The role of mundane mobility and contact in dialect death and dialect birth

Urry begins his 2007 book, Mobilities, by throwing some quite stunning statistics at his readers: in 2010, there were one billion legal international arrivals at ports and airports; in 1800 people in the US travelled on average 50 metres per day, today it is 50 kilometres per day; 8.7% of world employment is in tourism; and, at any one time, there are 360,000 passengers in flight above the United States (2007: 3-4). But very many of these mobilities for the individuals concerned are or have become rather unexceptional – a flight to a holiday in Majorca or Florida, a journey on a crowded commuter train into Madrid or Tokyo, a cross-Channel ferry to Calais in France to pick up some cheap wine and a camembert. Whilst much of the theoretically influential dialectological literature on mobility reports on long-distance, often permanent, often dangerous migrations, I turn our attention here to the dialectological consequences of this unexceptional everyday movement. I will argue here that, just as more dramatic and long-distance mobilities can trigger linguistic change, so too can the much more mundane movements we engage in in everyday life. I demonstrate that the linguistic consequences of that contact are similar if not the same – perhaps less dramatic, perhaps involving the convergence of an initially less divergent array of variants – but typologically of the same ilk. And I demonstrate that because these mobilities have been long-term, intensive and ongoing, their consequences on the dialect landscape have been highly significant. Important to remember, however, is that these mobilities are socially stratified and unevenly distributed. As Wolff put it: “the suggestion of free and equal mobility is … a deception, since we don’t all have the same access to the road” (1993: 253).

Characterisation of Gas Transport Properties of the Opalinus Clay, a Potential Host Rock Formation for Radioactive Waste Disposal

The Opalinus Clay in Northern Switzerland has been identified as a potential host rock formation for the disposal of radioactive waste. Comprehensive understanding of gas transport processes through this low-permeability formation forms a key issue in the assessment of repository performance. Field investigations and laboratory experiments suggest an intrinsic permeability of the Opalinus Clay in the order of 10(-20) to 10(-21) m(2) and a moderate anisotropy ratio < 10. Porosity depends on clay content and burial depth; values of similar to 0.12 are reported for the region of interest. Porosimetry indicates that about 10-30 of voids can be classed as macropores, corresponding to an equivalent pore radius > 25 nm. The determined entry pressures are in the range of 0.4-10 MPa and exhibit a marked dependence on intrinsic permeability. Both in situ gas tests and gas permeameter tests on drillcores demonstrate that gas transport through the rock is accompanied by porewater displacement, suggesting that classical flow concepts of immiscible displacement in porous media can be applied when the gas entry pressure (i.e. capillary threshold pressure) is less than the minimum principal stress acting within the rock. Essentially, the pore space accessible to gas flow is restricted to the network of connected macropores, which implies a very low degree of desaturation of the rock during the gas imbibition process. At elevated gas pressures (i.e. when gas pressure approaches the level of total stress that acts on the rock body), evidence was seen for dilatancy controlled gas transport mechanisms. Further field experiments were aimed at creating extended tensile fractures with high fracture transmissivity (hydro- or gasfracs). The test results lead to the conclusion that gas fracturing can be largely ruled out as a risk for post-closure repository performance.

Characterization of the beta-lactamase gene from {\it Enterococcus faecalis\/} strain HH22

The plasmid-encoded, constitutively produced $\beta$-lactamase gene from Enterococcus faecalis strain HH22 was genetically characterized. A restriction endonuclease map of the 5.1 kb EcoRI fragment encoding the enterococcal $\beta$-lactamase was prepared and compared with the restriction map of a cloned staphylococcal $\beta$-lactamase gene (from the naturally-occurring staphylococcal $\beta$-lactamase plasmid pI258). Comparison and hybridization studies showed that there were identical restriction sites in the region of the $\beta$-lactamase structural gene but not in the region surrounding this gene. Also the enterococcal $\beta$-lactamase plasmid did not encode resistance to mercury or cadmium which is encoded by the small, transducible staphylococcal $\beta$-lactamase plasmids. The nucleotide sequence of the enterococcal gene was shown to be identical to the published sequences of three of four staphylococcal type A $\beta$-lactamase genes; more differences were seen with the genes for staphylococcal type C and D enzymes. One hundred-forty nucleotides upstream of the $\beta$-lactamase start codon were also determined for the inducible staphylococcal $\beta$-lactamase gene on pI258; this sequence was identical to that of the constitutively expressed enterococcal gene indicating that the changes resulting in constitutive expression are not due to changes in the promoter or operator region. Moreover, complementation studies indicated that production of the enterococcal enzyme could be repressed. The gene for the enterococcal $\beta$-lactamase and an inducible staphylococcal $\beta$-lactamase were each cloned into a shuttle vector and then transformed into enterococcal and staphylococcal recipients. The major difference between the two host backgrounds was that more enzyme was produced by the staphylococcal host, regardless of the source of the gene but no qualitative difference was seen between the two genera. Also a difference in the level of resistance to ampicillin was seen between the two backgrounds with the cloned enzymes by MIC and time-kill studies. The location of the enzyme was found to be host dependent since each cloned gene generated extracellular (free) enzyme in the staphylococcus and cell bound enzyme in the enterococcus. Based on the identity of the enterococcal $\beta$-lactamase and several staphylococcal $\beta$-lactamases, these data suggest recent spread of $\beta$-lactamase to enterococci and also suggest loss of a functional repressor. ^

Dominance of chemokine ligand 2 and matrix metalloproteinase-2 and -9 and suppression of pro-inflammatory cytokines in the epidural compartment after intervertebral disc extrusion in a canine model

BACKGROUND CONTEXT In canine intervertebral disc (IVD) disease, a useful animal model, only little is known about the inflammatory response in the epidural space. PURPOSE To determine messenger RNA (mRNA) expressions of selected cytokines, chemokines, and matrix metalloproteinases (MMPs) qualitatively and semiquantitatively over the course of the disease and to correlate results to neurologic status and outcome. STUDY DESIGN/SETTING Prospective study using extruded IVD material of dogs with thoracolumbar IVD extrusion. PATIENT SAMPLE Seventy affected and 13 control (24 samples) dogs. OUTCOME MEASURES Duration of neurologic signs, pretreatment, neurologic grade, severity of pain, and outcome were recorded. After diagnostic imaging, decompressive surgery was performed. METHODS Messenger RNA expressions of interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, IL-10, tumor necrosis factor (TNF), interferon (IFN)γ, MMP-2, MMP-9, chemokine ligand (CCL)2, CCL3, and three housekeeping genes was determined in the collected epidural material by Panomics 2.0 QuantiGene Plex technology. Relative mRNA expression and fold changes were calculated. Relative mRNA expression was correlated statistically to clinical parameters. RESULTS Fold changes of TNF, IL-1β, IL-2, IL-4, IL-6, IL-10, IFNγ, and CCL3 were clearly downregulated in all stages of the disease. MMP-9 was downregulated in the acute stage and upregulated in the subacute and chronic phase. Interleukin-8 was upregulated in acute cases. MMP-2 showed mild and CCL2 strong upregulation over the whole course of the disease. In dogs with severe pain, CCL3 and IFNγ were significantly higher compared with dogs without pain (p=.017/.020). Dogs pretreated with nonsteroidal anti-inflammatory drugs revealed significantly lower mRNA expression of IL-8 (p=.017). CONCLUSIONS The high CCL2 levels and upregulated MMPs combined with downregulated T-cell cytokines and suppressed pro-inflammatory genes in extruded canine disc material indicate that the epidural reaction is dominated by infiltrating monocytes differentiating into macrophages with tissue remodeling functions. These results will help to understand the pathogenic processes representing the basis for novel therapeutic approaches. The canine IVD disease model will be rewarding in this process.

ON THE STABILITY OF SUPER-EARTH ATMOSPHERES

We investigate the stability of super-Earth atmospheres around M stars using a seven-parameter, analytical framework. We construct stability diagrams in the parameter space of exoplanetary radius versus semimajor axis and elucidate the regions in which the atmospheres are stable against the condensation of their major constituents, out of the gas phase, on their permanent nightside hemispheres. We find that super-Earth atmospheres that are nitrogen-dominated (Earth-like) occupy a smaller region of allowed parameter space, compared to hydrogen-dominated atmospheres, because of the dual effects of diminished advection and enhanced radiative cooling. Furthermore, some super-Earths which reside within the habitable zones of M stars may not possess stable atmospheres, depending on the mean molecular weight and infrared photospheric pressure of their atmospheres. We apply our stability diagrams to GJ 436b and GJ 1214b, and demonstrate that atmospheric compositions with high mean molecular weights are disfavored if these exoplanets possess solid surfaces and shallow atmospheres. Finally, we construct stability diagrams tailored to the Kepler data set, for G and K stars, and predict that about half of the exoplanet candidates are expected to harbor stable atmospheres if Earth-like conditions are assumed. We include 55 Cancri e and CoRoT-7b in our stability diagram for G stars

Structural Organization of the Corpus Callosum Predicts Attentional Shifts after Continuous Theta Burst Stimulation

Repetitive transcranial magnetic stimulation (rTMS) applied over the right posterior parietal cortex (PPC) in healthy participants has been shown to trigger a significant rightward shift in the spatial allocation of visual attention, temporarily mimicking spatial deficits observed in neglect. In contrast, rTMS applied over the left PPC triggers a weaker or null attentional shift. However, large interindividual differences in responses to rTMS have been reported. Studies measuring changes in brain activation suggest that the effects of rTMS may depend on both interhemispheric and intrahemispheric interactions between cortical loci controlling visual attention. Here, we investigated whether variability in the structural organization of human white matter pathways subserving visual attention, as assessed by diffusion magnetic resonance imaging and tractography, could explain interindividual differences in the effects of rTMS. Most participants showed a rightward shift in the allocation of spatial attention after rTMS over the right intraparietal sulcus (IPS), but the size of this effect varied largely across participants. Conversely, rTMS over the left IPS resulted in strikingly opposed individual responses, with some participants responding with rightward and some with leftward attentional shifts. We demonstrate that microstructural and macrostructural variability within the corpus callosum, consistent with differential effects on cross-hemispheric interactions, predicts both the extent and the direction of the response to rTMS. Together, our findings suggest that the corpus callosum may have a dual inhibitory and excitatory function in maintaining the interhemispheric dynamics that underlie the allocation of spatial attention. SIGNIFICANCE STATEMENT: The posterior parietal cortex (PPC) controls allocation of attention across left versus right visual fields. Damage to this area results in neglect, characterized by a lack of spatial awareness of the side of space contralateral to the brain injury. Transcranial magnetic stimulation over the PPC is used to study cognitive mechanisms of spatial attention and to examine the potential of this technique to treat neglect. However, large individual differences in behavioral responses to stimulation have been reported. We demonstrate that the variability in the structural organization of the corpus callosum accounts for these differences. Our findings suggest novel dual mechanism of the corpus callosum function in spatial attention and have broader implications for the use of stimulation in neglect rehabilitation.

The role of patch testing in the management of oral lichenoid reactions.

BACKGROUND AND OBJECTIVES The distinction of oral lichenoid reactions from oral lichen planus may be difficult in a clinical setting. Our aims were to ascertain the utility of patch testing to confirm the association of oral lichenoid reactions with dental restorations and to identify the benefits of replacement of restorations, primarily made of amalgam. METHODS Patients seen in an oral medicine unit over a 10-year period diagnosed with oral lichenoid reactions, with oral lichen planus resistant to treatment or with atypical lichenoid features were included in this study. All had been subjected to skin patch testing. Histopathology reports blinded to patch test results were scrutinized. Patch-test-positive subjects were advised to have their restorations replaced. All were followed up to determine disease resolution for at least 3 months thereafter. RESULTS Among 115 patients, 67.8% patients reacted positive to a dental material and nearly a quarter to mercury or amalgam. No correlation was found between pathology and skin patch testing results (P = 0.44). A total of 87 patients were followed up in clinic, and among 26 patch-test-positive patients who had their amalgam fillings replaced, moderate to complete resolution was noted in 81%. CONCLUSIONS Skin patch testing is a valuable tool to confirm clinically suspected oral lichenoid reactions. Pathology diagnoses of oral lichenoid reactions did not correlate with patch test results. Prospective studies are needed to ascertain that a clinically suspected oral lichenoid reaction with a positive patch test result may resolve after the replacement of amalgam fillings.

Scientific assessment of the quality of OSIRIS images

Context. OSIRIS, the scientific imaging system onboard the ESA Rosetta spacecraft, has been imaging the nucleus of comet 67P/Churyumov-Gerasimenko and its dust and gas environment since March 2014. The images serve different scientific goals, from morphology and composition studies of the nucleus surface, to the motion and trajectories of dust grains, the general structure of the dust coma, the morphology and intensity of jets, gas distribution, mass loss, and dust and gas production rates. Aims. We present the calibration of the raw images taken by OSIRIS and address the accuracy that we can expect in our scientific results based on the accuracy of the calibration steps that we have performed. Methods. We describe the pipeline that has been developed to automatically calibrate the OSIRIS images. Through a series of steps, radiometrically calibrated and distortion corrected images are produced and can be used for scientific studies. Calibration campaigns were run on the ground before launch and throughout the years in flight to determine the parameters that are used to calibrate the images and to verify their evolution with time. We describe how these parameters were determined and we address their accuracy. Results. We provide a guideline to the level of trust that can be put into the various studies performed with OSIRIS images, based on the accuracy of the image calibration.

Effects of exercise with oxygen prebreathe for decompression risk reduction

Astronauts performing extravehicular activities (EVA) are at risk for occupational hazards due to a hypobaric environment, in particular Decompression Sickness (DCS). DCS results from nitrogen gas bubble formation in body tissues and venous blood. Denitrogenation achieved through lengthy staged decompression protocols has been the mainstay of prevention of DCS in space. Due to the greater number and duration of EVAs scheduled for construction and maintenance of the International Space Station, more efficient alternatives to accomplish missions without compromising astronaut safety are desirable. ^ This multi-center, multi-phase study (NASA-Prebreathe Reduction Protocol study, or PRP) was designed to identify a shorter denitrogenation protocol that can be implemented before an EVA, based on the combination of adynamia and exercise enhanced oxygen prebreathe. Human volunteers recruited at three sites (Texas, North Carolina and Canada) underwent three different combinations (“PRP phases”) of intense and light exercise prior to decompression in an altitude chamber. The outcome variables were detection of venous gas embolism (VGE) by precordial Doppler ultrasound, and clinical manifestations of DCS. Independent variables included age, gender, body mass index, oxygen consumption peak, peak heart rate, and PRP phase. Data analysis was performed both by pooling results from all study sites, and by examining each site separately. ^ Ten percent of the subjects developed DCS and 20% showed evidence of high grade VGE. No cases of DCS occurred in one particular PRP phase with use of the combination of dual-cycle ergometry (10 minutes at 75% of VO2 peak) plus 24 minutes of light EVA exercise (p = 0.04). No significant effects were found for the remaining independent variables on the occurrence of DCS. High grade VGE showed a strong correlation with subsequent development of DCS (sensitivity, 88.2%; specificity, 87.2%). In the presence of high grade VGE, the relative risk for DCS ranged from 7.52 to 35.0. ^ In summary, a good safety level can be achieved with exercise-enhanced oxygen denitrogenation that can be generalized to the astronaut population. Exercise is beneficial in preventing DCS if a specific schedule is followed, with an individualized VO2 prescription that provides a safety level that can then be applied to space operations. Furthermore, VGE Doppler detection is a useful clinical tool for prediction of altitude DCS. Because of the small number of high grade VGE episodes, the identification of a high probability DCS situation based on the presence of high grade VGE seems justified in astronauts. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.