Permeability-porosity relationships in seafloor vent deposits : dependence on pore evolution processes

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): B05208, doi:10.1029/2006JB004716.Systematic laboratory measurements of permeability and porosity were conducted on three large vent structures from the Mothra Hydrothermal vent field on the Endeavor segment of the Juan de Fuca Ridge. Geometric means of permeability values obtained from a probe permeameter are 5.9 × 10−15 m2 for Phang, a tall sulfide-dominated spire that was not actively venting when sampled; 1.4 × 10−14 m2 for Roane, a lower-temperature spire with dense macrofaunal communities growing on its sides that was venting diffuse fluid of <300°C; and 1.6 × 10−14 m2 for Finn, an active black smoker with a well-defined inner conduit that was venting 302°C fluids prior to recovery. Twenty-three cylindrical cores were then taken from these vent structures. Permeability and porosity of the drill cores were determined on the basis of Darcy's law and Boyle's law, respectively. Permeability values range from ∼10−15 to 10−13 m2 for core samples from Phang, from ∼10−15 to 10−12 m2 for cores from Roane, and from ∼10−15 to 3 × 10−13 m2 for cores from Finn, in good agreement with the probe permeability measurements. Permeability and porosity relationships are best described by two different power law relationships with exponents of ∼9 (group I) and ∼3 (group II). Microstructural analyses reveal that the difference in the two permeability-porosity relationships reflects different mineral precipitation processes as pore space evolves within different parts of the vent structures, either with angular sulfide grains depositing as aggregates that block fluid paths very efficiently (group I), or by late stage amorphous silica that coats existing grains and reduces fluid paths more gradually (group II). The results suggest that quantification of permeability and porosity relationships leads to a better understanding of pore evolution processes. Correctly identifying permeability and porosity relationships is an important first step toward accurately estimating fluid distribution, flow rate, and environmental conditions within seafloor vent deposits, which has important consequences for chimney growth and biological communities that reside within and on vent structures.Support from the National Science Foundation under grants NSF OCE-9986456 (W.Z. and M.K.T.) and NSF OCE-0327488 (P.R.C.) is gratefully acknowledged. We also thank the WHOI summer student fellowship for providing support to H.G

The Cleft revealed: geologic, magnetic, and morphologic evidence for construction of upper oceanic crust along the southern Juan de Fuca Ridge

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 7 (2006): Q04003, doi:10.1029/2005GC001038.The geology and structure of the Cleft Segment of the Southern Juan de Fuca Ridge (JdFR) have been examined using high-resolution mapping systems, observations by remotely operated vehicle (ROV), ROV-mounted magnetometer, and the geochemical analysis of recovered lavas. Bathymetric mapping using multibeam (EM300) coupled with in situ observations that focused on near-axis and flank regions provides a detailed picture of 0 to 400 ka upper crust created at the southern terminus of the JdFR. A total of 53 rock cores and 276 precisely located rock or glass samples were collected during three cruises that included sixteen ROV dives. Our observations of the seafloor during these dives suggest that many of the unfaulted and extensive lava flows that comprise and/or cap the prominent ridges that flank the axial valley emanate from ridge parallel faults and fissures that formed in the highly tectonized zone that forms the walls of the axial valley. The geochemically evolved and heterogeneous nature of these near-axis and flank eruptions is consistent with an origin within the cooler distal edges of a crustal magma chamber or mush zone. In contrast, the most recent axial eruptions are more primitive (higher MgO), chemically homogeneous lobate, sheet, and massive flows that generate a distinct magnetic high over the axial valley. We suggest that the syntectonic capping volcanics observed off-axis were erupted from near-axis and flank fissures and created a thickened extrusive layer as suggested by the magnetic and seismic data. This model suggests that many of the lavas that comprise the elevated ridges that bound the axial valley of the Cleft Segment were erupted during the collapse of a magmatic cycle not during the robust phase that established a new magmatic cycle.This research has been partially supported by a NSF grant to M. Perfit (OCE-0221541). M. Tivey acknowledges support from WHOI’s Mellon grant for Independent Study. Support for D. Stakes, T. Ramirez, D. Caress, and N. Maher and for the entire field program was provided by funds to MBARI from the Lucille and David Packard Foundation

Small molecule inhibition of p38 MAP kinase extends the replicative life span of human ATR-Seckel syndrome fibroblasts

Ataxia-telangiectasia and rad3 (ATR)-related Seckel syndrome is associated with growth retardation and premature aging features. ATR-Seckel fibroblasts have a reduced replicative capacity in vitro and an aged morphology that is associated with activation of stress-associated p38 mitogen-activated protein kinase and phosphorylated HSP27. These phenotypes are prevented using p38 inhibitors, with replicative capacity restored to the normal range. However, this stressed phenotype is retained in telomerase-immortalized ATR-Seckel fibroblasts, indicating that it is independent of telomere erosion. As with normal fibroblasts, senescence in ATR-Seckel is bypassed by p53 abrogation. Young ATR-Seckel fibroblasts show elevated levels of p21WAF1, p16INK4A, phosphorylated actin-binding protein cofilin, and phosphorylated caveolin-1, with small molecule drug inhibition of p38 reducing p16INK4A and caveolin-1 phosphorylation. In conclusion, ATR-Seckel fibroblasts undergo accelerated aging via stress-induced premature senescence and p38 activation that may underlie certain clinical features of Seckel syndrome, and our data suggest a novel target for pharmacological intervention in this human syndrome

Sulfide geochronology along the Endeavour Segment of the Juan de Fuca Ridge

Forty-nine hydrothermal sulfide-sulfate rock samples from the Endeavour Segment of the Juan de Fuca Ridge, northeastern Pacific Ocean, were dated by measuring the decay of 226Ra (half-life of 1600 years) in hydrothermal barite to provide a history of hydrothermal venting at the site over the past 6000 years. This dating method is effective for samples ranging in age from ∼200 to 20,000 years old and effectively bridges an age gap between shorter- and longer-lived U-series dating techniques for hydrothermal deposits. Results show that hydrothermal venting at the active High Rise, Sasquatch, and Main Endeavour fields began at least 850, 1450, and 2300 years ago, respectively. Barite ages of other inactive deposits on the axial valley floor are between ∼1200 and ∼2200 years old, indicating past widespread hydrothermal venting outside of the currently active vent fields. Samples from the half-graben on the eastern slope of the axial valley range in age from ∼1700 to ∼2925 years, and a single sample from outside the axial valley, near the westernmost valley fault scarp is ∼5850 ± 205 years old. The spatial relationship between hydrothermal venting and normal faulting suggests a temporal relationship, with progressive younging of sulfide deposits from the edges of the axial valley toward the center of the rift. These relationships are consistent with the inward migration of normal faulting toward the center of the valley over time and a minimum age of onset of hydrothermal activity in this region of 5850 years

Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

Leaving surgical training : some of the reasons are in surgery

In 2014, the Royal Australasian College of Surgeons identified, through internal analysis, a considerable attrition rate within its Surgical Education and Training programme. Within the attrition cohort, choosing to leave accounted for the majority. Women were significantly over-represented. It was considered important to study these ‘leavers’ if possible. An external group with medical education expertise were engaged to do this, a report that is now published and titled ‘A study exploring the reasons for and experiences of leaving surgical training’. During this time, the Royal Australasian College of Surgeons came under serious external review, leading to the development of the Action Plan on Discrimination, Bullying and Sexual Harassment in the Practice of Surgery, known as the Building Respect, Improving Patient Safety (BRIPS) action plan. The ‘Leaving Training Report’, which involved nearly one-half of all voluntary ‘leavers’, identified three major themes that were pertinent to leaving surgical training. Of these, one was about surgery itself: the complexity, the technical, decision-making and lifestyle demands, the emotional aspects of dealing with seriously sick patients and the personal toll of all of this. This narrative literature review investigates these aspects of surgical education from the trainees’ perspective