-up duration was similar between both groups (182 days vs 195 days, p = 0.624). Patients in the ciNPT group had fewer total complications (57% vs. 83%, p = 0.004) and fewer SSO (47% vs. 69%, p = 0.025). However, no differences were noted when comparing individual complications (SSI, wound dehiscence, skin necrosis, chronic wound, seroma, and hematoma). There was no difference in return to the operating room (27% vs. 26%, p = 0.890) or hernia recurrence (21% vs 19%, p = 0.811). Multivariate analysis showed that ciNPT decreased the risk of SSOPI nearly fourfold (odds ratio 0.28, 95% CI = 0.09-0.87, p = 0.027).

CONCLUSIONS

This study showed that closed-incision negative-pressure therapy in ventral hernia repair with concurrent panniculectomy may decrease the rate of wound complications in this high-risk population.

Identification of BVDV2b and 2c subgenotypes in the United States: Genetic and antigenic characterization

Bovine viral diarrhea virus (BVDV), a ubiquitous pathogen of cattle, causes subclinical to severe acute disease. Two species of BVDV are recognized, BVDV1 and BVDV2 with BVDV1 divided into at least 21 subgenotypes and BVDV2 into 3-4 subgenotypes, most commonly using sequences from the 5' untranslated region (5' UTR). We report genomic sequencing of 8 BVDV2 isolates that did not segregate into the 2a subgenotype; but represented two additional BVDV2 subgenotypes. One BVDV2 subgenotype was previously recognized only in Asia. The other seven viruses fell into a second subgenotype that was first reported in Brazil and the U.S. in 2002. Neutralization assays using antiserum raised against vaccine strain BVDV2a 296c revealed varying degrees of neutralization of genetically diverse BVDV2 isolates. Neutralization titers decreased from 1.8 to more than a four log(2) decrease. This study illustrated the considerable genetic and antigenic diversity in BVDV2 circulating in the U.S.

Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.

[Effect of different medication time prior to corneal refractive surgery on tear film stability]

Objective: To investigate the effect of different medication time prior to corneal refractive surgery on tear film stability. Methods: Prospective cohort study. A total of 60 patients (60 eyes), including 38 males (63.3%) and 22 females (37.7%) with an average age of (24.2±5.1) years (form 18 to 37 years), who had planned for corneal refractive surgery with normal ocular surface disease index score were included in this study. The patients were divided into 1d group (medication of 1 day, 30 eyes) and 3d group (medication of 3 days, 30 eyes) randomly. The first tear break up time (FBUT), the average tear break up time (AVBUT) and the dry eye grade score were recorded on the examination day and the operation day with Keratograph 5M. The difference of FBUT and AVBUI between the two groups was compared with the independent sample t test. The difference of FBUT and AVBUT between the examination day and the operation day was compared with the paired t test. The difference of the dry eye classification between the two groups was compared using chi-square test. Results: The FBUT and AVBUT of 1d group and 3d group were (10.89±5.19)s and (10.88±6.82)s, (16.24±3.62)s and (16.21±4.74)s respectively in preoperative examination, and (10.65±6.03)s and (8.14±5.75)s, (15.14±5.30)s and (12.86±5.92)s respectively in operation day. There was no significant difference in FBUT and AVBUT between the two groups (t=0.01, 1,47, 0.02, 1.44; P>0.05). However, in the 3d group, the AVBUT of operation day decreased as compared with that of the examination day, and the difference was statistically significant (t=2.31, P<0.05). There was no significant difference in the distribution of dry eye classification between the two groups (χ(2)=0.07, 3.36; P>0.05). Conclusion: Both of medication of 1 day and medication of 3 days prior to corneal refractive surgery can provide a similar tear film stability, however more attention should be paid to the medication for patients with asymptomatic but abnormal BUT. (Chin J Ophthalmol, 2018, 54: 744-747).

Influenza C Virus in Cattle with Respiratory Disease, United States, 2016-2018

We identified influenza C virus (ICV) in samples from US cattle with bovine respiratory disease through real-time PCR testing and sequencing. Bovine ICV isolates had high nucleotide identities (≈98%) with each other and were closely related to human ICV strains (≈95%). Further research is needed to determine bovine ICV's zoonotic potential.

Self-consistent absorption correction for quantifying very noisy X-ray maps: group III nitride nanowires as an example

Energy-dispersive X-ray mapping in a scanning transmission electron microscope is a method to visualize the spatial distribution of chemical elements in a sample. Quantification of the signal intensities depends on proper background elimination and correction of the self-absorption and fluorescence of X-ray lines in the sample. The latter become particularly relevant for slightly thicker and rough samples, small take-off angles and low-energetic X-ray lines, for which we have recently introduced a self-consistent absorption correction based on effective k*-factors selected automatically from curves simulated as function of a K/L line intensity ratio of one of the heavier elements in the sample for ranges of different compositions. This has been shown to work well for thick and for rough samples. Correcting the background intensity to sub-pixel accuracy is necessary for reliable quantification of very noisy maps. In this study, we show how this self-consistent absorption correction method can be applied to InGaN and AlGaN layers in GaN nanowires, the net maps of which can be so noisy the layers can hardly be seen by the eye (a few counts per pixel) and the background is below a single count in each spectrum channel. The result indicates that background estimation for the Ga L-line intensity using fractional counts from an interpolation of maps from neighbouring X-ray lines of elements that are not actually present in the specimen is critical for quantification. The nanowires studied were between 66 and 375 nm thick.

LAY DESCRIPTION

Energy-dispersive X-ray mapping in a scanning transmission electron microscope is a method to visualize the spatial distribution of chemical elements in a sample. Quantification of the signal intensities depends on proper background elimination and correction of the self-absorption of X-ray lines in the sample. Here we show that our previously developed method of self-consistent effective absorption factors works well even with extremely noise elemental maps of a few net counts only where the human eye can hardly discern any pattern and the background signal is typically less than a single count in each spectrum channel. Correcting the background intensity to sub-pixel accuracy is then necessary for reliable quantification.

Seed targeting with tiny anti-miR-1297 inhibits EMT in melanoma cells

MicroRNAs (miRNAs) are small, noncoding RNAs that have tissue- and cell-specific expression. They have the ability to regulate the malignant proliferation and transformation of tumour cells. The research focussed on the expression and role of miR-1297 in melanoma. We firstly found that miR-1297 is up-regulated in melanoma tissues and cell lines. Functionally, phosphatase and tension homology deleted on chromsome ten gene (PTEN) was used as a potential target for miR-1297 and detected using Western blotting and immunohistochemistry (IHC). We then used chemical synthesis of anti-miR1297 to explore the influence on melanoma cells and examined the effects on A375 cell proliferation using MTT and western blotting methods. The results showed that anti-miR-1297 transfected A375 cells could inhibit the growth. Furthermore, transfection with anti-miR-1297 reduced PTEN protein expression and partially restrained A375 cells proliferation, migration and reversed Epithelial-Mesenchymal Transition (EMT) progression. In conclusion, we tentatively put forward that miR-1297 might be the key oncomiR in melanoma, and seed-targeted anti-miR-1297 might serve as a new tactic for miR-1297-based therapies.

Impact of upper respiratory tract infections on perioperative outcomes of children undergoing therapeutic cardiac catheterisation

BACKGROUND

Recent upper respiratory tract infection (URI) is associated with increased incidence of perioperative complications in children undergoing open heart surgery. As a result, surgery is often postponed. However, the effect of recent URI on the incidence of perioperative complications in children undergoing therapeutic cardiac catheterisation is unknown. We investigated the perioperative outcomes of congenital heart disease (CHD) children with recent URI who underwent elective therapeutic catheterisation.

METHODS

We prospectively included children treated for CHD. Before surgery, parents or legal guardians were interviewed to complete a questionnaire on the child's demographics, history of asthma and passive smoking, and URI symptoms. Recorded perioperative respiratory adverse events (PRAEs) included laryngospasm, bronchospasm, breath holding, oxygen desaturation, and severe cough. Information on postoperative dysphoria, fever, copious sputum, and vomiting was obtained by telephone 24 h after surgery.

RESULTS

Of 363 included children, 169 had recently (within 2 weeks) had a URI. The URI did not affect the incidence of laryngospasm, bronchospasm, breath holding, fever, or vomiting. The incidence of desaturation, severe cough, dysphoria, and copious sputum were significantly increased. Independent risk factors for PRAEs in children with a recent URI included age, passive smoking, and presence of rhinorrhoea or moist cough. The lengths of stay in the hospital and intensive care unit were not significantly different between groups.

CONCLUSION

Although recent URI increased the incidence of PRAEs in children undergoing therapeutic cardiac catheterisation, most CHD patients with recent URI can undergo elective therapeutic cardiac catheterisation without serious adverse events or prolonged hospitalisation.

Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces†

Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbE_O157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx₁ and stx₂) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbE_O157, stx₁, stx₂, and eae genes and a culture method. Detection limits of the CRISPR_O157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 10³ and 2.3 × 10⁰ CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPR_O157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPR_O157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbE_O157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.

Association between COMT SNP variation and timidity in Golden and Labrador Retrievers

Timidity in dogs is a trait with high heritability. However, the relevant genetic factors and markers associated with this condition are largely unknown. The function of the catechol-O-methyl transferase (COMT) gene has been found to be associated with human fearful or anxious emotions, and the COMT:p.Val158Met polymorphism locus is significantly related to anxious behavior. In the present study, the correlation between timidity and four single nucleotide polymorphism (SNP) variations (C.-1666C>G c.39A>G, c.216G>A, c.482G>A) of the COMT gene was investigated in dogs. The evaluation was based on the dog courage assessment assay and a genotype and haplotype analysis in Labrador Retrievers (LR) and Golden Retrievers (GR). The principal components analysis factor structure of the courage phenotype was invariant between LR and GR. Sex, breed and age had no statistically significant effect on the timidity of the dogs. All SNP loci detected were in Hardy-Weinberg equilibrium. The c.39A>G locus was removed in the subsequent association analysis due to the significant difference between LR and GR in genotype distributions. Intriguingly, the genotypes and haplotypes of the COMT gene were significantly and highly correlated with the timidity of LR and GR. The A alleles of the COMT:c.216G>A and c.482G>A loci appeared to play a dominant role in the timid behavior of the dogs. This result supports and broadens the warrior/worrier hypothesis and will have important implications for the understanding of the evolution of temperament in dogs. Additionally, the results provide predictive genetic markers for temperament in dogs.

Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes

A real-time PCR (qPCR) assay targeting on invA and pagC genes was developed and validated for the detection and quantification of Salmonella enterica strains (Bai et al., 2018) [1]. A host gene, normally an endogenous housekeeping gene (Beer-Davidson et al., 2018; Poon et al., 2004) [2,3], or an irrelevant exogenous gene (Cheng et al., 2015; Sedlak et al., 2014) [4,5] has been widely used as an internal control to monitor nucleic acid extraction efficiencies and potential PCR inhibitions in PCR-based detection assays. An endogenous internal control designed based on the 18S rRNA gene was used in the above-mentioned qPCR assay. This 18S rRNA internal control amplifies the target gene in multiple species including bovine, swine, ovine, caprine and cervine. Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has the 18S rRNA gene as internal control. Threshold cycle (Ct) data for the duplex and the triplex qPCR on the 138 samples were similar, and are presented in this brief report.