Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction

OBJECTIVE

To develop soft prompt-based learning architecture for large language models (LLMs), examine prompt-tuning using frozen/unfrozen LLMs, and assess their abilities in transfer learning and few-shot learning.

METHODS

We developed a soft prompt-based learning architecture and compared 4 strategies including (1) fine-tuning without prompts; (2) hard-prompting with unfrozen LLMs; (3) soft-prompting with unfrozen LLMs; and (4) soft-prompting with frozen LLMs. We evaluated GatorTron, a clinical LLM with up to 8.9 billion parameters, and compared GatorTron with 4 existing transformer models for clinical concept and relation extraction on 2 benchmark datasets for adverse drug events and social determinants of health (SDoH). We evaluated the few-shot learning ability and generalizability for cross-institution applications.

RESULTS AND CONCLUSION

When LLMs are unfrozen, GatorTron-3.9B with soft prompting achieves the best strict F1-scores of 0.9118 and 0.8604 for concept extraction, outperforming the traditional fine-tuning and hard prompt-based models by 0.6 ∼ 3.1 % and 1.2 ∼ 2.9 %, respectively; GatorTron-345 M with soft prompting achieves the best F1-scores of 0.8332 and 0.7488 for end-to-end relation extraction, outperforming other two models by 0.2 ∼ 2 % and 0.6 ∼ 11.7 %, respectively. When LLMs are frozen, small LLMs have a big gap to be competitive with unfrozen models; scaling LLMs up to billions of parameters makes frozen LLMs competitive with unfrozen models. Soft prompting with a frozen GatorTron-8.9B model achieved the best performance for cross-institution evaluation. We demonstrate that (1) machines can learn soft prompts better than hard prompts composed by human, (2) frozen LLMs have good few-shot learning ability and generalizability for cross-institution applications, (3) frozen LLMs reduce computing cost to 2.5 ∼ 6 % of previous methods using unfrozen LLMs, and (4) frozen LLMs require large models (e.g., over several billions of parameters) for good performance.

Generative large language models are all-purpose text analytics engines: text-to-text learning is all your need

OBJECTIVE

To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning.

METHODS

We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (ie, trainable vectors) with frozen LLM, where the LLM parameters were not updated (ie, frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models.

RESULTS AND CONCLUSION

The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ∼3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4%-10% for clinical abbreviation disambiguation, and 5.5%-9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the "one model for all" promise from training to deployment using a unified generative LLM.

A study of generative large language model for medical research and healthcare

There are enormous enthusiasm and concerns in applying large language models (LLMs) to healthcare. Yet current assumptions are based on general-purpose LLMs such as ChatGPT, which are not developed for medical use. This study develops a generative clinical LLM, GatorTronGPT, using 277 billion words of text including (1) 82 billion words of clinical text from 126 clinical departments and approximately 2 million patients at the University of Florida Health and (2) 195 billion words of diverse general English text. We train GatorTronGPT using a GPT-3 architecture with up to 20 billion parameters and evaluate its utility for biomedical natural language processing (NLP) and healthcare text generation. GatorTronGPT improves biomedical natural language processing. We apply GatorTronGPT to generate 20 billion words of synthetic text. Synthetic NLP models trained using synthetic text generated by GatorTronGPT outperform models trained using real-world clinical text. Physicians' Turing test using 1 (worst) to 9 (best) scale shows that there are no significant differences in linguistic readability (p = 0.22; 6.57 of GatorTronGPT compared with 6.93 of human) and clinical relevance (p = 0.91; 7.0 of GatorTronGPT compared with 6.97 of human) and that physicians cannot differentiate them (p < 0.001). This study provides insights into the opportunities and challenges of LLMs for medical research and healthcare.

Estradiol- and progesterone-associated changes in microRNA-induced silencing and reduced anti-seizure efficacy of an antagomir in female mice

About one third of individuals living with epilepsy have treatment-resistant seizures. Alternative therapeutic strategies are thus urgently needed. One potential novel treatment target is microRNA-induced silencing, which is differentially regulated in epilepsy. Inhibitors (antagomirs) of specific microRNAs have shown therapeutic promise in preclinical epilepsy studies; however, these studies were mainly conducted in male rodent models, and research into microRNA regulation in females and by female hormones in epilepsy is scarce. This is problematic because female sex and the menstrual cycle can affect the disease course of epilepsy and may, therefore, also alter the efficacy of potential microRNA-targeted treatments. Here, we used the proconvulsant microRNA miR-324-5p and its target, the potassium channel Kv4.2, as an example to test how microRNA-induced silencing and the efficacy of antagomirs in epilepsy are altered in female mice. We showed that Kv4.2 protein is reduced after seizures in female mice similar to male mice; however, in contrast to male mice, microRNA-induced silencing of Kv4.2 is unchanged, and miR-324-5p activity, as measured by the association with the RNA-induced silencing complex, is reduced in females after seizure. Moreover, a miR-324-5p antagomir does not consistently reduce seizure frequency or increase Kv4.2 in female mice. As a possible underlying mechanism, we found that miR-324-5p activity and silencing of Kv4.2 in the brain were differentially correlated with plasma levels of 17β-estradiol and progesterone. Our results suggest that hormonal fluctuations in sexually mature female mice influence microRNA-induced silencing and could alter the efficacy of potential future microRNA-based treatments for epilepsy in females.Significance StatementMicroRNA-induced silencing is currently investigated in preclinical studies as a potential novel class of treatment target for epilepsy; however, surprisingly little is known about if and how microRNA-induced silencing is regulated by biological sex and if microRNA therapeutics are as effective in females as they are in males. This study shows that microRNA silencing of the potassium channel Kv4.2 and the functional activity of its targeting microRNA, miR-324-5p, change with plasma levels of estrogens and progesterone and that an inhibitor of miR-324-5p is less effective in female mice to suppress seizures. These findings are significant as they suggest microRNA-induced silencing as a novel molecular mechanism contributing to sex differences in epilepsy that could impact future therapy development.

A large language model for electronic health records

There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model-GatorTron-using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on five clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve five clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og .

Public understandings of potential policy responses to health inequalities: Evidence from a UK national survey and citizens' juries in three UK cities

A substantial body of research describes the distribution, causes and potential reduction of health inequalities, yet little scholarship examines public understandings of these inequalities. Existing work is dominated by small-scale, qualitative studies of the experiences of specific communities. As a result, we know very little about what broader publics think about health inequalities; and even less about public views of potential policy responses. This is an important gap since previous research shows many researchers and policymakers believe proposals for 'upstream' policies are unlikely to attract sufficient public support to be viable. This mixed methods study combined a nationally representative survey with three two-day citizens' juries exploring public views of health inequalities and potential policy responses in three UK cities (Glasgow, Manchester and Liverpool) in July 2016. Comparing public opinion elicited via a survey to public reasoning generated through deliberative processes offers insight into the formation of public views. The results challenge perceptions that there is a lack of public support for upstream, macro-level policy proposals and instead demonstrate support for proposals aiming to tackle health inequalities via improvements to living and working conditions, with more limited support for proposals targeting individual behavioural change. At the same time, some macro-economic proposals, notably those involving tax increases, proved controversial among study participants and results varied markedly by data source. Our analysis suggests that this results from three intersecting factors: a resistance to ideas viewed as disempowering (which include, fundamentally, the idea that health inequalities exist); the prevalence of individualising and fatalistic discourses, which inform resistance to diverse policy proposals (but especially those that are more 'upstream', macro-level proposals); and a lack of trust in (local and national) government. This suggests that efforts to enhance public support for evidence-informed policy responses to health inequalities may struggle unless these broader challenges are also addressed.

Observation of Weakened V-V Dimers in the Monoclinic Metallic Phase of Strained VO_{2}

Emergent order at mesoscopic length scales in condensed matter can provide fundamental insight into the underlying competing interactions and their relationship with the order parameter. Using spectromicroscopy, we show that mesoscopic stripe order near the metal-insulator transition (MIT) of strained VO_{2} represents periodic modulations in both crystal symmetry and V-V dimerization. Above the MIT, we unexpectedly find the long-range order of V-V dimer strength and crystal symmetry become dissociated beyond ≈200  nm, whereas the conductivity transition proceeds homogeneously in a narrow temperature range.

Academic advocacy in public health: Disciplinary 'duty' or political 'propaganda'?

The role of 'advocacy' within public health attracts considerable debate but is rarely the subject of empirical research. This paper reviews the available literature and presents data from qualitative research (interviews and focus groups conducted in the UK in 2011-2013) involving 147 professionals (working in academia, the public sector, the third sector and policy settings) concerned with public health in the UK. It seeks to address the following questions: (i) What is public health advocacy and how does it relate to research?; (ii) What role (if any) do professionals concerned with public health feel researchers ought to play in advocacy?; and (iii) For those researchers who do engage in advocacy, what are the risks and challenges and to what extent can these be managed/mitigated? In answering these questions, we argue that two deeply contrasting conceptualisations of 'advocacy' exist within public health, the most dominant of which ('representational') centres on strategies for 'selling' public health goals to decision-makers and the wider public. This contrasts with an alternative (less widely employed) conceptualisation of advocacy as 'facilitational'. This approach focuses on working with communities whose voices are often unheard/ignored in policy to enable their views to contribute to debates. We argue that these divergent ways of thinking about advocacy speak to a more fundamental challenge regarding the role of the public in research, policy and practice and the activities that connect these various strands of public health research.

In situ observations of a possible skate nursery off the western Antarctic Peninsula

A dense aggregation of skate egg cases was imaged during a photographic survey of the sea floor along the western Antarctic Peninsula in November 2013. Egg cases were noted in a narrow band between 394 and 443 m depth. Although some skate species in other oceans are known to utilize restricted areas to deposit eggs in great numbers, such nurseries have not been described in the Southern Ocean.

Effects of rare-earth size on the electronic structure of La1−xLuxVO3

The electronic structure of La(1-x)Lu(x)VO(3)(x = 0, 0.2, 0.6 and 1) single crystals has been investigated using soft x-ray absorption spectroscopy, soft x-ray emission spectroscopy, and resonant soft x-ray inelastic scattering to study the effects of rare-earth size. The x-ray absorption and emission spectra at the O K-edge present a progressive evolution with R-site cation, in agreement with local spin density approximation calculations. This evolution with R, together with the temperature dependence of the O K-edge spectra, is attributed to changes in the crystal structure of La(1-x)Lu(x)VO(3). The crystal-field dd. excitations probed by resonant inelastic x-ray scattering at the V L(3)-edge exhibit an increase in energy and enhanced intensity with the decrease of R-site ionic radius, which is mainly attributed to the increased tilting magnitude of the VO(6) octahedra. Upon cooling to ~95 K, the dd* excitations are prominently enhanced in relative Intensity, in agreement with the formation of the Jahn.Teller distortion int he orbital ordering phase. Additionally, the dd* transitions of the mixed compounds are noticeably suppressed with respect to those of the pure compounds, possibly owing to the formation of C-type orbital ordering induced by large R-site size variances.

Direct observation of decoupled structural and electronic transitions and an ambient pressure monocliniclike metallic phase of VO2

We report the simultaneous measurement of the structural and electronic components of the metal-insulator transition (MIT) of VO2 using electron and photoelectron spectroscopies and microscopies. We show that these evolve over different temperature scales, and are separated by an unusual monocliniclike metallic phase. Our results provide conclusive evidence that the new monocliniclike metallic phase, recently identified in high-pressure and nonequilibrium measurements, is accessible in the thermodynamic transition at ambient pressure, and we discuss the implications of these observations on the nature of the MIT in VO2.

Low-energy V t2g orbital excitations in NdVO3

The electronic structure of NdVO(3) and YVO(3) has been investigated as a function of sample temperature using resonant inelastic soft x-ray scattering at the V L(3)-edge. Most of the observed spectral features are in good agreement with an atomic crystal-field multiplet model. However, a low energy feature is observed at ∼ 0.4 eV that cannot be explained by crystal-field arguments. The resonant behaviour of this feature establishes it as due to excitations of the V t(2g) states. Moreover, this feature exhibits a strong sample temperature dependence, reaching maximum intensity in the orbitally-ordered phase of NdVO(3), before becoming suppressed at low temperatures. This behaviour indicates that the origin of this feature is a collective orbital excitation, i.e. the bi-orbiton.

Determination of the individual atomic site contribution to the electronic structure of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA)

We have studied the element and orbital-specific electronic structure of thin films of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) using a combination of synchrotron radiation-exited resonant x-ray emission spectroscopy, x-ray absorption spectroscopy, x-ray photoelectron spectroscopy, as well as density functional theory calculations. Resonant and non-resonant x-ray emission spectroscopies were used to measure the C and O 2p partial densities of state in PTCDA. Furthermore, resonant x-ray emission at the C and O K-edges is shown to be able to measure the partial densities of states associated with individual atomic sites. The flat molecular orientation of PTCDA on various substrates is explained in terms of the carbonyl O atom acting as a hydrogen-bond acceptor leading to multiple in-plane intermolecular C=O···H-C hydrogen bonding between carbonyl groups and the perylene core of the neighboring PTCDA molecules. We support this conclusion by comparison of our calculations to measurements of the electronic structure using element-, site-, and orbital-selective C and O K-edge resonant x-ray emission spectroscopy, and photoemission spectroscopy.

Resonant soft-X-ray emission as a bulk probe of correlated electron behavior in metallic SrxCa1-xVO3

The evolution of electron correlation in SrxCa1-xVO3 has been studied using a combination of bulk-sensitive resonant soft x-ray emission spectroscopy, surface-sensitive photoemission spectroscopy, and ab initio band structure calculations. We show that the effect of electron correlation is enhanced at the surface. Strong incoherent Hubbard subbands are found to lie ∼20% closer in energy to the coherent quasiparticle features in surface-sensitive photoemission spectroscopy measurements compared with those from bulk-sensitive resonant soft x-ray emission spectroscopy, and a ∼10% narrowing of the overall bandwidth at the surface is also observed.

The band structure of WO3 and non-rigid-band behaviour in Na0.67WO3 derived from soft x-ray spectroscopy and density functional theory

The electronic structure of single-crystal WO3 and Na0.67WO3 (a sodium-tungsten bronze) has been measured using soft x-ray absorption and resonant soft x-ray emission oxygen K-edge spectroscopies. The spectral features show clear differences in energy and intensity between WO3 and Na0.67WO3. The x-ray emission spectrum of metallic Na0.67WO3 terminates in a distinct Fermi edge. The rigid-band model fails to explain the electronic structure of Na0.67WO3 in terms of a simple addition of electrons to the conduction band of WO3. Instead, Na bonding and Na 3s-O 2p hybridization need to be considered for the sodium-tungsten bronze, along with occupation of the bottom of the conduction band. Furthermore, the anisotropy in the band structure of monoclinic γ-WO3 revealed by the experimental spectra with orbital-resolved geometry is explained via density functional theory calculations. For γ-WO3 itself, good agreement is found between the experimental O K-edge spectra and the theoretical partial density of states of O 2p orbitals. Indirect and direct bandgaps of insulating WO3 are determined from extrapolating separations between spectral leading edges and accounting for the core-hole energy shift in the absorption process. The O 2p non-bonding states show upward band dispersion as a function of incident photon energy for both compounds, which is explained using the calculated band structure and experimental geometry.

Assessment of technical and biological parameters of volumetric quantitative computed tomography of the foot: a phantom study

SUMMARY

Few studies exist for bone densitometry of the whole foot. A phantom study demonstrated the sources of error and necessary controls for accurate quantitative computed tomography of the foot. A loss in bone mineral density (BMD) in the small foot bones may be an early indicator of diabetic foot complications.

INTRODUCTION

Volumetric quantitative computed tomography (vQCT) facilitates the assessment of pedal bone osteopenia, which, in the presence of peripheral neuropathy, may well be an early sign of diabetic foot deformity. To date, sources and magnitudes of error in foot vQCT measurements have not been reported.

METHODS

Foot phantoms were scanned using a 64-slice CT scanner. Energy (in kilovoltage peak), table height, phantom size and orientation, location of "bone" inserts, insert material, location of calibration phantom, and reconstruction kernel were systematically varied during scan acquisition.

RESULTS

Energy (in kilovoltage peak) and distance from the isocenter (table height) resulted in relative attenuation changes from -5% to 22% and -5% to 0%, respectively, and average BMD changes from -0.9% to 0.0% and -1.1% to 0.3%, respectively, compared to a baseline 120-kVp scan performed at the isocenter. BMD compared to manufacturer-specified values ranged, on average, from -2.2% to 0.9%. Phantom size and location of bone-equivalent material inserts resulted in relative attenuation changes of -1.2% to 1.4% compared to the medium-sized phantom.

CONCLUSION

This study demonstrated that variations in kilovoltage peak and table height can be controlled using a calibration phantom scanned at the same energy and height as a foot phantom; however, error due to soft tissue thickness and location of bones within a foot cannot be controlled using a calibration phantom alone.

Trends in the obstetric features and management of twin pregnancies

There are no reports outlining the trends in obstetric features and clinical management of twin pregnancies in an Irish obstetric population. The aim of this study was to investigate these factors for all twin pregnancies delivered during the 19 year period between 1989 and 2007, at Galway University Hospital (GUH). There were 52,199 infants delivered at GUH, of which 1594 infants (3.05% of births) were twins, related to 797 twin pregnancies. The overall incidence of twin pregnancies was 1.52%, increasing from 0.8%-1.0% in the early years of the study to 1.7-1.8% in the latter years of the study (P<0.001). There was a significant increase in incidence of twins born to mothers aged 30-39 years, alongside a significant reduction to mothers aged 20-29 years (P<0.01). The caesarean section rate overall was 41.5% (331/797), of which 54% (n=179) were elective, and 46% (n=152) were emergency, representing an emergency caesarean section rate of 19.1% of all twin pregnancies, and of 24.6% after exclusion of elective caesarean sections. The caesarean section rate for twins increased from 30% in 1989 to greater than 50% in the latter years of the study (P<0.01), related largely to a significant increase in elective caesarean sections (P<0.01). The combined vaginal-caesarean delivery rate was remarkably low at 0.75% of all twin pregnancies, and 1% after exclusion of elective caesarean sections. The preterm delivery rates were 4.1% (<32 weeks), and 16.3% (<36 weeks), with an overall perinatal mortality rate of 37 per 1000. These findings highlight the altered demographic and clinical aspects of twin pregnancies in an Irish obstetric population.

Patient perspectives of Condition Management Programmes as a route to better health, well-being and employability

BACKGROUND

Condition Management Programmes (CMPs), delivered through primary care settings, have been identified as possible vehicles to facilitate return to work for individuals with chronic health problems. There is little research, however, which examines how such programmes are received by patients.

OBJECTIVE

To explore patients' experiences of CMPs in terms of health, well-being and employability.

METHODS

Four focus groups and nine semi-structured interviews were conducted in order to capture patients' (n = 25) perceptions and experiences regarding participation in one of five different CMPs: Cardiac Rehabilitation, Counselling, Lower Back Pain Services, Smoking Cessation and a GP Exercise Referral Programme.

RESULTS

Experiences of the CMPs were generally positive. Respondents reported improved health behaviours (specifically better diets and increased exercise), positive psychosocial outcomes (including increased self-esteem, confidence and social support) and in some cases, return to work. However, concerns were expressed about the shortness of interventions and their accessibility.

CONCLUSIONS

Although condition management appears to have been well received by participants, the findings also illustrate that there is no 'one size fits all' template for CMPs. Rather, interventions should be adapted to take account of the dynamics of specific conditions, the context in which the intervention is based and the characteristics of the individuals involved.

Electronic excitations in the correlated metal BaV(0.98)Ti(0.02)S(3) studied using resonant inelastic soft x-ray scattering

Electronic excitations in the correlated metal BaTi(0.02)V(0.98)S(3) have been studied using resonant inelastic soft x-ray scattering at the V L edge. The intensities of the intra-atomic d-d(*) excitations and the elastic x-ray scattering feature are found to be temperature dependent, with the intensity increasing with decreasing temperature until saturation is reached near 100 K. The behavior of the spectral features is interpreted as evidence of a shift in the 3d electrons from more band-like states at higher temperature to more localized states at low temperature.

Comment on "Near-edge X-ray absorption fine-structure investigation of graphene"

A Comment on the Letter by D. Pacilé et al., Phys. Rev. Lett. 101, 066806 (2008)10.1103/PhysRevLett.101.066806. The authors of the Letter offer a Reply.

Electronic structure of the organic semiconductor Alq3 (aluminum tris-8-hydroxyquinoline) from soft x-ray spectroscopies and density functional theory calculations

The element-specific electronic structure of the organic semiconductor aluminum tris-8-hydroxyquinoline (Alq(3)) has been studied using a combination of resonant x-ray emission spectroscopy, x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory (DFT) calculations. Resonant and nonresonant x-ray emission spectroscopy were used to measure directly the carbon, nitrogen and oxygen 2p partial densities of states in Alq(3), and good agreement was found with the results of DFT calculations. Furthermore, resonant x-ray emission at the carbon K-edge is shown to be able to measure the partial density of states associated with individual C sites. Finally, comparison of previous x-ray emission studies and the present data reveal the presence of clear photon-induced damage in the former.

Health inequalities in England, Scotland and Wales: stakeholders' accounts and policy compared

OBJECTIVES

The election of a Labour government in 1997 brought the issue of health inequalities firmly back on to the policy agenda across the UK. Since then, in the wake of devolution, the need to tackle health inequalities has been highlighted as a policy priority in all three mainland UK countries, albeit with varying degrees of emphasis. This paper reports on a major cross-national study, funded by the Economic and Social Research Council, investigating how National Health Service bodies, local councils and partnerships make sense of their work on health inequalities, and examining the difference made by the contrasting approaches that have been taken to performance assessment in England, Wales and Scotland.

STUDY DESIGN

Case studies, semi-structured interviews and analysis of key policy statements.

METHODS

In order to explore how health inequalities have been approached by the three governments (noting that there was a change in governments in Wales and Scotland during this time), key policy statements published between May 1997 and May 2007 were analysed. Concurrently, data from stakeholder interviews carried out in 2006 in case study areas in each country were analysed to determine the extent of alignment between policy and practice at local level.

RESULTS

This paper suggests that claims about the extent of health policy divergence in post-devolution Britain may have been exaggerated. It finds that, whilst the three countries have taken differing approaches to performance assessment and the setting of targets, policy approaches to health inequalities up until 2007 appear to have been remarkably similar. Furthermore, the first round of interview data suggest that variations in local understandings of, and responses to, health inequalities cannot always be clearly distinguished along national lines.

CONCLUSIONS

Based on the policy analysis, devolution in the UK does not appear to have resulted in substantively different national policy approaches to health inequalities. Indeed, the overall analysis suggests that (prior to the 2007 elections in Scotland and Wales) the differences between local areas within countries may be of as much interest as those between countries.

A multi-state Salmonella Typhimurium outbreak associated with frozen vacuum-packed rodents used to feed snakes

From December 2005 through January 2006, the Minnesota Department of Health (MDH) identified four human clinical isolates of Salmonella Typhimurium that were indistinguishable by pulsed-field gel electrophoresis (PFGE). During routine interviews, three of the cases reported attending the same junior high school and two handled snakes in the science classroom. MDH collected environmental samples from the school's science classroom for Salmonella culturing; these included environmental samples and frozen vacuum-packed mice purchased over the internet to feed the classroom snakes. Through PulseNet, a national molecular subtyping surveillance network for enteric bacteria, 21 human S. Typhimurium isolates with indistinguishable PFGE patterns were identified in the United States since December 2005. Each state determined whether these human cases had recent exposure to snakes fed vacuum-packed rodents. Texas state officials conducted tracebacks of the vacuum-packed mice and collected samples at the breeding facility. Nineteen of 21 cases were interviewed, and seven reported contact with frozen vacuum-packed rodents from the same internet-based supplier in Texas. In Minnesota, the outbreak PFGE subtype of S. Typhimurium was isolated from the snakes, frozen feed rodents, and the classroom environment. Three human cases were identified in Michigan, Pennsylvania, and Wyoming. The outbreak PFGE subtype of S. Typhimurium was isolated from the Pennsylvania case's frozen rodents and the Michigan case's pet snake. The outbreak PFGE subtype of S. Typhimurium was also isolated from the supplier's rodent facility. This was a S. Typhimurium outbreak associated with frozen rodents. Human transmission likely occurred through direct contact with snakes and contaminated environmental surfaces. This report represents the second recent multi-state salmonellosis outbreak associated with commercially distributed rodents. Stronger oversight of the commercial rodent industry is warranted.

The UCSC Genome Browser Database: update 2009

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

Dissipation of PAHs in saturated, dredged sediments: a field trial

Sediments dredged from navigable rivers often contain elevated concentrations of recalcitrant, potentially toxic organic compounds such as polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). The presence of these compounds often requires that the sediments be stored in fully contained disposal facilities. A 3-year field study was conducted at the Jones Island disposal facility in Milwaukee, Wisconsin, to compare bioremediation of PAHs in contaminated dredged sediments in the absence of plants to phytoremediation with Salix nigra (black willow) (SX61), Spartina pectinata (prairie cord grass), Carex aquatalis (lake sedge), Lolium multiflorum (annual rye), and Scirpus fluviatilis (bulrush). Nine PAHs were detected initially in the sediments. Over the 3-year experiment, acenaphthene dissipation ranged from 94% to 100%, whereas anthracene, benzo[a]pyrene and indo[1,2,3-cd]pyrene generally had modest decreases in concentration (0-30% decrease). The remaining five PAHs ranged in degree of disappearance from 23% to 82%. Planted treatments did not enhance PAH dissipation relative to those without plants, but treatments with high biomass yield and high transpiration plant species had significantly less removal of PAHs than unplanted controls. Significant, negative correlations between nitrogen removal and decreases in PAH concentration suggest that competition for nutrients between plants and microorganisms may have impeded the microbial degradation of PAHs in the rhizosphere of the more rapidly growing plant species.

The UCSC Genome Browser Database: 2008 update

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

Inhibition of inducible nitric oxide synthase enhances anti-tumour immune responses in rats immunized with IFN-gamma-secreting glioma cells

Interferon gamma (IFN-gamma) has successfully been used in immunotherapy of different experimental tumours. Mechanistically, IFN-gamma has extensive effects on the immune system including release of nitric oxide (NO) by upregulation of the inducible nitric oxide synthase (iNOS). NO has putative immunosuppressive effects but could also play a role in killing of tumour cells. Therefore, the aim of the present study was to clarify whether inhibition of iNOS in rats immunized with glioma cells (N32) producing IFN-gamma (N32-IFN-gamma), could enhance the anti-tumour immune response. Initially, both a selective iNOS, l-N(6)-(1-Iminoethyl)-l-lysine (l-NIL), and non-selective, N-nitro-l-arginine methyl ester (l-NAME), inhibitor of NOS were tested in vitro. After polyclonal stimulation with LPS and SEA, both l-NIL and l-NAME enhanced proliferation and production of IFN-gamma from activated rat splenocytes and this effect was inversely correlated to the production of NO. However, l-NIL had a broader window of efficacy and a lower minimal effective dose. When rats were immunized with N32-IFN-gamma, and administered NOS inhibitors by intraperitoneal (i.p.) mini-osmotic pumps, only splenocytes of rats treated with l-NIL, but not l-NAME, displayed an enhanced proliferation and production of IFN-gamma when re-stimulated with N32 tumour cells. Based on these findings, l-NIL was administered concurrently with N32-IFN-gamma cells to rats with intracerebral (i.c.) tumours resulting in a prolonged survival. These results show that inhibition of iNOS can enhance an IFN-gamma-based immunotherapy of experimental i.c. tumours implying that NO released after immunization has mainly immunosuppressive net effects.

X-ray spectroscopic study of the charge state and local ordering of room-temperature ferromagnetic Mn-doped ZnO

The charge state and local ordering of Mn doped into a pulsed laser deposited single-phase thin film of ZnO are investigated by using x-ray absorption spectroscopy at the O K-edge, Mn K-edge and L-edge, and x-ray emission spectroscopy at the O K-edge and Mn L-edge. This film is ferromagnetic at room temperature. EXAFS measurement shows that Mn(2+) replaces the Zn site in tetrahedral symmetry, and there is no evidence for either metallic Mn or MnO in the film. Upon Mn doping, the top of O 2p valence band extends into the bandgap, indicating additional charge carriers being created.

Phytoremediation of polychlorinated biphenyl (PCB)-contaminated sediment: a greenhouse feasibility study

Contaminated sediments dredged from navigable waterways often are placed in confined disposal facilities to prevent further spread of the pollutants. Reducing contaminants to acceptable levels would allow for disposal of the sediments and further dredging activity. A greenhouse study was conducted to evaluate plant treatments and the addition of an organic amendment to decrease the concentration of PCB congeners found in Arochlor 1260. Sediment treated with the amendment and either low transpiring plants or no plants had the greatest removal of the PCB congeners. High-transpiring plants apparently prevented the highly reducing conditions required for reductive dechlorination of highly chlorinated PCBs. Most likely, the amendment provided labile carbon that initiated the reducing conditions needed for dechlorination. The sediment moisture content and moisture-related plant parameters were significant predictors of the PCB loss. Carex aquatalis and Spartina pectinata are predicted to be the most effective plant treatments for phytoremediation of PCBs.

The Trace Amine 1 receptor knockout mouse: an animal model with relevance to schizophrenia

Trace amines have been implicated in a number of neuropsychiatric disorders including depression and schizophrenia. Although long known to modulate neurotransmission indirectly through the release of catecholamines, the identification of the Trace Amine 1 receptor (TA1) offers a mechanism by which trace amines can influence synaptic activity directly. TA1 binds and is activated by trace amines such as beta-phenylethylamine and tyramine. Our pharmacological characterization of mouse TA1 showed that, as in rat and primate, amphetamine is an agonist at this receptor but with surprisingly high potency. Without selective ligands for TA1 that do not also possess catecholamine-releasing properties, however, it has not been possible to study its physiological role in the central nervous system. To that end, a line of mice lacking the TA1 receptor was generated to characterize its contribution to the regulation of behavior. Compared with wild-type littermates, TA1 knockout (KO) mice displayed a deficit in prepulse inhibition. Knockout animals, in which the TA1-agonist influence of amphetamine was absent, showed enhanced sensitivity to the psychomotor-stimulating effect of this drug, which was temporally correlated with significantly larger increases in the release of both dopamine and norepinephrine in the dorsal striatum and associated with a 262% increase in the proportion of striatal high-affinity D2 receptors. TA1 therefore appears to play a modulatory role in catecholaminergic function and represents a potentially novel mechanism for the treatment of neuropsychiatric disorders. Furthermore, the TA1 KO mouse may provide a useful model for the development of treatments for some positive symptoms of schizophrenia.

Risk factors for sporadic Shiga toxin-producing Escherichia coli O157 infections in FoodNet sites, 1999-2000

To monitor risk factors for illness, we conducted a case-control study of sporadic Shiga toxin-producing Escherichia coli O157 (STEC O157) infections in 1999-2000. Laboratory-confirmed cases of STEC O157 infection were identified through active laboratory surveillance in all or part of seven states. Patients and age-matched controls were interviewed by telephone using a standard questionnaire. Information was collected on demographics, clinical illness, and exposures to food, water, and animals in the 7 days before the patient's illness onset. During the 12-month study, 283 patients and 534 controls were enrolled. STEC O157 infection was associated with eating pink hamburgers, drinking untreated surface water, and contact with cattle. Eating produce was inversely associated with infection. Direct or indirect contact with cattle waste continues to be a leading identified source of sporadic STEC O157 infections.

The UCSC genome browser database: update 2007

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at .

Electronic origins of structural distortions in post-transition metal oxides: experimental and theoretical evidence for a revision of the lone pair model

Structural distortions in post-transition metal oxides are often explained in terms of the influence of sp hybrid "lone pairs." Evidence is presented here showing that this model must be revised. The electronic structures of prototypically distorted alpha-PbO and alpha-Bi2O3 have been measured by high-resolution x-ray photoemission and soft x-ray emission spectroscopies. In contrast with the expectations of the lone pair model, a high density of metal 6s states is observed at the bottom of the valence band. The measurements are consistent with the results of density functional theory calculations.

The UCSC Genome Browser Database: update 2006

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .

Quasiparticle spectra, charge-density waves, superconductivity, and electron-phonon coupling in 2H-NbSe2

High-resolution photoemission has been used to study the electronic structure of the charge-density wave (CDW) and superconducting dichalcogenide, 2H-NbSe2. From the extracted self-energies, important components of the quasiparticle interactions have been identified. In contrast to previously studied TaSe2, the CDW transition does not affect the electronic properties significantly. The electron-phonon coupling is identified as a dominant contribution to the quasiparticle self-energy and is shown to be very anisotropic (k dependent) and much stronger than in TaSe2.

Development and validation of a simulation model for blowfly strike of sheep

A comprehensive simulation model for sheep blowfly strike due to Lucilia sericata (Meigen) (Diptera: Calliphoridae), which builds on previously published versions but also incorporates important new empirical data, is used to explain patterns of lamb and ewe strike recorded on 370 farms in south-west, south-east and central England and Wales. The model is able to explain a significant percentage of the variance in lamb strike incidence in all four regions, and ewe strike in three of the four regions. The model is able to predict the start of seasonal blowfly strike within one week in three of the four regions for both ewes and lambs, and within 3 weeks in the fourth region. It is concluded that the accuracy of the model will allow it to be used to assess the likely efficacy of new control techniques and the effects of changes in existing husbandry practices on strike incidence. The model could also be used to give sheep farmers advance warning of approaching strike problems. However, the ability to forecast future strike patterns is dependent on the accuracy of the weather projections; the more long-term the forecast, the more approximate the prediction is likely to be. When applied on a regional basis, model forecasts indicate expected average patterns of strike incidence and may not therefore be appropriate for individual farmers whose husbandry practices differ substantially from the average.

How do mothers' childrearing histories, stress and parenting affect children's behavioural outcomes?

BACKGROUND

Information is needed to understand the role of low to moderate levels of mothers' emotional stress and child characteristics (i.e. prematurity) on parenting behaviours and their impact on children's behaviour that might be deemed 'challenging' but not 'disordered'.

METHODS

The direct and indirect relations of maternal childrearing history and emotional stress, and observed parenting practices when children were 3 years of age on 4-year child behavioural outcomes was examined in a sample of low-income families with a term (n=112) or preterm (n=180) child. Parenting practices included displays of warmth and restrictiveness when interacting with their children. Child outcomes at 4 years included observation of social initiations with their mothers and maternal report of social and attentional problems.

RESULTS

A Structural Equation Model building approach guided by specific hypotheses indicated that preterm as compared to full-term children had more maternal reported social and attentional problems but did not differ in observed social initiating skills. Greater negative maternal childrearing history indirectly influenced social initiating skills through its direct influence on maternal emotional stress. Greater maternal emotional stress directly influenced mothers' parenting that, in turn, directly influenced social initiating. Prematurity and a more negative childrearing history had a direct negative influence on the maternal report of social and attentional behavioural outcomes.

CONCLUSIONS

These findings delineate the effects of prematurity and maternal parenting on the behaviour of 4-year-old-children and extend current knowledge of the influence of parental emotional stress on parenting. Even milder levels can negatively influence parenting, and in turn, contribute to children's less well developed social skills. The issues raised in this study could help with the identification and prioritization of medical and psychological services.

Does early responsive parenting have a special importance for children's development or is consistency across early childhood necessary?

The role of early versus ongoing maternal responsiveness in predicting cognitive and social development was examined in home visits for mothers, full-term children (n = 103), and medically low-risk (n = 102) and high-risk (n = 77) preterm children at 5 ages. There were 4 maternal clusters based on warm and contingent responsiveness behaviors observed early (at 6, 12, and 24 months) and late (at 3 and 4 years): high early, high late; high early, low late; low early, moderate late; and low early, low late. Children, especially preterm children, showed faster cognitive growth when mothers were consistently responsive. Social growth was similar in the consistently responsive (high-high) and the early-responsive inconsistent (high-low) clusters, but greater deceleration at 4 years among children with mothers in the inconsistent cluster refuted the notion of a unique role for early responsiveness. The importance of consistent responsiveness, defined by an affective-emotional construct, was evident even when a broader constellation of parenting behaviors was considered.

Epidemiology and clonality of community-acquired methicillin-resistant Staphylococcus aureus in Minnesota, 1996-1998

Methicillin-resistant Staphylococcus aureus (MRSA) has emerged among patients in the general population who do not have established risk factors for MRSA. Records from 10 Minnesota health facilities were reviewed to identify cases of MRSA infection that occurred during 1996-1998 and to identify which cases were community acquired. Susceptibility testing and pulsed-field gel electrophoresis (PFGE) subtyping were performed on available isolates. A total of 354 patients (median age, 16 years) with community-acquired MRSA (CAMRSA) infection were identified. Most case patients (299 [84%]) had skin infections, and 103 (29%) were hospitalized. More than 90% of isolates were susceptible to all antimicrobial agents tested, with the exception of beta-lactams and erythromycin. Of 334 patients treated with antimicrobial agents, 282 (84%) initially were treated with agents to which their isolates were nonsusceptible. Of 174 Minnesota isolates tested, 150 (86%) belonged to 1 PFGE clonal group. CAMRSA infections were identified throughout Minnesota; although most isolates were genetically related and susceptible to multiple antimicrobials, they were generally nonsusceptible to initial empirical therapy.

Pre-adult mortality in the blowfly Lucilia sericata

Populations of the blowfly, Lucilia sericata (Meigen) (Diptera: Calliphoridae), have a considerable potential for rapid increase; the lifetime reproductive output of each adult female has been estimated to be between 130 and 172 eggs. Nevertheless, in the field, absolute population densities of this species are relatively low. To account for this difference, the levels of mortality affecting the eggs, feeding and wandering larvae and pupae of L. sericata were assessed in the field and laboratory. Percentage egg hatch was dependent on relative humidity with no egg eclosion at humidities below 50%; there was no significant effect of temperature on egg hatch. On infested sheep, the mean mortality of feeding larvae was 53%, but this ranged widely from 0% to 96%. There was no effect of atmospheric temperature or humidity on the mortality of feeding larvae in vivo. In the laboratory, only 10% of wandering larvae pupariated at 10 degrees C. At above 20 degrees C pupariation was consistently almost 100%. Percentage emergence increased from 0% at 10 degrees C to about 80% between 20 and 30 degrees C. The upper lethal temperature for pupae was approached at 35 degrees C. Analysis of the predation of pupae in the field revealed a weak, but significant curvilinear relationship between temperature and proportionate mortality and a median mortality of 0.49% per 24 h exposure (interquartile range = 5.2%). There was no evidence of density dependence in pupal predation. Overall, it is estimated that pre-adult mortality accounts for losses of approximately 97% of each generation, but this figure is subject to considerable variation depending on factors such as climate, time of year and host susceptibility.

Precision and accuracy of computed tomography foot measurements

OBJECTIVE

To test the accuracy and precision of computed tomography (CT) imaging for describing the 3-dimensional structure of the foot in patients with diabetes mellitus and peripheral neuropathy.

DESIGN

Experimental, test-retest.

SETTING

Clinical CT scanner at a local hospital.

SPECIMENS

Two tissue-equivalent phantoms and 6 cadaver feet.

MAIN OUTCOME MEASURES

Measurements taken from CT data of phantoms and cadaver feet were compared with physical (caliper) measurements. The feasibility of creating a computer-aided design/rapid prototyping 3-dimensional model from CT data was assessed by using 1 cadaver foot.

RESULTS

No bias was found for phantom or cadaver CT measurements compared with caliper measurements. The mean difference between repeat scans of cadaver feet (1 observer) was 0.1 +/- 0.8 mm and between observers, 0.4 +/- 0.8 mm. Comparing caliper measurements of the rapid prototype model and actual foot measurements revealed an error of 0.3 +/- 0.4 mm.

CONCLUSION

CT-based 3-dimensional imaging produced accurate and precise foot measurements, enabling description of internal and external structures. This capability will be coupled with plantar pressure measurements to improve our understanding and treatment of foot ulcers in people with diabetes.

Behavior of sewage sludge-derived PAHs on pasture

A field experiment was set up to investigate the retention of PAHs by pasture grass following sludge application. In addition to information on compound-specific loss rates, the influence of meteorological variables and sludge-pasture contact time on the weathering process were investigated. The rates of loss were compound specific with half-lives ranging from < 1 to 10 d. The lighter PAHs were rapidly lost from the grass surface primarily by volatilization. For the intermediate and heavier PAHs, loss was slower with rain playing an important role in the weathering process. Growth dilution was also important in reducing the contaminant levels in the grass. The effect of sludge-pasture contact time prior to weathering by rain on the residual levels remains unclear. In terms of risk of exposure, there is the potential for persistent organic contaminants to be introduced into the grazing animal food chain if sewage sludge is applied to pasture land.

Seasonal and species differences in the air--pasture transfer of PAHs

A field plot was established at a semirural site in the U.K. to investigate the atmospheric transfer of PAHs to different pasture species over the whole growing season. The PAHs displayed a range of partitioning behaviors in the atmosphere from exclusively gas phase to exclusively particle bound, resulting in different modes of deposition to the plant surface. The different pasture species had different plant and sward characteristics, e.g., leaf morphologies, yields, etc. For the majority of PAHs, the plant species displayed a seasonality in concentrations, with concentrations being higher in the winter than in the summer. For the lighter PAHs, this seasonality was absent with soil outgassing and/or summer sources of PAHs being implicated. Air-plant transfer factors (scavenging coefficients, with units m3/g dw) typically ranged between 4 and 52 during the summer, increasing to 8-88 during winter. Despite different plant and sward characteristics, the mixtures and concentrations of PAHs were similar for all the plant species. This indicates that there was little difference in the interception and retention behavior of the gas- and particle-phase PAHs. The implications of this for food chain transfer and air-vegetation modeling are discussed.

Microbial transformations of steroids--XII. Progesterone hydroxylation profiles are modulated by post-translational modification of an electron transfer protein in Streptomyces roseochromogenes

When Streptomyces roseochromogenes strain 10984 was incubated with exogenous progesterone for 25 h the major monohydroxylated metabolite, 16alpha-hydroxyprogesterone was produced in 3.6 fold excess to the minor metabolite 2beta,16alpha-dihydroxyprogesterone. In a reconstituted system containing highly purified progesterone 16alpha-hydroxylase cytochrome P-450, and electron transfer proteins ferredoxin-like redoxin (roseoredoxin) and redoxin reductase (roseoredoxin reductase), both metabolites were produced but in a 10:1 ratio. When S. roseochromogenes was pre-incubated for 8 h with 0.32 mM progesterone and the purified components of the hydroxylase system incubated as before, the ratio of 16alpha-hydroxyprogesterone to 2beta,16alpha-dihydroxyprogesterone produced decreased to 2.8:1, virtually identical to the ratio in whole cell transformations. Reconstitution assays containing all combinations of hydroxylase proteins purified from progesterone pre-incubated and control cells showed that the roseoredoxin was solely responsible for the observed changes in in vitro metabolite ratios. The fact that the lower 16alpha-hydroxyprogesterone to 2beta,16alpha-dihydroxyprogesterone ratio was also obtained when S. roseochromogenes was exposed to 0.335 mM cycloheximide for 8 h prior to the progesterone pre-incubation, pointed to post-translation modification of the roseoredoxin. Separation of two isoforms of roseoredoxin by isoelectric focusing supported this proposition.