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Recent erosion rates from tectonically active coasts provide evidence of rapid rock breakdown following coseismic uplift. These rates are needed to solve puzzles about 'missing' marine terraces that prevent accurate reconstruction of past sea levels, earthquakes and rock coast evolution. Yet little scientific effort has been put into investigating the impact of tectonism on shore platform development. It is also presently unclear if erosion records from one coast can be extrapolated to other regions with similar tectonic, geologic, or geomorphic characteristics. We present shore platform downwearing rates and processes measured using the traversing micro-erosion meter (TMEM) and Structure-from-Motion photogrammetry from an inter-tidal shore platform uplifted by 3.1 m between 100 to 300 years ago. The site is a mudstone platform at Kahutara Point, Māhia Peninsula, North Island, New Zealand. Over 1.43 years, the mean annual downwearing rate was 1.94 mm/yr, while the total erosion at individual TMEM stations ranged from 0.29 to 8.31 mm (equivalent to mean erosion rates of 0.07 to 5.82 mm/yr). We found a lack of any spatial pattern in erosion rates cross-shore, suggesting the equal efficiency of waves and weathering processes. Orthophotographs of the eroded rock surfaces support the combined role of marine processes (waves and tides), sub-aerial weathering processes, salt weathering and biological activity in the erosion of the mudstone platforms at Kahutara Point. The mean erosion rate of 1.94 mm/yr from the Māhia Peninsula is similar to the mean post-uplift rate of 2.25 mm/yr reported for the Kaikōura Peninsula, New Zealand, where platforms were uplifted by ~1 m in 2016. This result suggests a comparable pattern of erosion response at both sites following co-seismic uplift and provides the first field evidence to support the comparison of the Kaikōura and Māhia shore platforms, thus helping to inform marine terrace development and destruction.

Purpose:To determine if a targeted exome panel utilizing matched normal DNA can accurately detect germline and somatic HLA genes in patients with synovial sarcoma (SS) and whether select HLA-A*02 genotypes are prognostic or predictive of outcome in metastatic SS.Experimental Design:Patients with metastatic SS consented to HLA typing by a Clinical Laboratory Improvement Amendments (CLIA)-certified test to determine eligibility for a clinical trial of NY-ESO-1–specific engineered T cells restricted to carriers of HLA-A*02:01, -A*02:05, or -A*02:06 (HLA-A*02 eligible). HLA genotype was determined from Memorial Sloan Kettering Integrated Molecular Profiling of Actionable Cancer Targets (MSK-IMPACT), where feasible, and somatic loss of heterozygosity (LOH) in HLA alleles was identified. Overall survival (OS) was estimated and stratified by HLA-A*02 eligibility.Results:A total of 23 patients had HLA genotyping by a CLIA-certified lab and MSK-IMPACT. Ninety percent (108/110) of the sequenced alleles were concordant between IMPACT and the outside lab. LOH of HLA genes was detected in three tumors, one had loss of HLA-A*02:01. In total, 66 patients were screened for T-cell therapy and 20 (30%) were HLA-A*02 eligible on outside testing. Univariate analysis of OS from the time of metastasis found HLA-A*02 eligibility was marginally associated with shorter OS [HR = 1.95; 95% confidence interval (CI), 0.995–3.813; P = 0.052]. On multivariate analysis, older age and larger tumor size, but not HLA-A*02 eligibility, were significantly associated with decreased OS. HLA-A*02 eligibility did not impact OS after chemotherapy or pazopanib in the metastatic setting.Conclusions:Targeted gene panels like MSK-IMPACT may accurately report HLA type and identify loss of somatic HLA alleles. In a multivariable model, HLA-A*02 eligibility was not significantly associated with OS in patients with metastatic SS.

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IntroductionAmbulances services are asked to further reduce avoidable conveyances to emergency departments (EDs). Risk of Adverse Outcomes after a Suspected Seizure seeks to support this by: (1) clarifying the risks of conveyance and non-conveyance, and (2) developing a risk prediction tool for clinicians to use ‘on scene’ to estimate the benefits an individual would receive if conveyed to ED and risks if not.Methods and analysisMixed-methods, multi-work package (WP) project. For WP1 and WP2 we shall use an existing linked data set that tracks urgent and emergency care (UEC) use of persons served by one English regional ambulance service. Risk tools are specific to clinical scenarios. We shall use suspected seizures in adults as an exemplar.WP1: Form a cohort of patients cared for a seizure by the service during 2019/2020. It, and nested Knowledge Exchange workshops with clinicians and service users, will allow us to: determine the proportions following conveyance and non-conveyance that die and/or recontact UEC system within 3 (/30) days; quantify the proportion of conveyed incidents resulting in ‘avoidable ED attendances’ (AA); optimise risk tool development; and develop statistical models that, using information available ‘on scene’, predict the risk of death/recontact with the UEC system within 3 (/30) days and the likelihood of an attendance at ED resulting in an AA.WP2: Form a cohort of patients cared for a seizure during 2021/2022 to ‘temporally’ validate the WP1 predictive models.WP3: Complete the ‘next steps’ workshops with stakeholders. Using nominal group techniques, finalise plans to develop the risk tool for clinical use and its evaluation.Ethics and disseminationWP1a and WP2 will be conducted under database ethical approval (IRAS 307353) and Confidentiality Advisory Group (22/CAG/0019) approval. WP1b and WP3 have approval from the University of Liverpool Central Research Ethics Committee (11450). We shall engage in proactive dissemination and knowledge mobilisation to share findings with stakeholders and maximise evidence usage.

Satellite earth observation data has been frequently applied to monitor shoreline change at very large geographic scales. Techniques focus on the extraction of the instantaneous waterline boundary, a shoreline proxy that can be extracted from publicly available multispectral satellite data with sub-pixel accuracy. Interpreting coastal change through this proxy can be uncertain as the position of the waterline is dynamic, a function of beach gradient and constantly fluctuating marine processes, and might not capture information of the full spectrum of drivers influencing change for a given section of coast.Satellite data is acquired in raster format and there is useful information stored in each pixel across the entire coastal zone. Applying per-pixel change detection techniques could offer further insights to the role of drivers of coastal change beyond a vectorised land-water boundary. This paper describes a new method for monitoring coastal change at large geographic scales with public satellite remote sensing data through pixel-based change detection. The first step is the classification of pixels into specific coastal landcover classes. This is challenging at large scales owing to complex and diverse physical environmental characteristics. A methodology was developed and applied to New Zealand’s coastline, identifying 9 landcover types including sedimentary coast. A combination of Sentinel multispectral and synthetic-aperture-radar data were used to derive composite imagery for 2019 using Google Earth Engine cloud computing platform. This was classified using a set of hierarchal rules and machine learning in a Python programming environment. This was validated nationally against high-resolution aerial photography and commercial satellite imagery. This produced a coastal specific landcover classification from which per-pixel change detection techniques can be applied. Overall accuracy was 86.38% and exceeded 90% when normalised by class area.The outputs and code are available, and the framework has been designed to work with a range of earth observation datasets and can be applied to other regions around the world. Ongoing work includes implementing a framework to assess long-term change, at the coast in New Zealand. By investigating how specific coastal landcover types are changing, useful information can be acquired to better interpret drivers of coastal change and the impacts on coastal geomorphology at large geographic scales. Keywords: Satellite Remote Sensing, Multispectral, Synthetic Aperture Radar, Landcover classification, Change detection, Coastal change.

Oblique terrestrial laser scanning (TLS) enables topographic change detection at scales (10−1 –100 cm) that are appropriate for coastal cliff erosion monitoring. Despite this, its application has been limited to a select few regions around the world. Here we report new TLS point cloud datasets from 13 years of monitoring (2009-2022) at Rothesay Bay, Hauraki Gulf, New Zealand, which has a relatively low wave energy setting with a meso tidal range. The 120 m-long scan area includes cliffs of 10-30 m in height, formed of horizontally bedded soft sedimentary flysch rock. The cliffs are fronted by an ~140m wide near-horizontal shore platform that terminates in an abrupt seaward edge. Formation of such platform morphology is based on the assumption that: a) the platform has developed during several millennia of stable Holocene Sea level (around 6,000 years); b) the seaward edge of the shore platform does not erode; c) and the rate of cliff retreat reduces over time due to increased dissipation of wave energy across a widening shore platform. On this basis it has been previously assumed that the long-term cliff retreat rate at this field site is between 1.4±0.1 to 14.3±0.1 mm/year. In contrast, volumetric cliff-face erosion detected with intensive monthly TLS scanning (July 2021- April 2022) at this site indicates a cliff recession rate of 140-660 mm/year (during dry and wet seasons), and three scans over a 12-year window (2009, 2014, 2021) indicate an average erosion rate of 47 mm/year. If erosion had been constant at this rate over approximately 6,000 years, a total cliff retreat of 282 m would be expected, which presents a striking contrast to the width of the contemporary shore platform. The anomaly is even more pronounced given: a) the widely held assumption that cliff erosion rates should decline as platform width increases or that the long-term cliff retreat rates are constant, an assumption made previously for this site; and b) that Holocene Sea level appears to have been higher than present during the past 6,000 years. This presentation evaluates two possible hypotheses for the confounding width of the modern shore platform in comparison to current cliff erosion rates: 1) that current rates of cliff retreat are faster than past erosion rates (perhaps the TLS captured an unusually fast period of erosion, or perhaps there has been some modern acceleration in cliff erosion rates); 2) that the seaward edge has not remained in its original position or does not reliably indicate the original location of the cliff. These possibilities will be assessed through offshore bathymetric mapping and numerical model experiments.

IntroductionUnmet needs in patients with cancer and their carers are common but poorly identified and addressed. The Needs Assessment Tool-Cancer (NAT-C) is a structured consultation guide to identify and triage patient and carer unmet needs. The NAT-C is validated, but its effectiveness in reducing unmet patient and carer needs in primary care is unknown.Methods and analysisCluster randomised controlled trial with internal pilot and embedded process evaluation to test the clinical and cost effectiveness of the NAT-C in primary care for people with active cancer in reducing unmet patient and carer need, compared with usual care. We will recruit 1080 patients with active cancer (and carers if relevant) from 54 general practices in England.Participating practices will be randomised 1:1 to either deliver an NAT-guided clinical consultation plus usual care or to usual care alone. Consenting participants with active cancer and their carers (if nominated) will be asked to complete study questionnaires at baseline, 1 and 3 months for all, 6 months except for those recruited outside of the last 3 months of recruitment, and attend an NAT-C appointment if allocated to an intervention practice. An internal pilot will assess: site and participant recruitment, intervention uptake and follow-up rates. The primary outcome, the proportion of patients with an unmet need on the Supportive Care Needs Survey Short Form 34 at 3 months postregistration, will be analysed using a multilevel logistic regression. Mixed-methods process evaluation informed by Normalisation Process Theory will use quantitative survey and interview data from clinicians and key stakeholders in cancer care to develop an implementation strategy for nationwide rollout of the NAT-C if the intervention is cost-effective.Ethics and disseminationEthical approval from London-Surrey REC (20/LO/0312). Results will be peer-reviewed, published and made available to research participants.Trial registration numberISRCTN15497400.

Sequences of Holocene marine terraces are widely used in paleoseismic research to understand the timing and magnitude of earthquakes along tectonically active coastal margins worldwide. But the potential for marine terraces to be destroyed through erosion after uplift can result in incomplete records of paleoseismicity as derived from terrace chronologies, leading to misinterpretations of the paleoseismic history of a region. Here, we present measurements across a unique set of exposed bedrock marine terraces in the north-eastern South Island, NZ, to quantify the ages and erosion rates of the surfaces and produce a new chronology for paleoseismic interpretation. Surface exposure dating and multi-nuclide approaches offer the potential to quantify marine terrace preservation and destruction, potentially elucidating where terraces may be missing or removed from a sequence. Needles Point, Marlborough, NZ exhibits three well defined bare rock marine terraces and a gravel covered shore platform which was recently uplifted ~2.5m in the MW 7.8 2016 Kaikōura earthquake. 10Be-derived ages for the platform surface and terrace 1 (T1) align with known ground surface rupturing earthquakes on the Kekerengu fault. T2 and T3 preserve older events not previously identified, potentially extending the earthquake record in this region. However, other known ground surface rupturing earthquakes on the Kekerengu fault are not preserved as terraces at Needles indicating that the preserved terraces at Needles Point do not therefore represent a full record of local paleoseismicity. As such, estimates of fault throw derived from these terraces would over-estimate earthquake magnitude.

Satellite earth observation data has become fundamental in efforts to map coastal change at large geographic scales. Research has generally focussed on extracting the instantaneous waterline position from time-series of satellite images to interpret long-term trends. The use of this proxy can, however, be uncertain because the waterline is sensitive to marine conditions and beach gradient. In addition, the technique disregards potentially useful data stored in surrounding pixels. In this paper, we describe a pixel-based technique to analyse coastal change. A hybrid rule-based and machine learning methodology was developed using a combination of Sentinel multispectral and Synthetic Aperture Radar composite imagery. The approach was then used to provide the first national-scale pixel-based landcover classification for the open coast of New Zealand. Nine landcover types were identified including vegetation, rock, and sedimentary classes that are common on beaches (dark sand, light sand, and gravel). Accuracy was assessed at national scale (overall accuracy: 86%) and was greater than 90% when normalised for class area. Using a combination of optical and Synthetic Aperture Radar data improved overall accuracy by 14% and enhanced the separation of coastal sedimentary classes. Comparison against a previous classification approach of sandy coasts indicated improvements of 30% in accuracy. The outputs and code are freely available and open-source providing a new framework for per-pixel coastal landcover mapping for all regions where public earth observation data is available.

A hallmark of sarcomas is genetic, biologic, and clinical heterogeneity, which is a challenge for preclinical development of therapeutic targets, clinical trial design, and patient care. Because sarcomas comprise over 100 subtypes, a broad comparative genetic analysis of subtypes has been lacking and sarcoma genetic studies have by necessity focused on one or a few subtypes. We will report the results of a comprehensive analysis of somatic genetic alterations detected by a targeted sequencing platform in a single institution cohort of 2,138 patient-specific samples of soft tissue and bone sarcoma representing 45 distinct pathological entities. We determined subtype-specific mutation and copy number (arm and gene level) events with a focus on pathways in which there are therapeutic targets under clinical or preclinical investigation. The most commonly altered pathways are cell cycle control, TP53, PI3K, receptor tyrosine kinase/RAS, and epigenetic regulators (e.g. >40% of uterine leiomyosarcoma [n=165], undifferentiated pleomorphic sarcoma [UPS, n=145] and pleomorphic liposarcoma [n=22]). Subtype-specific associations in rare subtypes include TERT amplification in 41% of intimal sarcoma (n=18) and alterations in chromatin remodeling and histone modifying complexes in uterine adenosarcoma (43% and 36%, respectively; n=14). Epigenetic pathway alterations in common sarcomas were also noted, including an increased frequency of oncogenic alterations in epigenetic regulators in dedifferentiated liposarcoma (DDLS; n=167) (25%) vs. well differentiated liposarcoma (8%; n=48). We evaluated rates of whole genome doubling (WGD), which in subtypes such as UPS and osteosarcoma (n=129) were >45%, which is more frequent than many carcinomas. WGD associated with worse overall survival in metastatic (p=0.042) but not primary samples (p=0.391). Among specific subtypes, WGD was associated with worse overall survival in metastatic UPS (p=0.022). Unsupervised clustering of samples based on genetic features revealed that in some cases sarcomas are more similar to individual tumors of distinct histology than to other sarcomas of the same subtype. For example, UPS and soft tissue leiomyosarcoma (n=125) segregated into multiple genetic clusters (high entropy) compared to others with low entropy (DDLS), which could have implications for future clinical trial interpretation and/or design. We also determined the subtype-specific rate of tumor mutation burden, which was overall low compared to many carcinomas, but notably varied between and within subtypes, with some having a long tail in the upper range of the distribution. Lastly, we assessed targetable alterations on a subtype-specific basis. Together with other ‘multiomic’ approaches, we anticipate this work will motivate preclinical studies of subtype-specific sarcoma biology and potential therapeutic targets and will inform efforts to interpret outcomes in sarcoma clinical trials with respect to underlying genetic subtypes. Citation Format: Benjamin A. Nacev, Francisco Sanchez-Vega, Shaleigh Smith, Cristina Antonescu, Evan Rosenbaum, Hongyu Shi, Cerise Tang, Nicholas Socci, Satshil Rana, Rodrigo Gularte-Merida, Ahmet Zehir, Mrinal Gounder, Timothy Bowler, Anisha Luthra, Bhumika Jadeja, Azusa Okada, Jonathan Strong, Jake Stoller, Jason Chan, Ping Chi, Sandra D'Angelo, Mark Dickson, Ciara Kelly, Mary Louise Keohan, Sujana Movva, Katherine Thornton, Paul Meyers, Leonard Wexler, Emily Slotkin, Julia Glade Bender, Neerav Shukla, Martee Hensley, John Healey, Michael La Quaglia, Kaled Alektiar, Aimee Crago, Sam Yoon, Brian Untch, Sarah Chiang, Narasimhan Agaram, Meera Hameed, Michael Berger, David Solit, Nikolaus Schultz, Marc Ladanyi, Samuel Singer, William Tap. Targeted sequencing of 2,138 bone and soft tissue sarcomas reveals commonly altered pathways, subtype-independent genetic clusters, and potential therapeutic targets [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR012.

The use of geothermal energy for a snow-melting system can be classified into two categories: the direct use of geothermal energy and the extraction of shallow geothermal energy using a geothermal heat pump. The advantages of a snow-melting system that employs geothermal energy include, but are not limited to, that the system: (1) uses energy that is renewable and sustainable, (2) avoids the need for chemical treatments, (3) increases snow removal safety, and (4) lowers CO 2 emissions. Moreover, by providing a sustainable temperature higher than 0 °C, such a system can substantially reduce maintenance costs that are due to pavement freeze-thaw cycles. A few applications of snow-melting systems have been demonstrated successfully in different areas of the world, including the United States. However, the pilot studies for these systems usually involved a massive financial investment. Thus, simulations of a snow-melting system via numerical methods may provide insights about the important components that are needed to develop a successful system. This study employed the COMSOL finite element code to conduct numerical analysis of heat collection pipes in a heat collection system in order to simplify the complex heat transfer mechanisms associated with heat extraction. The study focused on heat production modeling and the simulation of heat collection pipes in a stabilized subsurface temperature zone. The measured data show that the temperature stabilizes at 7 °C six meters below the ground surface regardless of the season. Specifically, this paper presents the computations for the heat production that is required in a snow-melting system for eastern North Dakota based on the average climatic data and precipitation using Chapman and Katunich’s equation. A heat extraction process that utilizes heat collection pipes was simulated based on the seasonal heat requirements. The results of the numerical analysis also show the effects of the thermal properties of soils and fluid properties for a heat collection system. This study found that higher soil thermal conductivity values and a reasonable volumetric flow rate are favorable conditions for a successful heat collection system in design, and the system is feasible for eastern North Dakota.

Treatment records of 94 patients treated in an experimental home-based psychiatric service and 78 control patients in standard care were collected over one year. There was a substantial reduction in in-patient care in the experimental group, both in terms of proportion admitted and duration of admissions, despite similar out-patient and general practice care. The total treatment costs were significantly larger (>50%) for standard care when controlled for by diagnostic grouping. Costs were further examined by including all specialist psychiatric care, and by excluding patients with primary diagnoses of brain damage or alcoholism. Sensitivity analysis explored the effects of increasing the cost of home visits. The relative cost effectiveness of the experimental service persisted. Clinical and social outcome was similar in control and experimental groups.

The genetic basis for the acquisition and retention of innovative morphological structures is of wide interest to evolutionary biologists. Mammals possess specific anatomical features that are not found in other vertebrates, such as external ears, placenta, and hair. It has been inferred that genetic changes in developmental regulatory pathways may contribute, in part, to the evolution of such innovations. In particular, duplicated developmental genes (paralogs) play an important role in generating variations in evolutionarily important morphological structures via deployment of novel cis-regulatory elements. The use of comparative genomics together with mouse transgenic methods provides an effective strategy for interrogating the regulatory landscape of duplicated loci of major developmental genes, as reported here for one of the Dlx gene clusters. The Distal-less (Dlx) genes comprise a homeobox-containing multigene family. The mammalian Dlx gene family consists of six members that are orthologous to the Drosophila Distal-less gene and which are organized into three convergently transcribed (tail-to-tail) bigene clusters; it is presumed that the ancestral bigene cluster was generated initially by tandem gene duplication followed by whole genome duplications (Stock et al., ‘96). Bigene cluster pairs are Dlx1 and Dlx2, Dlx6 and Dlx5, and Dlx41 and Dlx3 (Simeone et al., ‘94; McGuinness et al., ‘96; Nakamura et al., ‘96; Ellies et al., ‘97b; Zerucha and Ekker, 2000), each of which is originally linked to a HOX cluster (HOXD, HOXA, and HOXB, respectively). Dlx expression patterns and functional studies by targeted Dlx deletions provide strong evidence that these transcription factors play major roles in patterning of multiple developmental structures (Merlo et al., 2000; Quint et al., 2000; Zerucha and Ekker, 2000; Zerucha et al., 2000; Depew et al., 2002; Panganiban and Rubenstein, 2002). Though vertebrate Distal-less genes were originally described as being primarily “head” homeobox genes (Duboule, ‘94), they have been shown also to be involved in development of many other structures, that is, limbs, peripheral neurons, whiskers/hair follicles, otic vesicles, teeth, median fins in zebrafish, cement glands in Xenopus, keratinocytes in Xenopus and mice, placenta, genital tubercle and hematopoietic cells in humans (Dirksen et al., ‘93; Akimenko et al., ‘94; Morasso et al., ‘94, ‘99; Porteus et al., ‘94; Shimamoto et al., ‘97; Zerucha et al., ‘97; Park and Morasso, ‘99; Hwang et al., 2008). cis-Regulatory elements confer cell and tissue specificity with regard to the transcriptional machinery and have been implicated as being important for morphological evolution, particularly in the context of embryonic transcription factor genes (Shashikant et al., ‘98; Carroll, 2008; Cretekos et al., 2008; Levine, 2010). Since Dlx genes have been co-opted recurrently in vertebrate evolution by acquisition of novel expression sites, their cis-regulatory element functionality and evolutionary history are of great interest in terms of bauplan divergences in mammals. Delineation of the genomic organization and overlapping expression patterns of the Dlx genes provides a window into understanding the genomic control of development of the many structures described above. Expression patterns of linked Dlx genes have suggested that cis-regulatory elements controlling spatio-temporal expression exist within their respective intergenic regions (Ellies et al., ‘97a). Functional analyses of the intergenic region between paired Dlx genes showed that this region indeed harbors important cis-regulatory elements (Zerucha et al., 2000; Sumiyama et al., 2002; Ghanem et al., 2003). In the Dlx3–4 cluster there are several evolutionarily conserved elements within about 20 kb of the intergenic non-coding region of human and mouse. Moreover, one of these was shown to be a vital enhancer element for branchial arch expression in a Dlx3 specific manner (Sumiyama and Ruddle, 2003). Global alignments using genomic sequences from multiple species is an effective means to identify potentially functional elements in the non-coding regions. The ENCODE project report has shown that a total of 5% of the bases in the genome can be confidently identified as being under evolutionary constraint in mammals, and that approximately 60% of these bases are biologically functional on the basis of experimental assays (ENCODE, 2007). The purpose of the current study was to investigate the rate of change of molecular evolution of cis-elements possibly related to mammalian specific characters of the Dlx3–4 bigene cluster using an extended dataset of 12 diverse mammalian species, including a marsupial and a monotreme. Large-scale sequence comparisons and subsequent constrained motif extraction were conducted with the aim of identifying molecular evolutionary trends in the respective elements. The analyses show that conserved nucleotide elements in intergenic region evolve at markedly different rates and highlight varying patterns of evolutionary divergence among the species. In transgenic mice experiments, we demonstrated that I37-2 cis-regulatory element for branchial arches showed theria-specific conservation and enhancer activity, whereas that of the platypus showed no enhancer activity in branchial arches. The findings serve as guideposts for our ultimate goal to examine the nature in which the cis-regulatory modules in the Dlx bigene clusters act to bring about developmental and gross morphological changes in vertebrate evolution.

Here, we demonstrate how comparative sequence analysis facilitates genome-wide base-pair-level interpretation of individual genetic variation and address two questions of importance for human personal genomics: first, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; and, second, whether population-specific or globally-present polymorphisms contribute more to functional variation in any given individual. Neither has been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair-level resolution for identifying functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary constraint and also analyzed variation within three published human genomes. We find that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments are strongly predictive of reductions in modern-day genetic diversity across a range of annotation categories and across the allele frequency spectrum from rare (10% minor allele frequency). Furthermore, we show that putatively functional variation in an individual genome is dominated by polymorphisms that do not change protein sequence and that originate from our shared ancestral population and commonly segregate in human populations. These observations show that common, noncoding alleles contribute substantially to human phenotypes and that constraint-based analyses will be of value to identify phenotypically relevant variants in individual genomes.

Background: The memory deficits in patients with temporal lobe epilepsy (TLE) are associated with epileptogenic lesions of the temporal lobes, especially hippocampal sclerosis. Memory deficits have been extensively studied in TLE, but the presence of pre-existing temporal lobe abnormality has confounded studies on the relationship between memory dysfunction and seizure activity. Idiopathic generalised epilepsy (IGE) is characterised by primary generalised seizures and is found to occur in the absence of any macroscopic brain abnormalities. IGE is therefore ideal for investigations on the effects of seizure activity on memory and cognition. Aim and methods: Magnetic resonance spectroscopy (MRS) and neuropsychological testing were used to investigate the relationship between epileptic seizures, memory performance and neuronal dysfunction in the temporal lobes of a group of patients with IGE. 30 patients and 15 healthy controls participated in the study. Results: Patients with IGE were found to perform worse than controls on tests of speed of information processing, general cognitive performance and a range of memory tests, including face recognition, word recognition, verbal recall and complex figure recall. The performance of the patient group on the visual recognition and verbal recall sections of the Doors and People Test was found to correlate with MRS ratios of N-acetyl aspartate:choline and N-acetyl aspartate:creatine in the temporal lobes. Conclusion: This result supports the hypothesis that memory deficits in epilepsy may be due to neuronal dysfunction secondary to epileptic activity itself in the absence of any macroscopic lesions in the temporal lobes.

The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (∼1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

The dramatic radiation of sticklebacks in different post-glacial environments provides a unique opportunity to study the molecular mechanisms that underlie rapid evolutionary change in vertebrates. We have developed a number of genomic and genetic tools to facilitate further study of a wide range of morphological, physiological and behavioral traits in sticklebacks. A large collection of microsatellite markers has previously been developed for use in genome-wide linkage mapping of interesting traits in crosses between different stickleback forms. cDNA libraries have been generated and EST sequencing projects have begun to isolate stickleback homologs of developmental control genes. Large insert BAC libraries have been built to compare chromosome regions of interest from both anadromous and freshwater stickleback populations. Large scale fingerprinting of one of these libraries has been used to assemble overlapping contigs of BAC clones for chromosome walking and positional cloning. Together with recent development of methods to make transgenic sticklebacks, these tools should make it possible to identify the molecular basis of many different evolutionary traits in stickleback, and to begin to answer longstanding questions about the numbers and types of mutations that control the appearance of new morphological, physiological, and behavioral traits during vertebrate evolution.

Attempts to identify regulatory sequences in the human genome have involved experimental and computational methods such as cross-species sequence comparisons and the detection of transcription factor binding-site motifs in coexpressed genes. Although these strategies provide information on which genomic regions are likely to be involved in gene regulation, they do not give information on their functions. We have developed a functional selection for promoter regions in the human genome that uses a retroviral plasmid library-based system. This approach enriches for and detects promoter function of isolated DNA fragments in an in vitro cell culture assay. By using this method, we have discovered likely promoters of known and predicted genes, as well as many other putative promoter regions based on the presence of features such as CpG islands. Comparison of sequences of 858 plasmid clones selected by this assay with the human genome draft sequence indicates that a significantly higher percentage of sequences align to the 500-bp segment upstream of the transcription start sites of known genes than would be expected from random genomic sequences. We also observed enrichment for putative promoter regions of genes predicted in at least two annotation databases and for clones overlapping with CpG islands. Functional validation of randomly selected clones enriched by this method showed that a large fraction of these putative promoters can drive the expression of a reporter gene in transient transfection experiments. This method promises to be a useful genome-wide function-based approach that can complement existing methods to look for promoters.

Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and oligonucleotide microarrays will accelerate the molecular analysis of zebrafish mutations.[Supplemental material is available online atwww.genome.org. The sequence data described in this paper have been submitted to dbSNP under accession nos. 5103507–5105537. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Postlethwait, C.-B. Chien, C. Kimmel, L. Maves, and M. Westerfield.]

Faujasite type zeolite membranes were synthesized on porous ceramic alumina supports by using direct (in situ) and secondary (seeded) growth methods. In the secondary growth method a seed layer of ZSM-2 nanocrystals (prepared according to a report by Schoeman et al. J. Colloid Interface Sci. 1995, 170, 449–456) was deposited on the surface of the support before the hydrothermal growth. For both in situ and secondary growth, the mixture composition was 4.17 Na 2 O:1.0 Al 2 O 3 :10 TEA (triethanol ammonium):1.87 SiO 2 :460 H 2 O. X-ray diffraction (XRD), scanning electron microscopy (SEM), and electron microprobe analysis (EPMA), indicate well intergrown 5–30 μm thick FAU films with Si/Al ∼1–1.5. The separation of saturated/unsaturated hydrocarbon mixtures is demonstrated over a range of temperatures (40–160°C). The mixtures examined (and the corresponding equimolar mixture separation factors) are benzene/cyclohexane (160), benzene/ n -hexane (144), toluene/ n -heptane (45), propylene/propane (6.2), and ethylene/methane (8.4). In all cases, the membranes are unsaturated hydrocarbon permselective. With equimolar feed mixtures (5 kPa/5 kPa benzene/cyclohexane) and in the temperature range 65–160°C, the membranes exhibit separation factor of 20–160 with the benzene flux in the range 10 −4 –10 −3 mol m −2 s −1 . Decreasing the total feed partial pressure (0.31/0.31 kPa benzene/cyclohexane) reduces both separation factor (12) and benzene flux. Similar trend is observed when the benzene/cyclohexane ratio in the feed mixture (0.5/9.5 kPa benzene/cyclohexane) is reduced. A sorption diffusion model based on the Stefan–Maxwell formulation has also been employed to show that the benzene/cyclohexane separation can mainly be attributed to differences of their adsorption properties.

Introduction: Patients (Pts) with asymptomatic (ASX) carotid stenosis have 3 treatment (Rx) options (surgery[CEA], stenting[CAS], and medical therapy alone[Med],) each with its own risks and benefits (R/Bs). In prior work, many ASX Pts who had CEA did not understand the disease (Dz), their Rx options, and associated R/Bs. Decision aids (DAs) have been shown in other conditions to foster more informed Rx choices. Objective: To develop and assess the impact of a DA on knowledge of Dz, Rx options, and DA satisfaction. Methods: We created a multimedia, web-based DA to explain ASX carotid Dz, Rx options, and associated R/Bs. The DA was refined and vetted by experts in neurology, vascular/neuro-surgery, internal medicine, decision making, and patient education. The DA included: text, anatomic graphics, pictographs of short term and long R/Bs of CEA v. Med, and Pt and MD video testimonials. We tested it in an online Pt panel in those: 55+ yrs with ≥ 1 risk factor for carotid Dz (HTN, DM, CHOL, CAD, PVD). Post-viewing knowledge of key educational messages incl. Rx options, associated R/Bs, and DA satisfaction were assessed with validated instruments. Results: Overall, 1778 of 1843 completed viewing the 40 minute DA (96%). Mean age was 67 yrs, 51% female, 91% White, and 24% ≤high school degree. Pts correctly answered 68% of the 19 knowledge items. The DA was well-liked with mean score of 4.4 (out of 5) on a 10 item DA satisfaction score and 4.3 (out of 5) on a 7 item DA helpfulness score. Pts correctly grasped most gist messages including that: not everyone needed CEA (99%), there was no best Rx it depends on the Pt (92%), they had time to make a decision (86%), CEA can cause stroke (92%), CEA can cause death (91%), and carotid Dz can cause stroke (83%). They had trouble understanding the time trade of CEA v. Med-only 55% correctly said CEA was riskier in the short term, and 50% that Med was riskier in the long term. Overall, 74% said they would choose Med. Pts who were younger, female, White, higher education, or with family/friends with stroke or CAD had higher knowledge scores. Conclusions: A web-based DA was effective in conveying most gist messages regarding making an informed decision in ASX carotid Dz. The next step is testing the impact of the DA in Pts facing a real decision about revascularization.

BACKGROUND: Uveal melanoma exhibits a high incidence of metastases; and, to date, there is no systemic therapy that clearly improves outcomes. The anticytotoxic T-lymphocyte-associated protein 4 (anti-CTLA-4) antibody ipilimumab is a standard of care for metastatic melanoma; however, the clinical activity of CTLA-4 inhibition in patients with metastatic uveal melanoma is poorly defined. METHODS: To assess ipilimumab in this setting, the authors performed a multicenter, retrospective analysis of 4 hospitals in the United States and Europe. Clinical characteristics, toxicities, and radiographic disease burden, as determined by central, blinded radiology review, were evaluated. RESULTS: Thirty-nine patients with uveal melanoma were identified, including 34 patients who received 3 mg/kg ipilimumab and 5 who received 10 mg/kg ipilimumab. Immune-related response criteria and modified World Health Organization criteria were used to assess the response rate (RR) and the combined response plus stable disease (SD) rate after 12 weeks, after 23 weeks, and overall (median follow-up, 50.4 weeks [12.6 months]). At week 12, the RR was 2.6%, and the response plus SD rate was 46.%; at week 23, the RR was 2.6%, and the response plus SD rate was 28.2%. There was 1 complete response and 1 late partial response (at 100 weeks after initial SD) for an immune-related RR of 5.1%. Immune-related adverse events were observed in 28 patients (71.8%) and included 7 (17.9%) grade 3 and 4 events. Immune-related adverse events were more frequent in patients who received 10 mg/kg ipilimumab than in those who received 3 mg/kg ipilimumab. The median overall survival from the first dose of ipilimumab was 9.6 months (95% confidence interval, 6.3-13.4 months; range, 1.6-41.6 months). Performance status, lactate dehydrogenase level, and an absolute lymphocyte count ≥ 1000 cells/μL at week 7 were associated significantly with survival. CONCLUSIONS: In this multicenter, retrospective analysis of 4 hospitals in the United States and Europe of patients with uveal melanoma, durable responses to ipilimumab and manageable toxicity were observed.

The mammalian Dlx3 and Dlx4 genes are configured as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that largely reside within the intergenic region of the cluster. Previous work revealed that there are conspicuously conserved elements within the intergenic region of the Dlx3–4 bigene clusters of mouse and human. In this paper we have extended these analyses to include 12 additional mammalian taxa (including a marsupial and a monotreme) in order to better define the nature and molecular evolutionary trends of the coding and non-coding functional elements among morphologically divergent mammals. Dlx3–4 regions were fully sequenced from 12 divergent taxa of interest. We identified three theria-specific amino acid replacements in homeodomain of Dlx4 gene that functions in placenta. Sequence analyses of constrained nucleotide sites in the intergenic non-coding region showed that many of the intergenic conserved elements are highly conserved and have evolved slowly within the mammals. In contrast, a branchial arch/craniofacial enhancer I37-2 exhibited accelerated evolution at the branch between the monotreme and therian common ancestor despite being highly conserved among therian species. Functional analysis of I37-2 in transgenic mice has shown that the equivalent region of the platypus fails to drive transcriptional activity in branchial arches. These observations, taken together with our molecular evolutionary data, suggest that theria-specific episodic changes in the I37-2 element may have contributed to craniofacial innovation at the base of the mammalian lineage.

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature., National Human Genome Research Institute (U.S.), National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568)

The value of "intelligent" (i.e., digital, automated) energy solutions is now undisputed. Across the industry, these solutions are known by different names, such as: I-Field, Digital Oilfield, Asset of the Future, Field of the Future, Integrated Operations, and Integrated Oilfield Solutions. But regardless of what name is used, the expectation remains the same: technical staff are now expected to work in new ways––with new or automated processes, with new people, with new technologies, in new office operational facilities, and with new responsibilities––and meet expectations of new levels of performance and effectiveness in their jobs.However, in the author's experience, there is widespread uncertainty among staff using the new technology. Specifically, there is confusion about job roles and responsibilities in the constantly changing technical work environment. While uncertainty eats away at staff morale, confusion poses a larger risk of failure, both at an individual and project level. Moreover, the success of hard-won Integrated Oilfield Solution project mandates comes under jeopardy––but this can be rectified if due care and attention is given to all stakeholders and end users who have an influence on the acceptance and use of the technology.This paper examines some of the most recent cases of Integrated Oilfield technology implementations, either individual projects or technology campaigns in terms of "the people aspects". The author proposes as a hypothesis, a model for Change Management and tests its completeness and exhaustiveness against these technology implementation cases.The paper concludes that if an all-inclusive Change Management Framework is adopted and therefore those issues relating to the engagement of people are addressed as a concerted effort at the beginning of an Integrated Oilfield Project, and these efforts are continued throughout the life of the project and into post implementation support, that projects will have a greater chance of success and sustainability.

The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a “living fossil.” An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth Latimeria menadoensis . Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species.

Results for the classification of jets obtained with the use feed-forward neural networks are reviewed with particular attention to model-dependence, flavor sensitivity and Et-dependence. First results obtained with a Kohonen-type network are also presented and both are compared with those obtained with a Fisher discriminant.

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view about chromatin structure has emerged, including its interrelationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded novel mechanistic and evolutionary insights about the functional landscape of the human genome. Together, these studies are defining a path forward to pursue a more-comprehensive characterisation of human genome function.

BackgroundAdvance care planning may help patients receive treatments that better align with their goals for care. We developed a Web-based decision aid called InformedTogether to facilitate shared advance care planning between chronic obstructive pulmonary disease (COPD) patients and their doctors. ObjectiveOur objective was to assess the usability of the InformedTogether decision aid, including whether users could interact with the decision aid to engage in tasks required for shared decision making, whether users found the decision aid acceptable, and implications for redesign. MethodsWe conducted an observational study with 15 patients and 8 doctors at two ethnically and socioeconomically diverse outpatient clinics. Data included quantitative and qualitative observations of patients and doctors using the decision aid on tablet or laptop computers and data from semistructured interviews. Patients were shown the decision aid by a researcher acting as the doctor. Pulmonary doctors were observed using the decision aid independently and asked to think aloud (ie, verbalize their thoughts). A thematic analysis was implemented to explore key issues related to decision aid usability. ResultsAlthough patients and doctors found InformedTogether acceptable and would recommend that doctors use the decision aid with COPD patients, many patients had difficulty understanding the icon arrays that were used to communicate estimated prognoses and could not articulate the definitions of the two treatment choices—Full Code and Do Not Resuscitate (DNR). Minor usability problems regarding content, links, layout, and consistency were also identified and corresponding recommendations were outlined. In particular, participants suggested including more information about potential changes in quality of life resulting from the alternative advance directives. Some doctor participants thought the decision aid was too long and some thought it may cause nervousness among patients due to the topic area. ConclusionsA decision aid for shared advance care planning for severe COPD was found acceptable to most COPD patients and their doctors. However, many patient participants did not demonstrate understanding of the treatment options or prognostic estimates. Many participants endorsed the use of the decision aid between doctors and their patients with COPD, although they desired more information about quality of life. The design must optimize comprehensibility, including revising the presentation of statistical information in the icon array, and feasibility of integration into clinical workflow, including shortening the decision aid.

Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling armor plate patterning in wild threespine sticklebacks. Mapping, sequencing, and transgenic studies show that the Ectodysplasin (EDA) signaling pathway plays a key role in evolutionary change in natural populations and that parallel evolution of stickleback low-plated phenotypes at most freshwater locations around the world has occurred by repeated selection of Eda alleles derived from an ancestral low-plated haplotype that first appeared more than two million years ago. Members of this clade of low-plated alleles are present at low frequencies in marine fish, which suggests that standing genetic variation can provide a molecular basis for rapid, parallel evolution of dramatic phenotypic change in nature.

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

Background: Many different environmental and genetic sex-determination mechanisms are found in nature. Closely related species can use different master sex-determination switches, suggesting that these developmental pathways can evolve very rapidly. Previous cytological studies suggest that recently diverged species of stickleback fish have different sex chromosome complements. Here, we investigate the genetic and chromosomal mechanisms that underlie sex determination in the threespine stickleback ( Gasterosteus aculeatus ). Results: Genome-wide linkage mapping identifies a single chromosome region at the distal end of linkage group (LG) 19, which controls male or female sexual development in threespine sticklebacks. Although sex chromosomes are not cytogenetically visible in this species, several lines of evidence suggest that LG 19 is an evolving sex chromosome system, similar to the XX female/XY male system in many other species: (1) males are consistently heterozygous for unique alleles in this region; (2) recombination between loci linked to the sex-determination region is reduced in male meiosis relative to female meiosis; (3) sequence analysis of X- and Y-specific bacterial artificial chromosome (BAC) clones from the sex-determination region reveals many sequence differences between the X- and Y-specific clones; and (4) the Y chromosome has accumulated transposable elements and local duplications. Conclusions: Taken together, our data suggest that threespine sticklebacks have a simple chromosomal mechanism for sex determination based on a nascent Y chromosome that is less than 10 million years old. Further analysis of the stickleback system will provide an exciting window into the evolution of sex-determination pathways and sex chromosomes in vertebrates.