Adverse event recording post hip fracture surgery

Accurate recording of adverse events post hip fracture surgery is vital for planning and allocating resources. The purpose of this study was to compare adverse events recorded prospectively at point of care with adverse recorded by the Hospital In-Patient Enquiry (HIPE) System. The study examined a two month period from August to September 2011 at University Hospital Limerick. Out of a sample size of 39, there were 7 males (17.9%) and 32 females (82.1%) with an age range of between 53 and 98 years. The mean age was 80.5 years. 55 adverse events were recorded, in contrast to the HIPE record of 13 (23.6%) adverse events. The most common complications included constipation 10 (18.2%), anaemia 8 (14.5%), urinary retention 8 (14.50%), pneumonia 5 (9.1%) and delirium 5 (9.1%). Of the female cohort, 24 (68.8%) suffered an adverse event, while only 4 (57%) males suffered an adverse event.

X-ray image enhancement via determinant based feature selection

Previous work has investigated the feasibility of using Eigenimage-based enhancement tools to highlight abnormalities on chest X-rays (Butler et al in J Med Imaging Radiat Oncol 52:244-253, 2008). While promising, this approach has been limited by computational restrictions of standard clinical workstations, and uncertainty regarding what constitutes an adequate sample size. This paper suggests an alternative mathematical model to the above referenced singular value decomposition method, which can significantly reduce both the required sample size and the time needed to perform analysis. Using this approach images can be efficiently separated into normal and abnormal parts, with the potential for rapid highlighting of pathology.

Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma

Chondrosarcoma is a heterogeneous collection of malignant bone tumors and is the second most common primary malignancy of bone after osteosarcoma. Recent work has identified frequent, recurrent mutations in IDH1 or IDH2 in nearly half of central chondrosarcomas. However, there has been little systematic genomic analysis of this tumor type, and, thus, the contribution of other genes is unclear. Here we report comprehensive genomic analyses of 49 individuals with chondrosarcoma (cases). We identified hypermutability of the major cartilage collagen gene COL2A1, with insertions, deletions and rearrangements identified in 37% of cases. The patterns of mutation were consistent with selection for variants likely to impair normal collagen biosynthesis. In addition, we identified mutations in IDH1 or IDH2 (59%), TP53 (20%), the RB1 pathway (33%) and Hedgehog signaling (18%).

Study Site Experiences and Attitudes Toward Prospective Assessments of Suicidal Ideation and Behavior in Clinical Trials: Results of an Internet-based Survey

OBJECTIVE

The International Society for CNS Clinical Trials and Methodology Suicidal Ideation and Behavior Assessment Working Group conducted an online survey regarding clinical trial site experiences and attitudes toward suicidal ideation and behavior data collection following the 2010 release of the initial United States Food and Drug Administration draft guidance on prospective assessment of suicidal ideation and behavior in clinical trials. Sites that had participated in at least one central nervous system clinical trial in the prior two years (N=6,058) were invited, via email, to complete a 20-item online assessment survey.

RESULTS

Nine hundred and seventy-nine evaluable responses were collected (42% United States). Respondents included principal investigators (36%), raters (28%), coordinators (25%), and others (10%). The majority were psychiatrists (43%) and reported using suicidal ideation and behavior assessments across many indications. Most respondents (80%) personally conducted suicidal ideation and behavior assessments. Overall, respondents indicated that suicidal ideation and behavior assessments were readily incorporated into the conduct of clinical trials and improved subject safety. The greatest challenge was obtaining an accurate baseline lifetime history (51%), while the greatest benefit was identifying subjects at risk of suicide (84%). Approximately a quarter of respondents reported implementation challenges such as training. Differences based on geographical region, respondents' roles, and responsibility for assessments were observed. Open-ended responses revealed additional challenges, e.g., use in cognitively impaired populations.

CONCLUSION

Prospective suicidal ideation and behavior monitoring was generally viewed positively, though specific challenges were identified. Limitations include self-report survey methodology and recruitment of only central nervous system clinical trials sites. These findings may help guide development of better methodologies for suicidal ideation and behavior assessment in clinical trials.

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.

Identifying environmental drivers of insect phenology across space and time: Culicoides in Scotland as a case study

Interpreting spatial patterns in the abundance of species over time is a fundamental cornerstone of ecological research. For many species, this type of analysis is hampered by datasets that contain a large proportion of zeros, and data that are overdispersed and spatially autocorrelated. This is particularly true for insects, for which abundance data can fluctuate from zero to many thousands in the space of weeks. Increasingly, an understanding of the ways in which environmental variation drives spatial and temporal patterns in the distribution, abundance and phenology of insects is required for management of pests and vector-borne diseases. In this study, we combine the use of smoothing techniques and generalised linear mixed models to relate environmental drivers to key phenological patterns of two species of biting midges, Culicoides pulicaris and C. impunctatus, of which C. pulicaris has been implicated in transmission of bluetongue in Europe. In so doing, we demonstrate analytical tools for linking the phenology of species with key environmental drivers, despite using a relatively small dataset containing overdispersed and zero-inflated data. We demonstrate the importance of landcover and climatic variables in determining the seasonal abundance of these two vector species, and highlight the need for more empirical data on the effects of temperature and precipitation on the life history traits of palearctic Culicoides spp. in Europe.

Artificial neural network processing of stripping analysis responses for identifying and quantifying heavy metals in the presence of intermetallic compound formation

Feed-forward neural networks have been trained to identify and quantify heavy metals in mixtures under conditions where there were significant complications due to intermetallic compound formation. The networks were shown to be capable of (i) correlating voltammetric responses with individual heavy metals in complex mixtures, (ii) determining the relationship between responses and concentrations (including nonlinear relationships due to overlapping peaks and intermetallic compound formation), and (iii) rapidly determining concentrations of individual components from mixtures once trained. Using simulated data, modeled after complex interactions experimentally observed in samples containing Cu and Zn, it has been demonstrated that networks containing two layers of neurons (a nonlinear hidden layer and a linear output layer) can be trained to calculate concentrations under a variety of complicated situations. These include, but are not limited to, cases where the response of the intermetallic compound formed is observed as a shoulder of one of the pure metals and cases where the response of the intermetallic compound formed is not observed in the potential window. In addition, the network described above was trained to simultaneously determine concentrations of four metals (Cu, Pb, Cd, and Zn) in a concentration range where all responses were complicated by intermetallic compound formation (1-500 ppb).

Preformed donor HLA-DP-specific antibodies mediate acute and chronic antibody-mediated rejection following renal transplantation

Donor-specific HLA alloantibodies may cause acute and chronic antibody-mediated rejection (AMR) and significantly compromise allograft survival. The clinical relevance of antibodies directed against some HLA class II antigens, particularly HLA-DP, is less clear with conflicting reports on their pathogenicity. We report two patients with high levels of pretransplant donor-specific HLA-DP antibodies who subsequently developed recurrent acute AMR and graft failure. In both cases, there were no other donor-specific HLA alloantibodies, suggesting that the HLA-DP-specific antibodies may be directly pathogenic.

Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes

The application of paired-end next generation sequencing approaches has made it possible to systematically characterize rearrangements of the cancer genome to base-pair level. Utilizing this approach, we report the first detailed analysis of ovarian cancer rearrangements, comparing high-grade serous and clear cell cancers, and these histotypes with other solid cancers. Somatic rearrangements were systematically characterized in eight high-grade serous and five clear cell ovarian cancer genomes and we report here the identification of > 600 somatic rearrangements. Recurrent rearrangements of the transcriptional regulator gene, TSHZ3, were found in three of eight serous cases. Comparison to breast, pancreatic and prostate cancer genomes revealed that a subset of ovarian cancers share a marked tandem duplication phenotype with triple-negative breast cancers. The tandem duplication phenotype was not linked to BRCA1/2 mutation, suggesting that other common mechanisms or carcinogenic exposures are operative. High-grade serous cancers arising in women with germline BRCA1 or BRCA2 mutation showed a high frequency of small chromosomal deletions. These findings indicate that BRCA1/2 germline mutation may contribute to widespread structural change and that other undefined mechanism(s), which are potentially shared with triple-negative breast cancer, promote tandem chromosomal duplications that sculpt the ovarian cancer genome.

Broadly reactive polymerase chain reaction for pathogen detection in canine granulomatous meningoencephalomyelitis and necrotizing meningoencephalitis

Background

Granulomatous meningoencephalomyelitis (GME) and necrotizing meningoencephalitis (NME) are common inflammatory conditions of the central nervous system of dogs. Infectious pathogens, particularly viruses, are suspected to contribute to the etiopathogenesis of GME and NME.

Hypothesis

Broadly reactive PCR might aid in the identification of infectious agents in GME and NME.

Animals

Sixty‐eight client‐owned dogs evaluated by necropsy at 1 university referral hospital.

Methods

A mixed prospective/retrospective case‐control study was performed. Brain tissue prospectively collected at necropsy from GME, NME, and control cases was evaluated by broadly reactive polymerase chain reaction (PCR) for adenoviruses, bunyaviruses, coronaviruses, enteroviruses, flaviviruses, herpesviruses, paramyxoviruses, and parechoviruses. In addition, these tissues were retrospectively evaluated for the presence of mycoplasmas by PCR, culture, and immunohistochemistry (IHC).

Results

Brain tissue was collected from 11 GME and 27 NME cases and 30 controls. Viral nucleic acids were not identified in the 6 GME cases, 25 NME cases, and 2 controls evaluated by viral PCR. Mycoplasma canis was identified by Mycoplasma genus PCR in 1/5 GME and 4/25 NME cases and subsequently was cultured from 4/5 GME and 4/8 NME cases as well as 2/9 controls. The IHC did not detect M. canis in any of the 11 GME and 27 NME cases or 14 controls evaluated with strain PG14 polyclonal antiserum.

Conclusions and Clinical Importance

The negative results suggest that viral pathogens are not common in the brain tissue of dogs with GME and NME. Further investigation is warranted to determine the importance of M. canis in cases of GME and NME.

The landscape of cancer genes and mutational processes in breast cancer

All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.

Systematic identification of genomic markers of drug sensitivity in cancer cells

Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers for responses to targeted agents. Here, to uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we screened a panel of several hundred cancer cell lines--which represent much of the tissue-type and genetic diversity of human cancers--with 130 drugs under clinical and preclinical investigation. In aggregate, we found that mutated cancer genes were associated with cellular response to most currently available cancer drugs. Classic oncogene addiction paradigms were modified by additional tissue-specific or expression biomarkers, and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. Unexpected relationships were revealed, including the marked sensitivity of Ewing's sarcoma cells harbouring the EWS (also known as EWSR1)-FLI1 gene translocation to poly(ADP-ribose) polymerase (PARP) inhibitors. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing

BACKGROUND

Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.

METHODS

To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression.

RESULTS

Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors.

CONCLUSIONS

Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.).

SIMS(DAIRY): a modelling framework to identify sustainable dairy farms in the UK. Framework description and test for organic systems and N fertiliser optimisation

Multiple demands are placed on farming systems today. Society, national legislation and market forces seek what could be seen as conflicting outcomes from our agricultural systems, e.g. food quality, affordable prices, a healthy environmental, consideration of animal welfare, biodiversity etc., Many of these demands, or desirable outcomes, are interrelated, so reaching one goal may often compromise another and, importantly, pose a risk to the economic viability of the farm. SIMS(DAIRY), a farm-scale model, was used to explore this complexity for dairy farm systems. SIMS(DAIRY) integrates existing approaches to simulate the effect of interactions between farm management, climate and soil characteristics on losses of nitrogen, phosphorus and carbon. The effects on farm profitability and attributes of biodiversity, milk quality, soil quality and animal welfare are also included. SIMS(DAIRY) can also be used to optimise fertiliser N. In this paper we discuss some limitations and strengths of using SIMS(DAIRY) compared to other modelling approaches and propose some potential improvements. Using the model we evaluated the sustainability of organic dairy systems compared with conventional dairy farms under non-optimised and optimised fertiliser N use. Model outputs showed for example, that organic dairy systems based on grass-clover swards and maize silage resulted in much smaller total GHG emissions per l of milk and slightly smaller losses of NO(3) leaching and NO(x) emissions per l of milk compared with the grassland/maize-based conventional systems. These differences were essentially because the conventional systems rely on indirect energy use for 'fixing' N compared with biological N fixation for the organic systems. SIMS(DAIRY) runs also showed some other potential benefits from the organic systems compared with conventional systems in terms of financial performance and soil quality and biodiversity scores. Optimisation of fertiliser N timings and rates showed a considerable scope to reduce the (GHG emissions per l milk too).

Old herbal remedies and modern combination therapy

The use of herbs as cures for human ailments is as old as modern man, but has now been replaced by synthetic drugs. However, the mixture of bioactive substances found in many traditional herbal remedies has similarities with modern combination therapies, like those developed by Sir John Crofton in Edinburgh for the treatment of tuberculosis. It is suggested that, in the development of these therapies, it might be possible to learn from the drug ‘cocktails’ found in plants.

Effect of ampicillin on bleeding time in very low birth-weight neonates during the first week after birth

OBJECTIVE

On the day of birth, the bleeding time of very low birth-weight (VLBW, <1500 g) neonates is generally prolonged, compared with term neonates. However, their bleeding time generally improves (shortens) over the next 7 to 10 days. Ampicillin can prolong the bleeding times of term and late preterm neonates, but its effect on VLBW neonates, who already have a somewhat prolonged bleeding time initially, is not known.

STUDY DESIGN

This was a prospective, single-centered, paired, before vs after test of the effect of ampicillin on template bleeding time and PFA-100 time (platelet function analyzer). Ampicillin was dosed at every 12 h intravenously, but decisions about discontinuation were made by the responsible clinician, independent of this study.

RESULT

A total of 20 VLBW neonates were studied. They ranged from 23- to 30-weeks gestation at birth and weighed 500 t 1410 g. Initial bleeding times averaged 166 s (95% CI, 138 to 194) and initial PFA-100 times averaged 119 s (95% CI, 90 to 148). In all, 10 had ampicillin dosing stopped after a shorter course (4 to 7 doses) and 10 had it continued for a longer course (10 to 15 doses). Blood cultures were sterile in all 20, and no differences in laboratory or clinical features were found between those treated with a shorter vs longer course. After stopping the ampicillin following a short course the bleeding times and PFA-100 times were similar to the initial values. However, after a longer course the bleeding times were prolonged by an average of 2 min, to 284 s (95% CI, 242 to 326; P=0.001 vs initial). The PFA-100 times also trended longer by an average of 44 s (P=0.07). The number of doses of ampicillin received in the first week correlated with the degree of prolongation in bleeding time (r=0.68).

CONCLUSION

Over the first week of life, a period when the bleeding time of VLBW neonates normally shortens, the opposite occurred (the bleeding time lengthened) if ≥ 10 doses of ampicillin were administered.

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ~3500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (KDM6A)1, JARID1C (KDM5C) and SETD22. These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control3. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodeling complex gene PBRM14 as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.