Deep seafloor arrivals : an unexplained set of arrivals in long-range ocean acoustic propagation

Author Posting. © Acoustical Society of America, 2009. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 126 (2009): 599-606, doi:10.1121/1.3158826.Receptions, from a ship-suspended source (in the band 50–100 Hz) to an ocean bottom seismometer (about 5000 m depth) and the deepest element on a vertical hydrophone array (about 750 m above the seafloor) that were acquired on the 2004 Long-Range Ocean Acoustic Propagation Experiment in the North Pacific Ocean, are described. The ranges varied from 50 to 3200 km. In addition to predicted ocean acoustic arrivals and deep shadow zone arrivals (leaking below turning points), “deep seafloor arrivals,” that are dominant on the seafloor geophone but are absent or very weak on the hydrophone array, are observed. These deep seafloor arrivals are an unexplained set of arrivals in ocean acoustics possibly associated with seafloor interface waves.The LOAPEX source deployments, the moored DVLA receiver deployments, and some post-cruise data reduction and analysis were funded by the Office of Naval Research under Award Nos. N00014-1403-1-0181, N00014-03-1-0182, and N00014-06-1-0222. Additional post-cruise analysis support was provided to RAS through the Edward W. and Betty J. Scripps Chair for Excellence in Oceanography. The OBS/Hs used in the experiment were provided by Scripps Institution of Oceanography under the U.S. National Ocean Bottom Seismic Instrumentation Pool (SIO-OBSIP—http://www.obsip.org). To cover the costs of the OBS/H deployments funds were paid to SIO-OBSIP from the National Science Foundation and from the Woods Hole Oceanographic Institution Deep Ocean Exploration Institute

Heritability and mechanisms of n-3 long chain polyunsaturated fatty acid deposition in the flesh of Atlantic salmon

N-3 long chain polyunsaturated fatty acids (n-3LC-PUFA) are essential components of vertebrate membrane lipids and are crucially deficient in modern Western diets. The main human dietary source for n-3LC-PUFA is fish and seafood, particularly oily fish and over 50% of global fish production is currently supplied by aquaculture. However, increasing pressure to include vegetable oils, which are devoid of n-3LC-PUFA, in aquaculture feeds reduces the content of these crucial nutrients in farmed fish flesh. The aim of this study was to measure the heritability and infer mechanisms determining flesh n-3LC-PUFA content in Atlantic salmon. This was achieved by analysing flesh lipid parameters in 48 families of Atlantic salmon, and by measuring differences in hepatic mRNA expression in families with high and low flesh n-3LC-PUFA. The results show that flesh n-3LC-PUFA level is a highly heritable trait (h2 = 0.77±0.14) and indicate the involvement of increased lipid transport, most likely in the form of very low density lipoprotein (VLDL) from liver. This increase in lipid transport may be associated with increased activity of a transcription factor, hepatic nuclear factor 4α (HNF4α), possibly as a result of family differences in transforming growth factor β1 (Tgfβ1) signalling. This study paves the way for identification of quantitative trait loci and gene interaction networks that are associated with levels of n-3LC-PUFA in fish flesh. Such markers can be used to assist the sustainable production of Atlantic salmon and provide optimal levels of critical nutrients for human consumers

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution

Mechanistic evaluation of primary human hepatocyte culture using global proteomic analysis reveals a selective dedifferentiation profile

© 2016 The Author(s)The application of primary human hepatocytes following isolation from human tissue is well accepted to be compromised by the process of dedifferentiation. This phenomenon reduces many unique hepatocyte functions, limiting their use in drug disposition and toxicity assessment. The aetiology of dedifferentiation has not been well defined, and further understanding of the process would allow the development of novel strategies for sustaining the hepatocyte phenotype in culture or for improving protocols for maturation of hepatocytes generated from stem cells. We have therefore carried out the first proteomic comparison of primary human hepatocyte differentiation. Cells were cultured for 0, 24, 72 and 168 h as a monolayer in order to permit unrestricted hepatocyte dedifferentiation, so as to reveal the causative signalling pathways and factors in this process, by pathway analysis. A total of 3430 proteins were identified with a false detection rate of <1 %, of which 1117 were quantified at every time point. Increasing numbers of significantly differentially expressed proteins compared with the freshly isolated cells were observed at 24 h (40 proteins), 72 h (118 proteins) and 168 h (272 proteins) (p < 0.05). In particular, cytochromes P450 and mitochondrial proteins underwent major changes, confirmed by functional studies and investigated by pathway analysis. We report the key factors and pathways which underlie the loss of hepatic phenotype in vitro, particularly those driving the large-scale and selective remodelling of the mitochondrial and metabolic proteomes. In summary, these findings expand the current understanding of dedifferentiation should facilitate further development of simple and complex hepatic culture systems

Small Molecule Activation by Uranium Tris(aryloxides): Experimental and Computational Studies of Binding of N-2, Coupling of CO, and Deoxygenation Insertion of CO2 under Ambient Conditions

Previously unanticipated dinitrogen activation is exhibited by the well-known uranium tris(aryloxide) U(ODtbp)(3), U(OC6H3-Bu-2(t)-2,6)(3), and the tri-tert-butyl analogue U(OTtbp)(3), U(OC6H2-Bu-3(t)-2,4,6)(3), in the form of bridging, side-on dinitrogen complexes [U(OAr)(3)](2)(mu-eta(2):eta(2)-N-2), for which the tri-tert-butyl N-2 complex is the most robust U-2(N-2) complex isolated to date. Attempted reduction of the tris(aryloxide) complex under N-2 gave only the potassium salt of the uranium(III) tetra(aryloxide) anion, K[U(OAr)(4)], as a result of ligand redistribution. The solid-state structure is a polymeric chain formed by each potassium cation bridging two arenes of adjacent anions in an eta(6) fashion. The same uranium tris(aryloxides) were also found to couple carbon monoxide under ambient conditions to give exclusively the ynediolate [OCCO](2-) dianion in [U(OAr)(3)](2)(mu-eta(1):eta(1)-C2O2), in direct analogy with the reductive coupling recently shown to afford [U{N(SiMe3)(2)}(3)](2)(mu-eta(1):eta(1)-C2O2). The related U-III complexes U{N(SiPhMe2)(2)}(3) and U{CH(SiMe3)(2)}(3) however do not show CO coupling chemistry in our hands. Of the aryloxide complexes, only the U(OC6H2-Bu-3(t)-2,4,6)(3) reacts with CO2 to give an insertion product containing bridging oxo and aryl carbonate moieties, U-2(OTtbp)(4)(mu-O)(mu-eta(1):eta(1)-O2COC6H2-Bu-3(t)-2,4,6)(2), which has been structurally characterized. The presence of coordinated N-2 in [U(OTtbp)(3)](2)(N-2) prevents the occurrence of any reaction with CO2, underscoring the remarkable stability of the N-2 complex. The di-tert-butyl aryloxide does not insert CO2, and only U(ODtbp)(4) was isolated. The silylamide also reacts with carbon dioxide to afford U(OSiMe3)(4) as the only uranium-containing material. GGA and hybrid DFT calculations, in conjunction with topological analysis of the electron density, suggest that the U-N-2 bond is strongly polar, and that the only covalent U -> N-2 interaction is pi backbonding, leading to a formal (U-IV)(2)(N-2)(2-) description of the electronic structure. The N-N stretching wavenumber is preferred as a metric of N-2 reduction to the N-N bond length, as there is excellent agreement between theory and experiment for the former but poorer agreement for the latter due to X-ray crystallographic underestimation of r(N-N). Possible intermediates on the CO coupling pathway to [U(OAr)(3)](2)(mu-C2O2) are identified, and potential energy surface scans indicate that the ynediolate fragment is more weakly bound than the ancillary ligands, which may have implications in the development of low-temperature and pressure catalytic CO chemistry

Diagnosing Appendicitis: Evidence-Based Review of the Diagnostic Approach in 2014

Introduction: Acute appendicitis is the most common abdominal emergency requiring emergency surgery. However, the diagnosis is often challenging and the decision to operate, observe or further work-up a patient is often unclear. The utility of clinical scoring systems (namely the Alvarado score), laboratory markers, and the development of novel markers in the diagnosis of appendicitis remains controversial. This article presents an update on the diagnostic approach to appendicitis through an evidence-based review. Methods: We performed a broad Medline search of radiological imaging, the Alvarado score, common laboratory markers, and novel markers in patients with suspected appendicitis. Results: Computed tomography (CT) is the most accurate mode of imaging for suspected cases of appendicitis, but the associated increase in radiation exposure is problematic. The Alvarado score is a clinical scoring system that is used to predict the likelihood of appendicitis based on signs, symptoms and laboratory data. It can help risk stratify patients with suspected appendicitis and potentially decrease the use of CT imaging in patients with certain Alvarado scores. White blood cell (WBC), C-reactive protein (CRP), granulocyte count and proportion of polymorphonuclear (PMN) cells are frequently elevated in patients with appendicitis, but are insufficient on their own as a diagnostic modality. When multiple markers are used in combination their diagnostic utility is greatly increased. Several novel markers have been proposed to aid in the diagnosis of appendicitis; however, while promising, most are only in the preliminary stages of being studied. Conclusion: While CT is the most accurate mode of imaging in suspected appendicitis, the accompanying radiation is a concern. Ultrasound may help in the diagnosis while decreasing the need for CT in certain circumstances. The Alvarado Score has good diagnostic utility at specific cutoff points. Laboratory markers have very limited diagnostic utility on their own but show promise when used in combination. Further studies are warranted for laboratory markers in combination and to validate potential novel markers. [West J Emerg Med. 2014;15(7):–0.

Diagnosing Appendicitis: Evidence-Based Review of the Diagnostic Approach in 2014

Introduction: Acute appendicitis is the most common abdominal emergency requiring emergency surgery. However, the diagnosis is often challenging and the decision to operate, observe or further work-up a patient is often unclear. The utility of clinical scoring systems (namely the Alvarado score), laboratory markers, and the development of novel markers in the diagnosis of appendicitis remains controversial. This article presents an update on the diagnostic approach to appendicitis through an evidence-based review. Methods: We performed a broad Medline search of radiological imaging, the Alvarado score, common laboratory markers, and novel markers in patients with suspected appendicitis. Results: Computed tomography (CT) is the most accurate mode of imaging for suspected cases of appendicitis, but the associated increase in radiation exposure is problematic. The Alvarado score is a clinical scoring system that is used to predict the likelihood of appendicitis based on signs, symptoms and laboratory data. It can help risk stratify patients with suspected appendicitis and potentially decrease the use of CT imaging in patients with certain Alvarado scores. White blood cell (WBC), C-reactive protein (CRP), granulocyte count and proportion of polymorphonuclear (PMN) cells are frequently elevated in patients with appendicitis, but are insufficient on their own as a diagnostic modality. When multiple markers are used in combination their diagnostic utility is greatly increased. Several novel markers have been proposed to aid in the diagnosis of appendicitis; however, while promising, most are only in the preliminary stages of being studied. Conclusion: While CT is the most accurate mode of imaging in suspected appendicitis, the accompanying radiation is a concern. Ultrasound may help in the diagnosis while decreasing the need for CT in certain circumstances. The Alvarado Score has good diagnostic utility at specific cutoff points. Laboratory markers have very limited diagnostic utility on their own but show promise when used in combination. Further studies are warranted for laboratory markers in combination and to validate potential novel markers. [West J Emerg Med. 2014;15(7):–0.

A combined Richter's and de Garengeot's hernia

INTRODUCTION: de Garengeot's hernia is very rare. Richter's hernia is responsible for 10% of acute strangulated hernias. PRESENTATION OF CASE: A 91-year-old woman with three days of abdominal distention was found on computed tomogram to have an incarcerated femoral hernia. Operation revealed a de Garengeot's hernia combined with a Richter's hernia of small bowel. Primary repair was performed along with appendectomy. DISCUSSION: We discuss these rare hernias, not previously reported in combination, and options for management. CONCLUSION: Combined de Garengeot's and Richter's hernias are rare, represent a significant diagnostic challenge, and should be repaired urgently to prevent ischemic bowel, or limit contamination if ischemia is already present. Use of computed tomography will likely lead to increased pre-operative diagnosis of this rare entity

Photoelectron spectroscopic determination of the energy bandwidths of high-order harmonics (7th–55th) produced by an ultrafast laser in neon

The energy bandwidths of high-order harmonics of a Ti:sapphire ultrafast laser are extracted from electron kinetic-energy measurements of the photoionization of gas-phase atoms and molecules. High-order harmonics of the 70 fs, 800 nm laser are produced by focusing &#8776;2.5 mJ pulses into a jet of neon gas and are frequency-separated by a grazing-incidence grating. Photoelectrons resulting from the ionization of gaseous samples are energy-analyzed with a magnetic bottle time-of-flight spectrometer. Energy broadening of the photoelectron peaks at low kinetic energies are a direct result of the energy bandwidths of the harmonics. The energy bandwidths of the harmonics are found to increase from 0.11(&#177;0.03) eV (7th harmonic) to 0.37(&#177;0.03) eV (45th harmonic) in a gradual manner. The higher-order harmonics (47th-55th) appear to reach a plateau at a value of &#8776;0.43 eV. Though a full theoretical treatment of bandwidths of the harmonics for the 70 fs driving pulse regime does not exist, the theories developed for shorter pulses(&#60;&#732;30 fs) can give insight into the observed results