Performance comparison: exome sequencing as a single test replacing Sanger sequencing

Next generation sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome sequencing as a single test replacing Sanger sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-sequencing results of 258 genes to those obtained from next generation sequencing (NGS) using two exome-sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different sequencing methods and DNA sources). Sanger sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger sequencing and 97-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger sequencing or NGS.

Towards Neutron Capture on Exotic Nuclei: Demonstrating (d,pγ) as a Surrogate Reaction for (n,γ)

The neutron-capture reaction plays a critical role in the synthesis of the elements in stars and is important for societal applications including nuclear power generation and stockpile-stewardship science. However, it is difficult-if not impossible-to directly measure neutron capture cross sections for the exotic, short-lived nuclei that participate in these processes. In this Letter we demonstrate a new technique which can be used to indirectly determine neutron-capture cross sections for exotic systems. This technique makes use of the (d,p) transfer reaction, which has long been used as a tool to study the structure of nuclei. Recent advances in reaction theory, together with data collected using this reaction, enable the determination of neutron-capture cross sections for short-lived nuclei. A benchmark study of the ^{95}Mo(d,p) reaction is presented, which illustrates the approach and provides guidance for future applications of the method with short-lived isotopes produced at rare isotope accelerators.

Fission fragment yields and total kinetic energy release in neutron-induced fission of235,238U,and239Pu

Different aspects of the nuclear fission process have been studied at Los Alamos Neutron Science Center (LANSCE) using various instruments and experimental techniques. Properties of the fragments emitted in fission have been investigated using Frisch-grid ionization chambers, a Time Projection Chamber (TPC), and the SPIDER instrument which employs the 2v-2E method. These instruments and experimental techniques have been used to determine fission product mass yields, the energy dependent total kinetic energy (TKE) release, and anisotropy in neutron-induced fission of U-235, U-238 and Pu-239.

Evidence for Gamow-Teller Decay of ^{78}Ni Core from Beta-Delayed Neutron Emission Studies

The β-delayed neutron emission of ^{83,84}Ga isotopes was studied using the neutron time-of-flight technique. The measured neutron energy spectra showed emission from states at excitation energies high above the neutron separation energy and previously not observed in the β decay of midmass nuclei. The large decay strength deduced from the observed intense neutron emission is a signature of Gamow-Teller transformation. This observation was interpreted as evidence for allowed β decay to ^{78}Ni core-excited states in ^{83,84}Ge favored by shell effects. We developed shell model calculations in the proton fpg_{9/2} and neutron extended fpg_{9/2}+d_{5/2} valence space using realistic interactions that were used to understand measured β-decay lifetimes. We conclude that enhanced, concentrated β-decay strength for neutron-unbound states may be common for very neutron-rich nuclei. This leads to intense β-delayed high-energy neutron and strong multineutron emission probabilities that in turn affect astrophysical nucleosynthesis models.

A MultiCenter Pilot Randomized Controlled Trial of Remote Ischemic Preconditioning in Major Vascular Surgery

A pilot randomized controlled trial that evaluated the effect of remote ischemic preconditioning (RIPC) on clinical outcomes following major vascular surgery was performed. Eligible patients were those scheduled to undergo open abdominal aortic aneurysm repair, endovascular aortic aneurysm repair, carotid endarterectomy, and lower limb revascularization procedures. Patients were randomized to RIPC or to control groups. The primary outcome was a composite clinical end point comprising any of cardiovascular death, myocardial infarction, new-onset arrhythmia, cardiac arrest, congestive cardiac failure, cerebrovascular accident, renal failure requiring renal replacement therapy, mesenteric ischemia, and urgent cardiac revascularization. Secondary outcomes were components of the primary outcome and myocardial injury as assessed by serum troponin values. The primary outcome occurred in 19 (19.2%) of 99 controls and 14 (14.1%) of 99 RIPC group patients ( P = .446). There were no significant differences in secondary outcomes. Our trial generated data that will guide future trials. Further trials are urgently needed.

Double-magic nature of 132Sn and 208Pb through lifetime and cross-section measurements

Single-neutron states in (133)Sn and (209)Pb, which are analogous to single-electron states outside of closed atomic shells in alkali metals, were populated by the ((9)Be, (8)Be) one-neutron transfer reaction in inverse kinematics using particle-γ coincidence spectroscopy. In addition, the s(1/2) single-neutron hole-state candidate in (131)Sn was populated by ((9)Be, (10)Be). Doubly closed-shell (132)Sn (radioactive) and (208)Pb (stable) beams were used at sub-Coulomb barrier energies of 3 MeV per nucleon. Level energies, γ-ray transitions, absolute cross sections, spectroscopic factors, asymptotic normalization coefficients, and excited-state lifetimes are reported and compared with shell-model expectations. The results include a new transition and precise level energy for the 3p(1/2) candidate in (133)Sn, new absolute cross sections for the 1h(9/2) candidate in (133)Sn and 3s(1/2) candidate in (131)Sn, and new lifetimes for excited states in (133)Sn and (209)Pb. This is the first report on excited-state lifetimes of (133)Sn, which allow for a unique test of the nuclear shell model and (132)Sn double-shell closure.

Correlations in intermediate energy two-proton removal reactions

We report final-state-exclusive measurements of the light charged fragments in coincidence with (26)Ne residual nuclei following the direct two-proton removal from a neutron-rich (28)Mg secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple-coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially correlated pair-removal mechanism. The fraction of such correlated events, 56(12)%, is consistent with the fraction of the calculated cross section, 64%, arising from spin S=0 two-proton configurations in the entrance-channel (shell-model) (28)Mg ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams.

Setting core standards: privacy, identity & interoperability

This position paper focuses on strategic developments and underlying concepts emerging out of the standards and associated domains. It addresses the issue of personal privacy in the wider context of interoperability across an ever-growing range of e-health and social care support systems and processes. These will increasingly be driven by major growth in the elderly segment of national populations where unambiguous identification of both patients and care staff both in hospitals and the community will become significant issues. This is particularly so where remote patient monitoring and access control to personal data is concerned, and is further complicated where racial, cultural and linguistic barriers are prevalent.

Management of spontaneous rupture of the oesophagus (Boerhaave’s syndrome): Single centre experience of 18 cases

BACKGROUND

Spontaneous oesophageal rupture (Boerhaave's syndrome) is rare, and carries a high attendant risk of mortality.

METHODS

A retrospective eight-year review from a tertiary unit.

RESULTS

Eighteen patients were managed, with a mean age of 57 (39 - 88 years). Eight patients presented early and underwent surgery, seven with primary closure and one with exclusion and diversion. There was one death in this group. Ten patients were managed conservatively. In this group, two underwent an oesophagectomy because of failed conservative measures, and four had an endoprosthesis inserted. One patient died in this group on the first admission, but two patients with stents in situ died from massive bleeding relating to an aorto-oesophageal fistula at 39 days and 189 days respectively following presentation.

CONCLUSIONS

Surgical intervention remains the gold standard when the diagnosis is made early. For late diagnoses, this series suggests caution in the use of endoprostheses.

Assistive technology--behaviourally assisted

In considering the recurrent problems involved in technology led initiatives within the public sector, this paper seeks to identify change management requirements needed to help avoid these latent pitfalls in the widespread introduction of Assistive Technology. It develops a change process approach based on current clinical psychology techniques used in assessing sources and level of resistance to behavioural change and applies them to managing effective benefits realisation.

The Influence of Subintimal Angioplasty on Level of Amputation and Limb Salvage Rates in Lower Limb Critical Ischaemia: A 15-year Experience

OBJECTIVES

The aim of this study is to assess the influence of subintimal angioplasty (SIA) on lower limb amputation rate and level in critically ischaemic limbs.

METHODS

Between January 1989 and March 2004, 1268 patients were admitted for treatment of lower limb critical ischaemia. Eight hundred and twenty-nine patients underwent revascularisation (bypass 671 and angioplasty 158), while 439 patients had primary amputations. A retrospective analysis of a prospectively maintained vascular registry was performed. Patients were divided into two groups, those who were admitted prior to the availability of subintimal angioplasty and those treated post-introduction of angioplasty. The two groups were compared with regards to age, sex, diabetes mellitus, ASA grade, Rutherford classification and level of disease. Outcome was assessed by the limb salvage rate, 30-day morbidity and mortality, and length of hospital stay.

RESULTS

The average number of revascularisation increased with the introduction of subintimal angioplasty, from 53 to 96 per year (p<0.001). The overall limb salvage rate increased significantly from 42 to 70% (p<0.001). The cumulative limb salvage rate following revascularisation rose from 72 to 86% (p<0.001). The level of amputation (AKA:BKA) did not vary significantly. Thirty-day morbidity, mortality and length of hospital stay were significantly lower in the post-angioplasty group.

CONCLUSIONS

Technical advances have resulted in a steadying of amputation numbers despite an ageing population.

Introducing handheld computing into a residency program: preliminary results from qualitative and quantitative inquiry

Although published reports describe specific handheld computer applications in medical training, we know very little yet about how, and how well, handheld computing fits into the spectrum of information resources available for patient care and physician training. This paper reports preliminary quantitative and qualitative results from an evaluation study designed to track changes in computer usage patterns and computer-related attitudes before and after introduction of handheld computing. Pre-implementation differences between residents and faculty s usage patterns are interpreted in terms of a "work role" construct. We hypothesize that over time residents and faculty will adopt, adapt, or abandon handheld computing according to how, and how well, this technology supports their successful completion of work role-related tasks. This hypothesis will be tested in the second phase of this pre- and post-implementation study.

The use of regenerable, affinity ligand-based surfaces for immunosensor applications

The regeneration of antibody-binding surfaces is of major importance for re-usable sensor formats such as required for direct 'real-time' biosensing technologies and is often difficult to achieve. Antibodies commonly bind the antigen with high avidity and may themselves be sensitive to regeneration conditions. The interaction of polyclonal anti-chlorpyriphos antibody with an immobilised chlorpyriphos-ovalbumin (chlor-oval) conjugate and the interaction of soluble recombinant CD4 with covalently immobilised anti-CD4 IgG are presented in order to highlight these difficulties. Affinity-capture is suggested as an alternative format as it facilitates surface regeneration, directed immobilisation and the attainment of interaction progress curves that conform to the ideal pseudo-first-order kinetic interaction model. Protein A, protein G and polyclonal anti-mouse Fe-coated surfaces were used to observe the interaction of captured anti-GST monoclonal antibody with glutathione-s-transferase (GST). It was shown that a protein A affinity-capture surface produced ideal interaction progress curves while both protein G and polyclonal anti-mouse Fe resulted in systemic deviations.

Time of onset of non-insulin-dependent diabetes mellitus and genetic variation in the beta 3-adrenergic-receptor gene

BACKGROUND

The beta 3-adrenergic receptor is expressed in visceral adipose tissue and is thought to contribute to the regulation of the resting metabolic rate and lipolysis.

METHODS

To investigate whether mutations in the gene for the beta 3-adrenergic receptor predispose patients to obesity and non-insulin-dependent diabetes mellitus (NIDDM), we studied this gene in 10 Pima Indians by analysis of single-stranded conformational polymorphisms and dideoxy sequence analysis. Association studies were performed in 642 Pima subjects (390 with NIDDM and 252 without NIDDM).

RESULTS

A missense mutation was identified in the gene for the beta 3-adrenergic receptor that results in the replacement of tryptophan by arginine (Trp64Arg) in the first intracellular loop of the receptor. This mutation was detected with allelic frequencies of 0.31 in Pima Indians, 0.13 in 62 Mexican Americans, 0.12 in 49 blacks, and 0.08 in 48 whites in the United States. Among Pimas, the frequency of the Trp64Arg mutation was similar in nondiabetic and diabetic subjects. However, in subjects homozygous for the mutation the mean (+/- SD) age at the onset of NIDDM was significantly lower (36 +/- 10 years) than in Trp64Arg heterozygotes (40 +/- 10 years) or normal homozygotes (41 +/- 11 years; P = 0.02). Furthermore, subjects with the mutation tended to have a lower adjusted resting metabolic rate (P = 0.14 by analysis of covariance).

CONCLUSIONS

Pima subjects homozygous for the Trp64Arg beta 3-adrenergic-receptor mutation have an earlier onset of NIDDM and tend to have a lower resting metabolic rate. This mutation may accelerate the onset of NIDDM by altering the balance of energy metabolism in visceral adipose tissue.

Immunosensors in medical diagnostics--major hurdles to commercial success

In the last few years the format of commercial immunoassays has dramatically changed. Automated instruments running up to 180 samples per hour and dry strip or film immunochemistry products are now available. These changes have been precipitated by the need for immunoassays that require less time and skill to perform. To date, no immunosensor technology has been successfully commercialized although a few are purported to be on the brink of being released for sale. Here, B. Manning and T. Maley evaluate the major factors affecting the success of immunosensors.

Comparative neuromuscular blocking actions of levamisole and pyrantel-type anthelmintics on rat and gastrointestinal nematode somatic muscle

The basis for the comparative toxicity to parasitic nematodes and their mammalian hosts of the anthelmintics levamisole, pyrantel, and several related analogs on somatic nicotinic cholinergic transmission was examined. Measurements of muscle contractility and membrane potential were made using the isolated hemidiaphragm preparation of the rat and isolated axial muscle segments from the gastrointestinal nematode Haemonchus contortus. Pyrantel caused a dose- and time-dependent reduction of nerve-evoked twitches in the rat diaphragm. These effects were exacerbated by increasing the frequency of phrenic nerve stimulation from 0.5 to 50 Hz. Levamisole was less potent and the onset of its effects slower than pyrantel. Neither drug significantly affected twitches evoked from d-tubocurarine-blocked preparations following direct stimulation of the diaphragm. Twitch depression was reversed by washing, but not by application of physostigmine. In H. contortus, both drugs stimulated a spastic contraction and sustained paralysis in the concentration range of 1-10 microM, mimicking the action of nicotine. Neither nicotinic nor muscarinic antagonists blocked these responses. Moreover, neither nicotinic antagonists nor muscarinic agonists or antagonists had any independent effect on contractility of the parasite muscle segments. The blocking actions of levamisole and pyrantel on H. contortus axial muscle were associated with membrane depolarization at the muscle. In the rat-isolated hemidiaphragm, pyrantel, but not levamisole, depolarized end-plate regions of muscle fibers. d-Tubocurarine blocked the depolarizing action of pyrantel but not levamisole on rat-isolated hemidiaphragm. In axial muscle fibers of H. contortus, d-tubocurarine did not block the depolarizing actions of pyrantel, levamisole, or nicotine. 3-Bromo and 3-amino derivatives of levamisole were equipotent with and mimicked the actions of the parent compound on H. contortus axial muscle contractility. In the rat preparation, the 3-bromo derivative was more potent than levamisole or 3-amino-levamisole. 3-Amino-levamisole, but not 3-bromo-levamisole, depolarized muscle end-plate membrane in the rat diaphragm. Results of the present study are consistent with the following conclusions: (a) both levamisole and pyrantel block contractility of nematode axial muscle by causing sustained depolarization of the muscle membrane; (b) both drugs block neuromuscular transmission at the mammalian neuromuscular junction but their mechanisms appear to differ; (c) levamisole and pyrantel are more potent blockers of neuromuscular transmission in H. contortus than in the rat. These results suggest that potentially important pharmacological differences exist between nematode and mammalian somatic nicotinic receptors.

Syphilis in pregnant black women

Serological tests for syphilis (with rapid plasma reagin) were performed in 2 767 women attending the antenatal clinic of King Edward VIII Hospital, Durban, for their first, booking visit. The test was repeated at the 36th week of pregnancy. A total of 152 women (5,5%) were assumed to have syphilis. In addition, 4 (11,8%) of 34 patients who were seronegative at less than 32 weeks of pregnancy had a positive serological test result at 36 weeks.

Lysine needs of rapidly growing turkeys from 12-22 weeks of age

Two experiments were conducted with Large White male turkeys to investigate the lysine requirement from 12 to 22 weeks of age. Six pens of 20 turkeys were fed each of the experimental diets. In experiment 1, a basal diet containing wheat, meat meal, cottonseed meal and distillers dried grains with solubles was supplemented with four levels of L-lysine. Lysine at 4.27% of protein and 2.31 g./mcal. of metabolizable energy from 16 to 20 weeks of age, and 1.83 g. from 20 to 22 weeks of age was inadequate for optimum growth and feed efficiency (16-22 weeks). Supplementing the diet with lysine from soybean meal gave performance equivalent to synthetic lysine, indicating that it was fully available. Performance of turkeys fed a diet containing 88% triticale from 16 to 20 weeks of age, and 72% from 20 to 22 weeks of age was equivalent to that of turkeys fed a more complex ration with an equivalent level of lysine. In experiment 2, Large White male turkeys were fed a basal diet composed largely of triticale and soybean meal from 12 to 20 weeks of age with different levels of added lysine. From 12 to 16 weeks of age, 3.11 g. lysine/mcal. of M.E. (4.9% of protein) was adequate for optimum growth and feed efficiency. From 16-20 weeks of age 2.36 g. lysine/mcal. of M.E. (4.3% of protein) was adequate for optimum performance. Although the estimated requirement from 16 to 20 weeks of age based on the two experiments differs (perhaps because of differences in lysine availability), the results suggest that the current N.R.C. recommendation may be higher than necessary.

Chemotherapy, BCG, and serum from tumor-bearing mice: comparative effects on growth and spread of mouse Lewis lung cancer

In 101 mice, Lewis lung tumor (25 mg apiece) was implanted subcutaneously in the right hind limb and the mice separated into various groups and protocols to test treatment with immunotherapeutic and chemotherapeutic agents. In those treated intralesionally with BCG, the growth of primary tumor was retarded (P smaller than or equal to .05). Tumor growth in animals treated with systemic BCG and serum from tumor-bearing mice was not different from controls. In 14 of 20 mice treated with chemotherapy (semustine and cyclophosphamide), there was no primary or metastatic growth (P smaller than or equal to .01). The observations show that this sort of systemic immunotherapy had no effect on mouse Lewis lung tumor, that intralesionally there was a retarding effect of BCG (although it did not influence metastases), and that this protocol of chemotherapy was strikingly effective.