Yield of clinically reportable genetic variants in unselected cerebral palsy by whole genome sequencing.

Cerebral palsy (CP) is the most common cause of childhood physical disability, with incidence between 1/500 and 1/700 births in the developed world. Despite increasing evidence for a major contribution of genetics to CP aetiology, genetic testing is currently not performed systematically. We assessed the diagnostic rate of genome sequencing (GS) in a clinically unselected cohort of 150 singleton CP patients, with CP confirmed at >4 years of age. Clinical grade GS was performed on the proband and variants were filtered, and classified according to American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines. Variants classified as pathogenic or likely pathogenic (P/LP) were further assessed for their contribution to CP. In total, 24.7% of individuals carried a P/LP variant(s) causing or increasing risk of CP, with 4.7% resolved by copy number variant analysis and 20% carrying single nucleotide or indel variants. A further 34.7% carried one or more rare, high impact variants of uncertain significance (VUS) in variation intolerant genes. Variants were identified in a heterogeneous group of genes, including genes associated with hereditary spastic paraplegia, clotting and thrombophilic disorders, small vessel disease, and other neurodevelopmental disorders. Approximately 1/2 of individuals were classified as likely to benefit from changed clinical management as a result of genetic findings. In addition, no significant association between genetic findings and clinical factors was detectable in this cohort, suggesting that systematic sequencing of CP will be required to avoid missed diagnoses.

Targeted resequencing identifies genes with recurrent variation in cerebral palsy.

A growing body of evidence points to a considerable and heterogeneous genetic aetiology of cerebral palsy (CP). To identify recurrently variant CP genes, we designed a custom gene panel of 112 candidate genes. We tested 366 clinically unselected singleton cases with CP, including 271 cases not previously examined using next-generation sequencing technologies. Overall, 5.2% of the naïve cases (14/271) harboured a genetic variant of clinical significance in a known disease gene, with a further 4.8% of individuals (13/271) having a variant in a candidate gene classified as intolerant to variation. In the aggregate cohort of individuals from this study and our previous genomic investigations, six recurrently hit genes contributed at least 4% of disease burden to CP: COL4A1, TUBA1A, AGAP1, L1CAM, MAOB and KIF1A. Significance of Rare VAriants (SORVA) burden analysis identified four genes with a genome-wide significant burden of variants, AGAP1, ERLIN1, ZDHHC9 and PROC, of which we functionally assessed AGAP1 using a zebrafish model. Our investigations reinforce that CP is a heterogeneous neurodevelopmental disorder with known as well as novel genetic determinants.

Tracing biogeochemical subsidies from glacier runoff into Alaska's coastal marine food webs.

Nearly half of the freshwater discharge into the Gulf of Alaska originates from landscapes draining glacier runoff, but the influence of the influx of riverine organic matter on the trophodynamics of coastal marine food webs is not well understood. We quantified the ecological impact of riverine organic matter subsidies to glacier-marine habitats by developing a multi-trophic level Bayesian three-isotope mixing model. We utilized large gradients in stable (δ13 C, δ15 N, δ2 H) and radiogenic (Δ14 C) isotopes that trace riverine and marine organic matter sources as they are passed from lower to higher trophic levels in glacial-marine habitats. We also compared isotope ratios between glacial-marine and more oceanic habitats. Based on isotopic measurements of potential baseline sources, ambient water and tissues of marine consumers, estimates of the riverine organic matter source contribution to upper trophic-level species including fish and seabirds ranged from 12% to 44%. Variability in resource use among similar taxa corresponded to variation in species distribution and life histories. For example, riverine organic matter assimilation by the glacier-nesting seabirds Kittlitz's murrelet (Brachyramphus brevirostris) was greater than that of the forest-nesting marbled murrelet (B. marmoratus). The particulate and dissolved organic carbon in glacial runoff and near surface coastal waters was aged (12100-1500 years BP 14 C-age) but dissolved inorganic carbon and biota in coastal waters were young (530 years BP 14 C-age to modern). Thus terrestrial-derived subsidies in marine food webs were primarily composed of young organic matter sources released from glacier ecosystems and their surrounding watersheds. Stable isotope compositions also revealed a divergence in food web structure between glacial-marine and oceanic sites. This work demonstrates linkages between terrestrial and marine ecosystems, and facilitates a greater understanding of how climate-driven changes in freshwater runoff have the potential to alter food web dynamics within coastal marine ecosystems in Alaska.

Experimental determination of multiple thermodynamic and kinetic risk factors for nephrolithiasis in the urine of healthy controls and calcium oxalate stone formers: does a universal discriminator exist?

Nephrolithiasis is thought to be governed by urinary thermodynamic and kinetic risk factors. However, identification of one or more of these factors which consistently and unambiguously differentiates between healthy subjects (N) and calcium oxalate (CaOx) renal stone patients (SF) remains elusive. The present study addresses this challenge. 24 h urines were collected from 15 N and 10 SF. Urine compositions were used to compute thermodynamic risk indices including urinary ratios, quotients and supersaturation (SS) values, while CaOx metastable limits (MSL) were determined experimentally. Crystallisation kinetics was determined by measuring rates of particle formation (number, volume, size) using a Coulter counter multisizer (CC) and a Coulter flow cytometer (FC). Particle shapes were qualitatively differentiated by FC and were viewed directly by scanning electron microscopy. Several urinary composition ratios and risk quotients were significantly different between the groups. However, there were no significant differences between CaOx MSL or SS values. Using transformed FC data, the rate of CaOx crystallisation in SF was significantly greater than in N. This was not supported by CC measurements. There were no significant differences between the groups with respect to particle size or CaOx crystal growth rates. Single and aggregated CaOx dihydrate crystals were observed in both groups with equal frequency and there were no differences in the kinetic properties of these deposits. A few CaOx monohydrate crystals were observed in SF. Although several risk factors were found to be significantly different between the groups, none of them were consistently robust when compared to other cognate factors. Arguments were readily invoked which demonstrated inter-factor inconsistencies and conflicts. We suspect that a unique discriminatory factor, such as any of those which we investigated in the present study, may not exist.

Efficient derivation of NPCs, spinal motor neurons and midbrain dopaminergic neurons from hESCs at 3% oxygen.

This protocol has been designed to generate neural precursor cells (NPCs) from human embryonic stem cells (hESCs) using a physiological oxygen (O(2)) level of 3% (previously termed hypoxia) and chemically defined conditions. The first stage involves suspension culture of hESC colonies at 3% O(2), where they acquire a neuroepithelial identity over a period of 2 weeks. This timescale is comparable to that observed at 20% O(2), but survival is enhanced. Sequential application of retinoic acid and purmorphamine (PM), from day 14 to day 28, directs differentiation toward spinal motor neurons. Alternatively, addition of fibroblast growth factor-8 and PM generates midbrain dopaminergic neurons. OLIG2 (encoding oligodendrocyte lineage transcription factor 2) induction in motor neuron precursors is twofold greater than that at 20% O(2), whereas EN1 (encoding engrailed homeobox 1) expression is enhanced fivefold. NPCs (at 3% O(2)) can be differentiated into all three neural lineages, and such cultures can be maintained long term in the absence of neurotrophins. The ability to generate defined cell types at 3% O(2) should represent a significant advancement for in vitro disease modeling and potentially for cell-based therapies.

Measurement of the positive muon lifetime and determination of the Fermi constant to part-per-million precision.

We report a measurement of the positive muon lifetime to a precision of 1.0 ppm; it is the most precise particle lifetime ever measured. The experiment used a time-structured, low-energy muon beam and a segmented plastic scintillator array to record more than 2×10(12) decays. Two different stopping target configurations were employed in independent data-taking periods. The combined results give τ(µ(+)) (MuLan)=2 196 980.3(2.2) ps, more than 15 times as precise as any previous experiment. The muon lifetime gives the most precise value for the Fermi constant: G(F) (MuLan)=1.166 378 8(7)×10(-5) GeV(-2) (0.6 ppm). It is also used to extract the µ(-)p singlet capture rate, which determines the proton's weak induced pseudoscalar coupling g(P).

Derivation of neural precursor cells from human ES cells at 3% O(2) is efficient, enhances survival and presents no barrier to regional specification and functional differentiation.

In vitro stem cell systems traditionally employ oxygen levels that are far removed from the in vivo situation. This study investigates whether an ambient environment containing a physiological oxygen level of 3% (normoxia) enables the generation of neural precursor cells (NPCs) from human embryonic stem cells (hESCs) and whether the resultant NPCs can undergo regional specification and functional maturation. We report robust and efficient neural conversion at 3% O(2), demonstration of tri-lineage potential of resultant NPCs and the subsequent electrophysiological maturation of neurons. We also show that NPCs derived under 3% O(2) can be differentiated long term in the absence of neurotrophins and can be readily specified into both spinal motor neurons and midbrain dopaminergic neurons. Finally, modelling the oxygen stress that occurs during transplantation, we demonstrate that in vitro transfer of NPCs from a 20 to 3% O(2) environment results in significant cell death, while maintenance in 3% O(2) is protective. Together these findings support 3% O(2) as a physiologically relevant system to study stem cell-derived neuronal differentiation and function as well as to model neuronal injury.

Calciuria, oxaluria and phosphaturia after ingestion of glucose, xylitol and sorbitol in two population groups with different stone-risk profiles.

The effects of glucose, sorbitol and xylitol ingestion on calciuria, oxaluria and phosphaturia in healthy black and white males on a standardized diet were investigated. After ingestion, they collected urine hourly for 3 h. Glucose decreased phosphaturia in blacks. Sorbitol decreased phosphaturia in both groups and increased oxaluria in whites. Xylitol increased oxaluria in blacks. Decreases in phosphaturia are attributed to penetration by phosphate into cells leading to decreases in phosphatemia and the renal filtered load. We suggest that this mechanism is more sensitive in blacks. We speculate that the increase in oxaluria after sorbitol ingestion occurs via its conversion to glyoxylate and that this pathway may be blocked in blacks. For the increase in oxaluria after xylitol ingestion, it is hypothesized that ketohexokinase and aldolase may be more active in blacks. Our results demonstrate, for the first time, a urinary effect due to sorbitol ingestion and an ethnic dependency of these and other effects.

Effects of direct transplantation of multipotent mesenchymal stromal/stem cells into the demyelinated spinal cord.

The adult bone marrow contains a population of multipotent mesenchymal stromal cells (MSCs), defined by plastic adherence, expression of stromal cell surface markers, and differentiation into mesenchymal lineages. There has been much interest in the possible therapeutic use of MSCs in the treatment of demyelinating diseases of the central nervous system. One therapeutic possibility is that these cells may be able to remyelinate when directly injected into the demyelinated spinal cord. Here we examine the effects of direct transplantation of green fluorescent protein (GFP)-labeled MSCs into a model of focal spinal cord demyelination induced by ethidium bromide. We demonstrate that direct intralesional injection of undifferentiated MSCs does not lead to remyelination. Furthermore, we report that transplanted MSCs migrate into areas of normal tissue, deposit collagen, and are associated with axonal damage. These findings support the need for further experimental evaluation of the safety and efficacy of direct parenchymal injection of MSCs into demyelinated lesions and highlight an important issue regarding potential clinical consequences of culture heterogeneity of MSCs between centers.

Schwann cell precursors transplanted into the injured spinal cord multiply, integrate and are permissive for axon growth.

There is a strong current interest in the use of cell transplantation for the treatment of spinal cord injuries. We report here the novel and potentially useful properties of an early cell in the Schwann cell lineage, the Schwann cell precursor (SCP). The experiments reveal a striking difference between these cells and Schwann cells when transplanted into the CNS. Unlike Schwann cells, SCPs thrive in the CNS where they initially proliferate rapidly but then fall out of division, thus effectively filling up the large cystic cavities formed following crush injury, while avoiding tumor formation. By 8 weeks, SCPs had started to express S100beta protein, a marker that differentiates Schwann cells from SCPs and had formed an apparently stable, vascularized cell mass, which created a continuous cellular bridge across the cystic cavities. The formation of the surrounding glial scar was reduced by local spread of the transplanted cells into the surrounding CNS tissue, where the cells integrated intimately with astrocytes and attenuated the physical barrier they normally form. SCP transplantation also altered and reduced the expression of chondroitin sulfate proteoglycans around the injury site. Caudal to the SCP transplants there was a large increase in the number of axons, compared with that seen in nontransplanted control tissue, showing that the implants effectively support axonal growth or sprouting. SCPs have advantageous attributes for CNS repair, despite the fact that sticky tape removal and ladder crossing tests at 8 weeks did not reveal significant functional improvements when compared with control animals.

Improved measurement of the positive-muon lifetime and determination of the Fermi constant.

The mean life of the positive muon has been measured to a precision of 11 ppm using a low-energy, pulsed muon beam stopped in a ferromagnetic target, which was surrounded by a scintillator detector array. The result, tau(micro)=2.197 013(24) micros, is in excellent agreement with the previous world average. The new world average tau(micro)=2.197 019(21) micros determines the Fermi constant G(F)=1.166 371(6)x10(-5) GeV-2 (5 ppm). Additionally, the precision measurement of the positive-muon lifetime is needed to determine the nucleon pseudoscalar coupling g(P).

Cilomilast (Ariflo) does not potentiate the cardiovascular effects of inhaled salbutamol.

We investigated the safety and potential pharmacodynamic interactions arising from the co-administration of inhaled beta(2)-agonist salbutamol and cilomilast (Ariflo), a new oral phosphodiesterase 4 inhibitor for the treatment of chronic obstructive pulmonary disease and asthma. This was a randomised, double-blind, placebo-controlled, multiple-dose, three-period crossover study involving non-smoking volunteers between the ages of 18 and 50 years. Volunteers were randomly assigned to receive cilomilast plus nebulised salbutamol, cilomilast plus nebulised placebo or placebo plus nebulised salbutamol. Each volunteer received cilomilast (10 mg twice daily) or placebo for 5 days. On day 5, the morning dose of cilomilast or placebo was followed 1 h later with a single dose of nebulised salbutamol (2.5 mg) or placebo. Primary variables were average change from pre- to 1.5 h post-salbutamol or placebo inhalation in blood pressure, pulse rate, 12-lead ECG and total number of heartbeats measured by 4-h Holter ECG. Thirteen volunteers completed the study. There was no evidence of a clinically important pharmacodynamic interaction between cilomilast and salbutamol in healthy volunteers. Both agents were well tolerated. In conclusion, the pharmacodynamic effects associated with salbutamol inhalation were unaffected by co-administration of cilomilast.

Beyond U(crit): matching swimming performance tests to the physiological ecology of the animal, including a new fish 'drag strip'.

Locomotor performance of animals is of considerable interest from management, physiological, ecological and evolutionary perspectives. Yet, despite the extensive commercial exploitation of fishes and interest in the health of various fish stocks, the relationships between performance capacity, natural selection, ecology and physiology are poorly known for fishes. One reason may be the technical challenges faced when trying to measure various locomotor capacities in aquatic species, but we will argue that the slow pace of developing new species-appropriate swim tests is also hindering progress. A technique developed for anadromous salmonids (the U(crit) procedure) has dominated the fish exercise physiology field and, while accounting for major advances in the field, has often been used arbitrarily. Here we propose criteria swimming tests should adhere to and report on several attempts to match swimming tests to the physiological ecology of the animal. Sprint performance measured with a laser diode/photocell timed 'drag strip' is a new method employing new technology and is reported on in some detail. A second new test involves accelerating water past the fish at a constant rate in a traditional swim tunnel/respirometer. These two performance tests were designed to better understand the biology of a bentho-pelagic marine fish, the Atlantic cod (Gadus morhua). Finally, we report on a modified incremental velocity test that was developed to better understand the biology of the blacknose dace (Rhinichthys atratulus), a Nearctic, lotic cyprinid.

Once a fast cod, always a fast cod: maintenance of performance hierarchies despite changing food availability in cod (Gadus morhua).

To examine whether Atlantic cod maintain constant hierarchies of sprint speeds and muscle metabolic capacities under different feeding regimes, the physiological capacities of individual cod were followed through a starvation-feeding-starvation cycle. We examined sprint speeds and maximal enzyme activities in white-muscle biopsies at each period. We measured the glycolytic enzymes, phosphofructokinase (PFK) and lactate dehydrogenase (LDH), the mitochondrial enzyme, cytochrome C oxidase (CCO), and the biosynthetic enzyme, nucleotide diphosphate kinase (NDPK). Sprint speeds were measured in a laser diode/photocell-timed raceway. As expected, the feeding regime had a marked impact on the physiological capacities of cod, but the responses differed for sprint-swimming and muscle metabolic capacities. The different enzyme activities as well the condition index generally decreased during the first starvation, improved with feeding, and fell again during the second starvation. In contrast, sprint performance improved after feeding but did not fall with the second starvation. Although both the enzyme activities and the sprint speeds showed considerable interindividual variation, sprint speeds were not significantly correlated with the enzyme activities. The hierarchy of sprint performance of the cod was maintained, regardless of the preceding feeding regime, whereas those of muscle metabolic capacities were not.

Caudal differential pressure as a predictor of swimming speed of cod (Gadus morhua).

We report the results of an experiment designed to investigate the feasibility of using differential pressure to estimate the swimming speed and metabolic rate of Atlantic cod (Gadus morhua). Seven cod were fitted with a miniature differential pressure sensor mounted on one side of the caudal peduncle immediately anterior to the base of the caudal fin rays. Relationships between differential pressure, tailbeat frequency, tailbeat amplitude, swimming speed and rate of oxygen consumption ((O(2))) were determined as a function of the swimming speed of cod swimming at 5 degrees C in a recirculating 'Brett-style' respirometer. Tailbeat differential pressure, tailbeat amplitude and tailbeat frequency were highly correlated with swimming speed. The average or integrated pressure ranged from 0 to 150 Pa for speeds up to 0.8 m s(-1) (1.1 L s(-1), where L is total body length), while the 'pressure difference' (maximum minus minimum pressure) ranged from 0 to 900 Pa. Small changes in swimming speed of less than 0.05 m s(-1) were readily detected as differences in tailbeat pressure. Burst swimming in the respirometer resulted in huge pressure 'bursts' of up to 5000 Pa 'pressure difference'. The rate of oxygen consumption increased exponentially and was highly correlated with swimming speed (r(2)=0.77). The rate of oxygen consumption was also correlated with tailbeat integrated pressure (r(2)=0.68) and with differential pressure (r(2)=0.43); regression correlations were always greater for individuals than for combined data from all cod. The results detailed in this study indicate that an ultrasonic differential pressure transmitter would enable accurate estimates of the swimming speed, rates of oxygen consumption and activity patterns of free-ranging fish in nature.

Perspectives on stimulating industrial research and development for neglected infectious diseases.

This paper summarizes recent thinking on stimulating industrial research and development (R&D) for neglected infectious diseases and argues that it is critical to enlarge the value of the market for medicines and vaccines through, for example, global purchase funds. The most important economic barriers to R&D are that the commercial markets are small and that individual purchasing power is severely limited, even though the number of patients may be very large. Since R&D costs for all diseases are high, this means that returns will not cover investments. Various mechanisms have been proposed to address this economic imbalance (accepting that other barriers will also need to be considered). Economic devices which reduce the costs of R&D--push factors--are useful, but our review suggests that high costs do not explain the shortfall in R&D. Economic devices which address the lack of viable markets have been termed pull factors and are designed to create or secure a market, thereby improving the likelihood of a return on investments. One pull mechanism is the commitment in advance to purchase a product that meets specified criteria, if invented. The purchase-precommitment approach has a number of attractive features. For example, it only rewards successful outputs rather than supporting research that may not succeed. Pull programmes effectively mimic the market and lead companies to favour lines of attack that they believe will lead to marketable products. Overall, a combination of push and pull mechanisms is likely to represent an attractive approach. This could combine, for example, increased funding for public laboratories, public-private partnerships in R&D, purchases of underutilized existing products, and a precommitment to purchase new drugs and vaccines when developed.

An overview of the pharmacokinetics of cilomilast (Ariflo), a new, orally active phosphodiesterase 4 inhibitor, in healthy young and elderly volunteers.

The oral pharmacokinetics of cilomilast (Ariflo) were investigated in five separate studies in healthy volunteers. Cilomilast was rapidly absorbed, and pharmacokinetics were dose proportional after single and repeat dosing. The elimination half-life was 7 to 8 hours; accordingly, steady state was reached on the 3rd day of dosing. The degree of accumulation following repeat twice-daily dosing was predictable from the data following a single dose. Although systemic exposure (AUC) was, on average, 21% higher in elderly (65-84 years) compared with young subjects, values for Cmax and t(1/2) were similar, and no difference in tolerability was noted. Single and repeat doses of cilomilast up to and including 15 mg (dosed before or taken between meals) were well tolerated. Dosing with food reduced the rate of absorption without affecting total bioavailability. Hence, tolerability was optimal in the fed state; repeat doses up to and including 30 mg twice daily aftermeals were well tolerated following dose titration.

Enhancing recall of information from a patient education booklet: a trial using cardiomyopathy patients.

A quasi-experimental trial was conducted to compare the effect on information recall of: (a) the use of adjunct questions (AQ) in printed materials; and (b) a procedure (the 5Rs) for integrating printed patient education materials into face-to-face teaching. A total of 51 patients with severe left ventricular failure (cardiomyopathy) was assigned to one of three groups (n=17). Each group worked with a purpose-prepared booklet, the first in association with the 5Rs procedure; the second group with a version of the booklet containing adjunct questions; and the third with a text only version of the booklet. Recall of information from the booklet was measured using a checklist scored on the basis of responses secured in a standardised interview. Improved recall was associated with both the adjunct questions and the 5Rs procedure, with the latter achieving a substantially superior outcome. The practical implications of these findings are presented and directions for further research indicated.

Bioavailability of the oral selective phosphodiesterase 4 inhibitor cilomilast.

STUDY OBJECTIVE: To determine the absolute bioavailability of cilomilast, and assess the effects of food, dosing time, and coadministration of antacid agents on its bioavailability and pharmacokinetics in healthy volunteers. SETTING: Clinical pharmacology unit. DESIGN: Five prospective pharmacokinetic studies: one single-blind, dose-escalating, placebo-controlled trial; four open-label, randomized studies. SUBJECTS: Ninety-six healthy adult volunteers who were nonsmokers. INTERVENTION: In the first study, four subjects received intravenous cilomilast 1, 2, and 4 mg. In the second study, 16 subjects received oral cilomilast 15 mg or intravenous cilomilast 4 mg. In the other three studies, a total of 76 subjects were given single oral 15-mg doses; one study compared its effects in fed versus fasted subjects, one looked for differences of morning versus evening dosing, and one examined coadministration with aluminum hydroxide-magnesium hydroxide. MEASUREMENTS AND MAIN RESULTS: After intravenous administration of cilomilast, plasma concentrations increased in an approximately dose-proportional manner; the half-life, approximately 6.5 hours, was dose independent. Cilomilast clearance and volume of distribution were small. After oral dosing, the absolute bioavailability was consistently close to 100%. Absorption was slower in fed subjects than in fasted (median 2-hr delay in time to reach maximum plasma concentration, average 39% reduction in maximum plasma concentration), but the area under the concentration-time curve from time zero to infinity (systemic availability) was unaffected. Pharmacokinetic parameters were not influenced by time of dosing or coadministration of antacid. CONCLUSION: The absolute bioavailability of oral cilomilast was 100%; it was not adversely affected by time of dosing or coadministration with food or antacid.

Surgical confirmation of ProstaScint abnormalities in two patients with high risk prostate cancer.

We describe our initial experience using ProstaScint scanning in addition to conventional imaging modalities for staging of high risk prostate cancer. Using our protocol, ProstaScint images detected abnormalities in pelvic lymph nodes not seen on CT scan or magnetic resonance imaging (MRI) in two patients. Subsequent surgical pelvic lymphadenectomy confirmed these abnormalities. Further patients will be accrued on this study to estimate the sensitivity and specificity of ProstaScint scanning.