Measurement of Gas Exchange, Stream Metabolism, and Carbon Fluxes of Headwater Streams

Freshwater systems are an important component of the global carbon cycle as they outgas disproportionately large quantities of carbon compared to the terrestrial landscape. Of particular importance are headwater streams, which represent roughly 90% of the channel network by length and have been conservatively estimated to outgas roughly 36% of the carbon dioxide (CO2) that is evaded from rivers and streams globally. We investigated carbon fluxes of a second order headwater stream that drains a 96 ha forested watershed in western Oregon, USA. Total inorganic carbon imports and exports were estimated to be 1294 kg C yr-1 (130 kg C ha-1yr-1). Influx from hillslope runoff and groundwater was measured to be 65.6 kg C ha-1yr-1, 50% of total imports. The remaining imports were split between stream metabolism at 26% (33.8 kg C ha-1yr-1) and near stream riparian sources at 23% (29.9 kg C ha-1yr-1). Exports of inorganic carbon as CO2 from the stream to the atmosphere were estimated to be 59% (76.9 kg C ha-1yr-1) of total exports. Streamflow exported the remaining 41% (53.1 kg C ha-1yr-1) of basin-scaled flux. Results highlight the importance of both external and internal carbon sources to the stream carbon budget. Aeration rate is an integral parameter for the measurement of CO2 evasion. It is also needed to measure instream metabolic processing. Common field methods to estimate the aeration rate have strengths and weaknesses, and researchers continue to search for better techniques, particularly for steep streams with high rates of gas exchange and low productivity. We developed the oxygen carbon (OC) method for calculating gas-exchange rates from simultaneous measurement of oxygen (O2) and dissolved inorganic carbon (DIC). Gas-exchange rates are calculated by solving the combined stream transport equation for O2 and DIC. The output is a time series of aeration rates at the same sampling frequency as the input O2 and carbon (C) data. Field tests in a fourth order montane stream in Oregon, USA, were a success. The OC method estimated the aeration rate to 3.25 h-1, which agreed well with the value from direct gas injection of 3.22 h-1. Sensitivity analysis indicated that application of the OC method is limited to reaches with a suitable change in combined O2 and CO2 concentration ≥ ~4 μmol/L and combined O2 and CO2 saturation deficits ≈ 4 μmol/L. The OC method was then applied in a second order headwater stream over a wide range of flow conditions, allowing for development of a site-specific regression between discharge and aeration rate

Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

Material-specific gap function in the high-temperature superconductors

We present theoretical arguments and experimental support for the idea that high-Tc superconductivity can occur with s-wave, d-wave, or mixed-wave pairing in the context of a magnetic mechanism. The size and shape of the gap is different for different materials. The theoretical arguments are based on the t-J model as derived from the Hubbard model so that it necessarily includes three-site terms. We argue that this should be the basic minimal model for high-Tc systems. We analyze this model starting with the dilute limit which can be solved exactly, passing then to the Cooper problem which is numerically tractable, then ending with a mean field approach. It is found that the relative stability of s-wave and d-wave depends on the size and the shape of the Fermi surface. We identify three striking trends. First, materials with large next-nearest-neighbor hopping (such as YBa(2)Cu(3)O(7-x)) are nearly pure d-wave, whereas nearest-neighbor materials (such as La(2-x)Sr(x)CuO(4)) tend to be more s-wave-like. Second, low hole doping materials tend to be pure d-wave, but high hole doping leads to s-wave. Finally, the optimum hole doping level increases as the next-nearest-neighbor hopping increases. We examine the experimental evidence and find support for this idea that gap function in the high-temperature superconductors is material-specific.Comment: 20 pages; requires revtex.sty v3.0, epsf.sty; includes 6 EPS figures; Postscript version also available at http://lifshitz.physics.wisc.edu/www/koltenbah/papers/gapfunc2.ps . This version contains an extensive amount of new work including theoretical background, an additional mean field treatment with new figures, and a more thorough experimental surve

What makes you not a Sikh? : a preliminary mapping of values

This study sets out to establish which Sikh values contrasted with or were shared by non-Sikh adolescents. A survey of attitude toward a variety of Sikh values was fielded in a sample of 364 non-Sikh schoolchildren aged between 13 and 15 in London. Values where attitudes were least positive concerned Sikh duties/code of conduct, festivals, rituals, prayer Gurdwara attendance, listening to scripture recitation, the amrit initiation. Sikh values empathized with by non-Sikhs concerned family pride, charity, easy access to ordination and Gurdwaras, maintaining the five Ks, seeing God in all things, abstaining from meat and alcohol and belief in the stories of Guru Nanak. Further significant differences of attitude toward Sikhism were found in comparisons by sex, age and religious affiliation. Findings are applied to teaching Sikhism to pupils of no faith adherence. The study recommends the extension of values mapping to specifically Sikh populations

Nursing work and sensory experiences of hospital design: A before and after qualitative study following a move to all-single room inpatient accommodation

The embodied experience of nursing practice is rarely studied. Drawing on data from an internationally relevant larger study conducted in 2013–14, here we explore the sensory dimension of the embodied experiences of nursing staff working on two acute NHS hospital wards before and after a move to all-single room inpatient accommodation. We undertook a secondary analysis of 25 interviews with nursing staff (12 before and 13 after the move with half [13/25] using photographs taken by participants) from a mixed-method before-and-after study. This analysis focused on the sensory dimensions of nursing staff's experiences of their working practices and the effect of the built environment upon these. Drawing on Pallasmaa's theoretocal insights, we report how the all-single room ward design prioritises ‘focused vision’ and hinders peripheral perception, whilst the open ward environment is rich in contextual and preconscious information. We suggest all-single room accommodation may offer staff an impoverished experience of caring for patients and of working with each other

Genome Sequence of E. coli O104:H4 Leads to Rapid Development of a Targeted Antimicrobial Agent against This Emerging Pathogen

A recent widespread outbreak of Escherichia coli O104:H4 in Germany demonstrates the dynamic nature of emerging and re-emerging food-borne pathogens, particularly STECs and related pathogenic E. coli. Rapid genome sequencing and public availability of these data from the German outbreak strain allowed us to identify an O-antigen-specific bacteriophage tail spike protein encoded in the genome. We synthesized this gene and fused it to the tail fiber gene of an R-type pyocin, a phage tail-like bacteriocin, and expressed the novel bacteriocin such that the tail fiber fusion was incorporated into the bacteriocin structure. The resulting particles have bactericidal activity specifically against E. coli strains that produce the O104 lipopolysaccharide antigen, including the outbreak strain. This O-antigen tailspike-R-type pyocin strategy provides a platform to respond rapidly to emerging pathogens upon the availability of the pathogen's genome sequence

PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism

<p>Abstract</p> <p>Background</p> <p>Genetic analysis of the human prion protein gene (<it>PRNP</it>) in suspect cases of Creutzfeldt-Jakob disease (CJD) is necessary for accurate diagnosis and case classification. Previous publications on the genetic variation at the <it>PRNP </it>locus have highlighted the presence of numerous polymorphisms, in addition to the well recognised one at codon 129, with significant variability between geographically distinct populations. It is therefore of interest to consider their influence on susceptibility or the clinico-pathological disease phenotype. This study aimed to characterise the frequency and effect of <it>PRNP </it>open reading frame polymorphisms other than codon 129 in both disease and control samples sourced from the United Kingdom population.</p> <p>Methods</p> <p>DNA was extracted from blood samples and genetic data obtained by full sequence analysis of the prion protein gene or by restriction fragment length polymorphism analysis using restriction enzymes specific to the gene polymorphism under investigation.</p> <p>Results</p> <p>147 of 166 confirmed cases of variant CJD (vCJD) in the UK have had <it>PRNP </it>codon 129 genotyping and all are methionine homozygous at codon 129; 118 have had full <it>PRNP </it>gene sequencing. Of the latter, 5 cases have shown other polymorphic loci: at codon 219 (2, 1.69%), at codon 202 (2, 1.69%), and a 24 bp deletion in the octapeptide repeat region (1, 0.85%). E219K and D202D were not found in sporadic CJD (sCJD) cases and therefore may represent genetic risk factors for vCJD.</p> <p>Genetic analysis of 309 confirmed UK sCJD patients showed codon 129 genotype frequencies of MM: 59.5% (n = 184), MV: 21.4% (n = 66), and VV: 19.1% (n = 59). Thirteen (4.2%) had the A117A polymorphism, one of which also had the P68P polymorphism, four (1.3%) had a 24 bp deletion, and a single patient had a novel missense variation at codon 167. As the phenotype of this latter case is similar to sCJD and in the absence of a family history of CJD, it is unknown whether this is a form of genetic CJD, or simply a neutral polymorphism.</p> <p>Conclusions</p> <p>This analysis of <it>PRNP </it>genetic variation in UK CJD patients is the first to show a comprehensive comparison with healthy individuals (n = 970) from the same population, who were genotyped for the three most common variations (codon 129, codon 117, and 24 bp deletion). These latter two genetic variations were equally frequent in UK sCJD or vCJD cases and a normal (healthy blood donor) UK population.</p

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.National Institutes of Health (U.S.) (New Innovator Award 1DP2OD008435)National Centers for Systems Biology (U.S.) (Grant 1P50GM098792)United States. Defense Threat Reduction Agency (HDTRA1-14-1-0007)Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (W911NF13D0001)National Institute of General Medical Sciences (U.S.) (Interdepartmental Biotechnology Training Program 5T32 GM008334)Fonds de la recherche en sante du Quebec (Master's Training Award

Heritability of non-speech auditory processing skills

Recent insight into the genetic bases for autism spectrum disorder, dyslexia, stuttering, and language disorders suggest that neurogenetic approaches may also reveal at least one etiology of auditory processing disorder (APD). A person with an APD typically has difficulty understanding speech in background noise despite having normal pure-tone hearing sensitivity. The estimated prevalence of APD may be as high as 10% in the pediatric population, yet the causes are unknown and have not been explored by molecular or genetic approaches. The aim of our study was to determine the heritability of frequency and temporal resolution for auditory signals and speech recognition in noise in 96 identical or fraternal twin pairs, aged 6–11 years. Measures of auditory processing (AP) of non-speech sounds included backward masking (temporal resolution), notched noise masking (spectral resolution), pure-tone frequency discrimination (temporal fine structure sensitivity), and nonsense syllable recognition in noise. We provide evidence of significant heritability, ranging from 0.32 to 0.74, for individual measures of these non-speech-based AP skills that are crucial for understanding spoken language. Identification of specific heritable AP traits such as these serve as a basis to pursue the genetic underpinnings of APD by identifying genetic variants associated with common AP disorders in children and adults