Intragenic CFTR Duplication and 5T/12TG Variant in a Patient with Non-Classic Cystic Fibrosis

Cystic fibrosis (CF) is an autosomal recessive disorder characterized by the accumulation of sticky and heavy mucus that can damage several organs. CF shows variable expressivity in affected individuals, but it typically causes respiratory and digestive complications as well as congenital bilateral absence of the vas deferens in males. Individuals with classic CF usually have variants that produce a defective protein from both alleles of the CFTR gene. Individuals with other variants may present with classic, non-classic, or milder forms of CF due to lower levels of functional CFTR protein. This article reports the genetic analysis of a female with features of asthma and mild or non-classic CF. CFTR sequencing demonstrated that she is a carrier for a maternally derived 5T/12TG variant. Deletion/duplication analysis by multiplex ligation-dependent probe amplification (MLPA) showed the presence of an intragenic paternally derived duplication involving exons 7-11 of the CFTR gene. This duplication is predicted to result in the production of a truncated CFTR protein lacking the terminal part of the nucleotide-binding domain 1 (NBD1) and thus is likely to be a non-functioning allele. The combination of this large intragenic duplication and 5T/12TG is the probable cause of the mild or non-classic CF features in this individual.

Individual personality differences in Port Jackson sharks Heterodontus portusjacksoni

This study examined interindividual personality differences between Port Jackson sharks Heterodontus portusjacksoni utilizing a standard boldness assay. Additionally, the correlation between differences in individual boldness and stress reactivity was examined, exploring indications of individual coping styles. Heterodontus portusjacksoni demonstrated highly repeatable individual differences in boldness and stress reactivity. Individual boldness scores were highly repeatable across four trials such that individuals that were the fastest to emerge in the first trial were also the fastest to emerge in subsequent trials. Additionally, individuals that were the most reactive to a handling stressor in the first trial were also the most reactive in a second trial. The strong link between boldness and stress response commonly found in teleosts was also evident in this study, providing evidence of proactive-reactive coping styles in H. portusjacksoni. These results demonstrate the presence of individual personality differences in sharks for the first time. Understanding how personality influences variation in elasmobranch behaviour such as prey choice, habitat use and activity levels is critical to better managing these top predators which play important ecological roles in marine ecosystems.

US college and university student health screening requirements for tuberculosis and vaccine-preventable diseases, 2012

OBJECTIVE

Colleges are at risk for communicable disease outbreaks because of the high degree of person-to-person interactions and relatively crowded dormitory settings. This report describes the US college student health screening requirements among US resident and international students for tuberculosis (TB) and vaccine-preventable diseases (VPDs) as they relate to the American College Health Association (ACHA) guidelines. Methods/Participants: In April 2012, US college health administrators (N = 2,858) were sent online surveys to assess their respective school's TB screening and immunization requirements.

RESULTS

Surveys were completed by 308 (11%) schools. Most schools were aware of the ACHA immunization (78%) and TB screening (76%) guidelines. Schools reported having policies related to immunization screening (80.4%), immunization compliance (93%), TB screening (55%), and TB compliance (87%).

CONCLUSION

Most colleges were following ACHA guidelines. However, there are opportunities for improvement to fully utilize the recommendations and prevent outbreaks of communicable diseases among students in colleges.

Surrogate markers of long-term outcome in primary total hip arthroplasty: A systematic review

Objectives

High failure rates of metal-on-metal hip arthroplasty implants have highlighted the need for more careful introduction and monitoring of new implants and for the evaluation of the safety of medical devices. The National Joint Registry and other regulatory services are unable to detect failing implants at an early enough stage. We aimed to identify validated surrogate markers of long-term outcome in patients undergoing primary total hip arthroplasty (THA).

Methods

We conducted a systematic review of studies evaluating surrogate markers for predicting long-term outcome in primary THA. Long-term outcome was defined as revision rate of an implant at ten years according to National Institute of Health and Care Excellence guidelines. We conducted a search of Medline and Embase (OVID) databases. Separate search strategies were devised for the Cochrane database and Google Scholar. Each search was performed to include articles from the date of their inception to June 8, 2015.

Results

Our search strategy identified 1082 studies of which 115 studies were included for full article review. Following review, 17 articles were found that investigated surrogate markers of long-term outcome. These included one systematic review, one randomised control trial (RCT), one case control study and 13 case series. Validated surrogate markers included Radiostereometric Analysis (RSA) and Einzel-Bild-Röntgen-Analyse (EBRA), each measuring implant migration and wear. We identified five RSA studies (one systematic review and four case series) and four EBRA studies (one RCT and three case series). Patient Reported Outcome Measures (PROMs) at six months have been investigated but have not been validated against long-term outcomes.

Conclusions

This systematic review identified two validated surrogate markers of long-term primary THA outcome: RSA and EBRA, each measuring implant migration and wear. We recommend the consideration of RSA in the pre-market testing of new implants. EBRA can be used to investigate acetabular wear but not femoral migration. Further studies are needed to validate the use of PROMs for post-market surveillance.

Cite this article: T. T. Malak, J. A. J. Broomfield, A. J. R. Palmer, S. Hopewell, A. Carr, C. Brown, D. Prieto-Alhambra, S. Glyn-Jones. Surrogate markers of long-term outcome in primary total hip arthroplasty: A systematic review. Bone Joint Res 2016;5:206–214. DOI: 10.1302/2046-3758.56.2000568.

Lessons learned from implementing Clostridium difficile-focused antibiotic stewardship interventions

OBJECTIVE

To determine whether controlling the prescription of targeted antibiotics would translate to a measurable reduction in hospital-onset Clostridium difficile infection (CDI) rates.

DESIGN

A multicenter before-and-after intervention comparative study.

SETTING/PARTICIPANTS

Ten medical centers in the greater New York region. Intervention group comprised of 6 facilities with early antimicrobial stewardship programs (ASPs). The 4 facilities without ASPs made up the nonintervention group.

INTERVENTIONS/METHODS

Intervention facilities identified target antibiotics using case-control studies and implemented ASP-based strategies to control their use. Pre- and postintervention hospital-onset CDI rates and antibiotic consumption were compared for a 20-month period from June 2010 to January 2012. Antibiotic usage was compared using defined daily dose, days of therapy, and number of courses prescribed. Comparisons used bivariate and regression techniques.

RESULTS

Intervention facilities identified piperacillin/tazobactam, fluoroquinolones, or cefepime (odds ratio, 2.0-9.8 in CDI case patients compared with those without CDI) as intervention targets and selected several interventions (all included a component of audit and feedback). Varying degrees of success were observed in reducing antibiotic consumption over time. Total target antibiotic use significantly decreased (P < .05) when measured by days of therapy and number of courses but not by defined daily dose. Intravenous moxifloxacin and oral ciprofloxacin use showed significant reduction when measured by defined daily dose and days of therapy (P ≤ .01). Number of courses with all forms of these antibiotics was reduced (P < .005). Intervention hospitals reported fewer hospital-onset CDI cases (2.8 rate point difference) compared with nonintervention hospitals; however, we were unable to show statistically significant decreases in aggregate hospital-onset CDI either between intervention and nonintervention groups or within the intervention group over time.

CONCLUSIONS

Although decreases in target antibiotic consumption did not translate into reductions of hospital-onset CDI in this study, many valuable lessons (including implementation strategies and antibiotic consumption measures) were learned. The findings can inform potential policy decisions regarding incorporating control of CDI and ASP as healthcare quality measures.

Evidence of an association between brain cellular injury and cognitive decline after non-cardiac surgery

BACKGROUND

Postoperative cognitive dysfunction (POCD) is common after non-cardiac surgery, but the mechanism is unclear. We hypothesized that decrements in cognition 1 month after non-cardiac surgery would be associated with evidence of brain injury detected by elevation of plasma concentrations of S100β, neuron-specific enolase (NSE), and/or the brain-specific protein glial fibrillary acid protein (GFAP).

METHODS

One hundred and forty-nine patients undergoing shoulder surgery underwent neuropsychological testing before and then 1 month after surgery. Plasma was collected before and after anaesthesia. We determined the relationship between plasma biomarker concentrations and individual neuropsychological test results and a composite cognitive functioning score (mean Z-score).

RESULTS

POCD (≥-1.5 sd decrement in Z-score from baseline) was present in 10.1% of patients 1 month after surgery. There was a negative relationship between higher plasma GFAP concentrations and lower postoperative composite Z-scores {estimated slope=-0.14 [95% confidence interval (CI) -0.24 to -0.04], P=0.005} and change from baseline in postoperative scores on the Rey Complex Figure Test copy trial (P=0.021), delayed recall trial (P=0.010), and the Symbol Digit Modalities Test (P=0.004) after adjustment for age, sex, history of hypertension and diabetes. A similar relationship was not observed with S100β or NSE concentrations.

CONCLUSIONS

Decline in cognition 1 month after shoulder surgery is associated with brain cellular injury as demonstrated by elevated plasma GFAP concentrations.

Effects of simulated neural mobilization on fluid movement in cadaveric peripheral nerve sections: implications for the treatment of neuropathic pain and dysfunction

BACKGROUND AND PURPOSE

Neural mobilization techniques are used clinically to treat neuropathic pain and dysfunction. While selected studies report efficacy of these techniques, the mechanisms of benefit are speculative. The purpose of this study was to evaluate the effects of in vitro simulated stretch/relax neural mobilization cycles on fluid dispersion within sections of unembalmed cadaveric peripheral nerve tissue.

METHODS

Bilateral sciatic nerve sections were harvested from six cadavers. Matched pairs of nerve sections were secured in a tissue tester and injected with a plasma/Toluidine Blue dye solution. Once the initial dye spread stabilized, the experimental nerve sections underwent 25 stretch/relaxation cycles (e.g. simulated neural mobilization) produced by a mechanical tissue tester. Post-test dye spread measurements were compared to pre-test measurements as well as control findings (no simulated mobilization). Data were analyzed using paired t-tests.

RESULTS

Individual dye spread measurements were reliable [ICC(3,1) = 0·99]. The post-test intraneural fluid movement (dye spread) in the experimental section increased significantly with simulated neural mobilization compared to pre-test measurements (3·2±2·1 mm; P = 0·015) and control measurements (3·3±2·7 mm; P = 0·013).

CONCLUSION

Repetitive simulated neural mobilization, incorporating stretch/relax cycles, of excised cadaveric peripheral nerve tissue produced an increase in intraneural fluid dispersion. Neural mobilization may alter nerve tissue environment, promoting improved function and nerve health, by dispersing tissue fluid and diminishing intraneural swelling and/or pressure.

Abstract P6-07-11: On the origin of T&gt;C transition mutations in breast cancer

Background: Mutations in cancer driver genes are thought to occur early in tumorigenesis. Examination of the sequence context enables the inference of causality. For example, C&gt;A transversions in lung malignancies are ascribed to tobacco smoke. A large proportion of clonal and subclonal mutations in breast cancer are attributed to the APOBEC cytidine deaminases. However, 26% of clonal mutations in cancer genes in the breast and 15% of subclonal mutations are T&gt;C transitions [Sci Transl Med. 2015;7:283ra54]. The purpose of this study was to determine if the T&gt;C transitions are likely an early event in breast carcinogenesis and look for clues to the mechanism by which they are produced.

Methods: Histologically normal tissue adjacent to a cancer provides a window into the early steps of oncogenesis. BAM files of exome sequencing data from 11 matched trios of tumor, adjacent normal tissue and blood (leukocyte DNA) from the TCGA (The Cancer Genome Atlas) breast cancer dataset were downloaded from the UCSC cgHUB repository. Mutations were called using the MuTect software (Broad Institute, Cambridge, MA). As a validation cohort, data was downloaded from 29 additional specimens that had been added to TCGA subsequent to the initial data set, and analyzed as above.

RNA-Seq data from the initial adjacent normal was downloaded from the TCGA data portal. The epithelia from 20 frozen tissue cores from healthy premenopausal donors to the Susan G. Komen Tissue Bank were microdissected and the RNA isolated. RNA-sequencing was carried out using the Life Technologies SOLiD Platform. RPKM gene expression values from TCGA and sequencing of the Komen normal tissues were merged, quantile normalized, and batch effect corrected. Normalization and differential gene expression was performed using Partek Genomics Suite.

Results: C&gt;T and T&gt;C transition mutations make up the majority of the mutations in histologically normal tissue adjacent to breast cancer. Displaying mutations in their trinucleotide context, i.e., by the sequence context immediately 5' and 3' to the mutated base revealed that T&gt;C mutations most frequently occur in the 5'-ATG-3', 5'-CTG-3' and 5'-ATA-3' contexts. Analysis of the RNA-Seq data discovered 1821 genes to be differentially expressed (FDR&lt;5%). Relevant to the questions being addressed in this study, the expression of Nitric Oxide Synthase 3, an enzyme that synthesizes nitric oxide from L-arginine, is 4-times greater in adjacent normal (p= 4.55E-03). [Of note, published data reveals no significant contamination of adjacent normal with tumor in the TCGA breast data.]

Conclusions: NOS3 expression is enhanced in certain inflammatory environments as well as by estrogen. Nitric oxide induces DNA damage; one mechanism is through the N2O3 pathway. Reaction of DNA with N2O3 leads to the deamination adenine to form hypoxanthine. Thymine-DNA glycosylase (TDG) initiates base excision repair (BER). Talhaoui et al [Nucleic Acids Res. 2014;42:6300-13] have recently shown that TDG excises T when it is paired with hypoxanthine. Downstream in this aberrant BER pathway the abasic site is repaired to a C resulting in the T&gt;C transition. The excision of the T is efficient only in a specific nucleotide context, which is 5'-TpG-3', as was observed in our study.

Citation Format: Choi M, Radovich M, Brown C, Clare SE. On the origin of T&gt;C transition mutations in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-11.

Gross, histological and ultrastructural morphology of the aglomerular kidney in the lined seahorse Hippocampus erectus

Histologic evaluation of the renal system in the lined seahorse Hippocampus erectus reveals a cranial kidney with low to moderate cellularity, composed of a central dorsal aorta, endothelial lined capillary sinusoids, haematopoietic tissue, fine fibrovascular stroma, ganglia and no nephrons. In comparison, the caudal kidney is moderately to highly cellular with numerous highly convoluted epithelial lined tubules separated by interlacing haematopoietic tissue, no glomeruli, fine fibrovascular stroma, numerous capillary sinusoids, corpuscles of Stannius and clusters of endocrine cells adjacent to large calibre vessels. Ultrastructural evaluation of the renal tubules reveals minimal variability of the tubule epithelium throughout the length of the nephron and the majority of tubules are characterized by epithelial cells with few apical microvilli, elaborate basal membrane infolding, rare electron dense granules and abundant supporting collagenous matrix.

Engineering enhanced vaccine cell lines to eradicate vaccine preventable diseases: the polio endgame (VAC9P.1107)

Advances in genomic screening and gene editing technologies provide a means to create the next generation of vaccine manufacturing cell lines. A genome-wide RNAi screen was used to identify gene knock-down events that enhance poliovirus replication with the aim of increasing vaccine yield and reducing the costs and time associated with vaccine production. Primary screen hits were validated with several attenuated and wild poliovirus strains in a Vero cell line employed in vaccine production. Multiple genes were identified that upon silencing increased titers &gt;20-fold, and in some instances, knockdown of a gene or gene combination increased virus titers by &gt;50-fold. Importantly, stable knockout of top candidates from the screen and validation studies using CRISPR technology provided equivalent or improved viral production of multiple serotypes. Several of these gene knockdowns also enhanced titer of enterovirus 71, a clinically relevant virus for which vaccines are being targeted. Host gene silencing events that facilitate poliovirus replication mapped to several cell pathways, and in all cases, gene silencing did not affect poliovirus antigenicity. This study suggests that modulating host genes to increase vaccine production can significantly enhance vaccine production at reduced costs, a finding that should greatly facilitate global implementation of inactivated poliovirus vaccine for polio eradication, and change the paradigm in mammalian vaccine cell line production.

Microhabitat use affects goby (Gobiidae) cue choice in spatial learning task

This study investigated whether spatial learning ability and cue use of gobies (Gobiidae) from two contrasting habitats differed in a spatial task. Gobies were collected from the spatially complex rock pools and dynamic, homogenous sandy shores. Fishes were trained to locate a shelter under the simulated threat of predation and it was determined whether they used local or extra-maze (global) and geometric cues to do so. It was hypothesized that fishes from rock pools would outperform fishes from sandy shores in their ability to relocate shelter and the two groups would differ in their cue use. It was found that rock-pool species learnt the location of the correct shelter much faster, made fewer errors and used a combination of all available cues to locate the shelter, while sand species relied significantly more on extra-maze and geometric cues for orientation. The results reported here support the hypothesis that fishes living in complex habitats have enhanced capacity for spatial learning and are more likely to rely on local landmarks as directional cues than fishes living in mundane habitats where local cues such as visual landmarks are unreliable.

The 6-min Walk Test Reflects Functional Capacity in Primary Care and Obese Patients

The main purpose of this study was to determine the association between the 6-min walk test distance (6MWTD) and physical functional capacity (PF) in primary care patients, as well as in obese individuals. We studied 351 subjects (age=56.8±14.6 years; BMI=29.4±5.7 kg/m(2); 68% women), including 141 obese subjects (BMI≥30 kg/m(2)), recruited in 10 different family practices. Physical (PCS) and mental component summary of the health-related quality of life (HRQOL) and the 8 sub-scores were measured using the Short Form-36 Health Survey. Anthropometry, vital signs and physical testing were measured according to standardized protocols. Recreational physical activity (LPA) and sedentary levels were determined using the Canadian Community Health Survey. In a stepwise multivariate analysis, 65% of the 6MWTD variance was explained by PF of the HRQOL, age, quadriceps strength, number of chronic diseases, LPA categories, BMI, resting heart rate, PCS, height and TV-viewing categories in primary care subjects. In the obese individuals, PF, age, quadriceps strength and BMI explained 57% of the 6MWTD variance. In these 2 groups, 44% of the 6MWTD variance is explained by PF only. To conclude, the 6MWTD is strongly associated with PF of the HRQOL. Thus, it adequately reflects physical limitations in daily life activities of primary care patients, including obese individuals.

Clinical outcomes associated with high, intermediate, and low rates of failed extubation in an intensive care unit

PURPOSE

Extubation failure is associated with adverse outcomes in mechanically ventilated patients, and it is believed that high rates of failed planned extubation (FPE) should be avoided. However, many believe that very low rates may also correlate with adverse outcomes if resulting from overly conservative weaning practices. We examined the relationship between the percentage of FPE (%FPE) and associated outcomes, with the aim of elucidating a favorable middle range.

METHODS

A total of 1395 extubations were analyzed in mechanically ventilated subjects. Monthly %FPE values were separated into tertiles. Ventilator-free days (VFDs), intensive care unit-free days (IFDs), and mortality were compared among tertiles.

RESULTS

Monthly %FPE tertiles were as follows: low, less than 7%; intermediate, 7% to 15%; and high, greater than 15%. There were significant differences in VFDs and IFDs by tertile from low to high (VFDs: low, 11.8; intermediate, 12.1; high, 9.9 [P = .003]; IFDs: low, 10.5; intermediate, 10.7; high, 9.0 [P = .033]). Post hoc comparisons demonstrated significant differences between the middle and high tertiles for both VFDs and IFDs.

CONCLUSIONS

Although exact rates may vary depending on setting, this suggests that a high %FPE (>15) should be avoided in the intensive care unit and that there may be an intermediate range where ventilator outcomes are optimized.

Start of the 2014/15 influenza season in Europe: drifted influenza A(H3N2) viruses circulate as dominant subtype

The influenza season 2014/15 started in Europe in week 50 2014 with influenza A(H3N2) viruses predominating. The majority of the A(H3N2) viruses characterised antigenically and/or genetically differ from the northern hemisphere vaccine component which may result in reduced vaccine effectiveness for the season. We therefore anticipate that this season may be more severe than the 2013/14 season. Treating influenza with antivirals in addition to prevention with vaccination will be important.

Mapping the landscape of climate engineering

In the absence of a governance framework for climate engineering technologies such as solar radiation management (SRM), the practices of scientific research and intellectual property acquisition can de facto shape the development of the field. It is therefore important to make visible emerging patterns of research and patenting, which we suggest can effectively be done using bibliometric methods. We explore the challenges in defining the boundary of climate engineering, and set out the research strategy taken in this study. A dataset of 825 scientific publications on climate engineering between 1971 and 2013 was identified, including 193 on SRM; these are analysed in terms of trends, institutions, authors and funders. For our patent dataset, we identified 143 first filings directly or indirectly related to climate engineering technologies-of which 28 were related to SRM technologies-linked to 910 family members. We analyse the main patterns discerned in patent trends, applicants and inventors. We compare our own findings with those of an earlier bibliometric study of climate engineering, and show how our method is consistent with the need for transparency and repeatability, and the need to adjust the method as the field develops. We conclude that bibliometric monitoring techniques can play an important role in the anticipatory governance of climate engineering.