Controlling Fragmentation of the Acetylene Cation in the Vacuum Ultraviolet via Transient Molecular Alignment.

An open-loop control scheme of molecular fragmentation based on transient molecular alignment combined with single-photon ionization induced by a short-wavelength free electron laser (FEL) is demonstrated for the acetylene cation. Photoelectron spectra are recorded, complementing the ion yield measurements, to demonstrate that such control is the consequence of changes in the electronic response with molecular orientation relative to the ionizing field. We show that stable C2H2+ cations are mainly produced when the molecules are parallel or nearly parallel to the FEL polarization, while the hydrogen fragmentation channel (C2H2+ → C2H+ + H) predominates when the molecule is perpendicular to that direction, thus allowing one to distinguish between the two photochemical processes. The experimental findings are supported by state-of-the art theoretical calculations.

Elemental composition of aquaculture fish from West Bengal, India: nutrition versus food safety.

Aquaculture production continues to grow in West Bengal, where on average people consume 8.2 kg capita-1 of fish each year, and an extensive mosaic of aquaculture ponds has developed along the River Hugli as clay pits are repurposed. The adjacent brickworks and industry (especially tanneries) are a source of environmental pollution, with potential for bioaccumulation of potentially harmful elements (PHEs) in fish farmed in these ponds. Fish from aquaculture present an opportunity to meet food sufficiency in West Bengal; however, an investigation to assess their effectiveness for micronutrient supply balanced against food safety is required. Five ponds close to industrial brick manufacture (urban) and three from rural areas were assessed for the degree of pollution within their pond sediments and waters. Fish were also sampled from each location including a subset from the market in Kolkata to determine the concentrations of PHEs in their fish muscle tissue. Dietary intake and PHE loading were calculated for four fish species to evaluate their nutrient content with respect to recommended daily intakes for adults, e.g. calcium (Ca), potassium (K), magnesium (Mg), iron (Fe), zinc (Zn) and selenium (Se), and to establish whether the provisional maximum tolerable intakes (PMTIs) are exceeded for PHEs, e.g. aluminium (Al), arsenic (As), mercury (Hg), chromium (Cr), tin (Sn), copper (Cu) and lead (Pb). Preliminary results suggest that aquaculture is making an important contribution to nutrition, with fish being a good source of Se. However, in contrast to small wild-caught fish, aquaculture fish in the present study were poor sources of Fe, Ca and Zn. The fish also made substantial contributions (> 10%) to the PMTI of Hg and As. Therefore, there is an urgent need for ongoing monitoring and an expanded sampling programme, as well as research into approaches which might improve the nutritional quality of the farmed fish.

Threats to intact tropical peatlands and opportunities for their conservation.

Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services and maintain their resilience to future environmental change. We explored threats to and opportunities for conserving remaining intact tropical peatlands; thus, we excluded peatlands of Indonesia and Malaysia, where extensive deforestation, drainage, and conversion to plantations means conservation in this region can protect only small fragments of the original ecosystem. We focused on a case study, the Pastaza-Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and is representative of peatland vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. There remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land-use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection does not include the most carbon-dense (domed pole forest) areas. New carbon-based conservation instruments (e.g., REDD+, Green Climate Fund), developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and elsewhere, such as those in New Guinea and Central Africa which remain, for the moment, broadly beyond the frontier of commercial development.

Upper airway obstruction in a patient with Ehlers-Danlos syndrome.

We report a case of recurrent airway obstruction episodes resulting from laryngeal hypermobility in a patient with Ehlers-Danlos syndrome. A 44-year-old woman, with known Ehlers-Danlos syndrome, presented with recent onset of episodes of upper airway obstruction due to hypermobility of her larynx. A suitable conservative management strategy proved elusive and the patient finally underwent a thyrohyoidopexy. The patient remains symptom free nine months after the procedure. This is the first report of spontaneous life threatening upper airway obstruction due to hypermobility of the suprahyoid suspensory soft tissues in Ehlers-Danlos syndrome.

Sensitivity of nonlinear photoionization to resonance substructure in collective excitation.

Collective behaviour is a characteristic feature in many-body systems, important for developments in fields such as magnetism, superconductivity, photonics and electronics. Recently, there has been increasing interest in the optically nonlinear response of collective excitations. Here we demonstrate how the nonlinear interaction of a many-body system with intense XUV radiation can be used as an effective probe for characterizing otherwise unresolved features of its collective response. Resonant photoionization of atomic xenon was chosen as a case study. The excellent agreement between experiment and theory strongly supports the prediction that two distinct poles underlie the giant dipole resonance. Our results pave the way towards a deeper understanding of collective behaviour in atoms, molecules and solid-state systems using nonlinear spectroscopic techniques enabled by modern short-wavelength light sources.

Toward Visualization for Games: Theory, Design Space, and Patterns.

Electronic games are starting to incorporate in-game telemetry that collects data about player, team, and community performance on a massive scale, and as data begins to accumulate, so does the demand for effectively analyzing this data. In this paper, we use examples from both old and new games of different genres to explore the theory and design space of visualization for games. Drawing on these examples, we define a design space for this novel research topic and use it to formulate design patterns for how to best apply visualization technology to games. We then discuss the implications that this new framework will potentially have on the design and development of game and visualization technology in the future.

LIAD-fs scheme for studies of ultrafast laser interactions with gas phase biomolecules.

Laser induced acoustic desorption (LIAD) has been used for the first time to study the parent ion production and fragmentation mechanisms of a biological molecule in an intense femtosecond (fs) laser field. The photoacoustic shock wave generated in the analyte substrate (thin Ta foil) has been simulated using the hydrodynamic HYADES code, and the full LIAD process has been experimentally characterised as a function of the desorption UV-laser pulse parameters. Observed neutral plumes of densities >10(9) cm(-3) which are free from solvent or matrix contamination demonstrate the suitability and potential of the source for studying ultrafast dynamics in the gas phase using fs laser pulses. Results obtained with phenylalanine show that through manipulation of fundamental femtosecond laser parameters (such as pulse length, intensity and wavelength), energy deposition within the molecule can be controlled to allow enhancement of parent ion production or generation of characteristic fragmentation patterns. In particular by reducing the pulse length to a timescale equivalent to the fastest vibrational periods in the molecule, we demonstrate how fragmentation of the molecule can be minimised whilst maintaining a high ionisation efficiency.

A 2D flow visualization user study using explicit flow synthesis and implicit task design.

This paper presents a 2D flow visualization user study that we conducted using new methodologies to increase the objectiveness. We evaluated grid-based variable-size arrows, evenly spaced streamlines, and line integral convolution (LIC) variants (basic, oriented, and enhanced versions) coupled with a colorwheel and/or rainbow color map, which are representative of many geometry-based and texture-based techniques. To reduce data-related bias, template-based explicit flow synthesis was used to create a wide variety of symmetric flows with similar topological complexity. To suppress task-related bias, pattern-based implicit task design was employed, addressing critical point recognition, critical point classification, and symmetric pattern categorization. In addition, variable-duration and fixed-duration measurement schemes were utilized for lightweight precision-critical and heavyweight judgment intensive flow analysis tasks, respectively, to record visualization effectiveness. We eliminated outliers and used the Ryan REGWQ post-hoc homogeneous subset tests in statistical analysis to obtain reliable findings. Our study shows that a texture-based dense representation with accentuated flow streaks, such as enhanced LIC, enables intuitive perception of the flow, while a geometry-based integral representation with uniform density control, such as evenly spaced streamlines, may exploit visual interpolation to facilitate mental reconstruction of the flow. It is also shown that inappropriate color mapping (e.g., colorwheel) may add distractions to a flow representation.

Efficacy of liquid spray decontaminants for inactivation of Bacillus anthracis spores on building and outdoor materials.

AIMS: To obtain data on the efficacy of various liquid and foam decontamination technologies to inactivate Bacillus anthracis Ames and Bacillus subtilis spores on building and outdoor materials. METHODS AND RESULTS: Spores were inoculated onto test coupons and positive control coupons of nine different materials. Six different sporicidal liquids were spray-applied to the test coupons and remained in contact for exposure times ranging from 10 to 70 min. Following decontamination, spores were recovered from the coupons and efficacy was quantified in terms of log reduction. CONCLUSIONS: The hydrogen peroxide/peracetic acid products were the most effective, followed by decontaminants utilizing hypochlorous acid chemistry. Decontamination efficacy varied by material type. SIGNIFICANCE AND IMPACT OF THE STUDY: The study results may be useful in the selection of technologies to decontaminate buildings and outdoor areas in the event of contamination with B. anthracis spores. These results may also facilitate selection of decontaminant liquids for the inactivation of other spore-forming infectious disease agents.

GOModeler--a tool for hypothesis-testing of functional genomics datasets.

BACKGROUND: Functional genomics technologies that measure genome expression at a global scale are accelerating biological knowledge discovery. Generating these high throughput datasets is relatively easy compared to the downstream functional modelling necessary for elucidating the molecular mechanisms that govern the biology under investigation. A number of publicly available 'discovery-based' computational tools use the computationally amenable Gene Ontology (GO) for hypothesis generation. However, there are few tools that support hypothesis-based testing using the GO and none that support testing with user defined hypothesis terms.Here, we present GOModeler, a tool that enables researchers to conduct hypothesis-based testing of high throughput datasets using the GO. GOModeler summarizes the overall effect of a user defined gene/protein differential expression dataset on specific GO hypothesis terms selected by the user to describe a biological experiment. The design of the tool allows the user to complement the functional information in the GO with his/her domain specific expertise for comprehensive hypothesis testing. RESULTS: GOModeler tests the relevance of the hypothesis terms chosen by the user for the input gene dataset by providing the individual effects of the genes on the hypothesis terms and the overall effect of the entire dataset on each of the hypothesis terms. It matches the GO identifiers (ids) of the genes with the GO ids of the hypothesis terms and parses the names of those ids that match to assign effects. We demonstrate the capabilities of GOModeler with a dataset of nine differentially expressed cytokine genes and compare the results to those obtained through manual analysis of the dataset by an immunologist. The direction of overall effects on all hypothesis terms except one was consistent with the results obtained by manual analysis. The tool's editing capability enables the user to augment the information extracted. GOModeler is available as a part of the AgBase tool suite (http://www.agbase.msstate.edu). CONCLUSIONS: GOModeler allows hypothesis driven analysis of high throughput datasets using the GO. Using this tool, researchers can quickly evaluate the overall effect of quantitative expression changes of gene set on specific biological processes of interest. The results are provided in both tabular and graphical formats.

Exploratory visual analysis of conserved domains on multiple sequence alignments.

BACKGROUND: Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. This insight can be augmented by joint display of conserved domains along the sequences. By fusing this metadata visually, biologists can analyze sequence conservation and functional motifs simultaneously and efficiently. RESULTS: We present MSAVis, a new approach combining luminance and hue for simultaneous visualization of conserved motifs and sequence alignment. Input for the algorithm is a multiple sequence alignment in a standard format. The NCBI Conserved Domain Database (CDD) is used for finding conserved domains along the alignment. The visualization quickly identifies conserved domains, and allows both macro (sequence-long) and micro (small amino-acid neighborhood) views. CONCLUSION: MSAVis utilizes two visual cues, luminance and hue, to facilitate at-a-glance summary of the conservation of a user-provided protein alignment while enabling multiple comparisons among functional domains. These visual cues are preattentive and separable so that the relationship between conservation strength and domain membership can be understood. The MSAVis software, written in Python and using BioPython and OpenGL, can be found at http://agbase.msstate.edu/tools/MSAVis.html.

Minor salivary gland inflammation in Devic's disease and longitudinally extensive myelitis.

Devic's disease is often considered as a variant of multiple sclerosis (MS). However, evidence suggests that Devic's disease may be distinct from MS. Devic's disease can coexist with connective tissue diseases, particularly Sjögren's disease, but this association is rare with MS. Diagnosis of Sjögren's disease in patients with neurological symptoms is often difficult. During early stages of Sjögren's disease, patients may not fulfill all criteria for Sjögren's disease. A high percentage of patients with Sjögren's disease have inflammatory infiltrates in minor salivary glands, and this may be a reliable indicator of early or subclinical disease. We show high prevalence (80%) of salivary gland inflammation in Devic's disease and longitudinally extensive transverse myelitis (LETM). We diagnosed 16 patients with Devic's disease, and 2 of these satisfied criteria for Sjögren's disease as did 2 of 9 patients with LETM. Anti-SSA/B titers were infrequently elevated. Although most did not satisfy criteria for Sjögren's disease. 9 of 12 Devic's disease patients and 7 of 8 LETM patients had severe salivary gland inflammation. Thus: (1) patients with Devic's disease or with LETM who have positive labial biopsies but do not satisfy criteria for Sjögren's disease could have subclinical Sjögren's diseases. Alternatively, (2) as patients with Devic's disease have elevated titers of several autoantibodies, so there may exist a set of antibodies that react with antigens in minor salivary glands and cause inflammation. Minor salivary gland biopsy is more sensitive than anti-SSA/B serology in providing histological evidence for possible Sjögren's disease with CNS lesions.

Transfusion support for a patient with McLeod phenotype without chronic granulomatous disease and with antibodies to Kx and Km.

BACKGROUND AND OBJECTIVES: Kell antigens are encoded by the KEL gene on the long arm of chromosome 7. Kx antigen is encoded by the XK gene on the short arm of the X chromosome. Kell and Kx proteins in the red cell membrane are covalently linked by a disulphide bond. The McLeod phenotype is characterized by weakened expression of antigens in the Kell blood group system, absence of Km and Kx antigens, and acanthocytosis. It has an X-linked mode of inheritance with transmission through carrier females. Some males with the McLeod syndrome also have chronic granulomatous disease (CGD). It is generally believed that patients with non-CGD McLeod may develop anti-Km but not anti-Kx, but that those with CGD McLeod can develop both anti-Km and anti-Kx. MATERIALS AND METHODS: We present serological data, DNA genotyping and gene sequencing, monocyte monolayer assay and neutrophil oxidative burst test from a patient with the McLeod phenotype without clinical evidence of CGD. RESULTS: We report here the second example of a patient with non-CGD McLeod who developed anti-Kx in addition to anti-Km. Sequencing of our patient's XK gene confirmed the presence of a mutation resulting in a premature stop codon and lack of Kx protein in the red cell membrane, which is consistent with the diagnosis of McLeod syndrome. Neutrophil oxidative burst test was normal, indicating that our patient did not have CGD. The challenge of providing 10 compatible blood units for multiple surgeries was met. CONCLUSION: The second case of a rare entity, a patient with non-CGD McLeod who developed anti-Kx and anti-Km, was managed successfully with a combination of autologous donations and procurement of compatible units from national and international sources.

A model and framework for visualization exploration.

Visualization exploration is the process of extracting insight from data via interaction with visual depictions of that data. Visualization exploration is more than presentation; the interaction with both the data and its depiction is as important as the data and depiction itself. Significant visualization research has focused on the generation of visualizations (the depiction); less effort has focused on the exploratory aspects of visualization (the process). However, without formal models of the process, visualization exploration sessions cannot be fully utilized to assist users and system designers. Toward this end, we introduce the P-Set Model of Visualization Exploration for describing this process and a framework to encapsulate, share, and analyze visual explorations. In addition, systems utilizing the model and framework are more efficient as redundant exploration is avoided. Several examples drawn from visualization applications demonstrate these benefits. Taken together, the model and framework provide an effective means to exploit the information within the visual exploration process.

Detection and visualization of defects in 3D unstructured models of nematic liquid crystals.

A method for the semi-automatic detection and visualization of defects in models of nematic liquid crystals (NLCs) is introduced; this method is suitable for unstructured models, a previously unsolved problem. The detected defects-also known as disclinations-are regions were the alignment of the liquid crystal rapidly changes over space; these defects play a large role in the physical behavior of the NLC substrate. Defect detection is based upon a measure of total angular change of crystal orientation (the director) over a node neighborhood via the use of a nearest neighbor path. Visualizations based upon the detection algorithm clearly identifies complete defect regions as opposed to incomplete visual descriptions provided by cutting-plane and isosurface approaches. The introduced techniques are currently in use by scientists studying the dynamics of defect change.

Superellipsoid-based, real symmetric traceless tensor glyphs motivated by nematic liquid crystal alignment visualization.

A glyph-based method for visualizing the nematic liquid crystal alignment tensor is introduced. Unlike previous approaches, the glyph is based upon physically-linked metrics, not offsets of the eigenvalues. These metrics, combined with a set of superellipsoid shapes, communicate both the strength of the crystal's uniaxial alignment and the amount of biaxiality. With small modifications, our approach can visualize any real symmetric traceless tensor.

Colonic pouchography is not routinely required prior to stoma closure.

BACKGROUND: Colonic pouch formation with pouch-anal anastomosis is now regarded as the procedure of choice for restoration of intestinal continuity following anterior resection for low rectal cancers. The aim of this study was to review the necessity for routine colonic pouchography prior to closure of a diverting loop stoma. METHODS: This was a prospective study of 52 consecutive patients who underwent colonic pouch formation between 1 June 1999 and 31 May 2002, four of whom have subsequently died. Each pouch was assessed clinically and radiologically prior to stoma closure. RESULTS: There were no clinical anastomotic leaks. Forty-six of 48 surviving patients have had a colonic pouchogram and in no case was either a pouch or pouch-anal anastomotic defect identified. To date 40 patients have undergone stoma closure without an anastomosis-related complication. CONCLUSION: Following successful colonic pouch formation, routine study of the pouch by contrast radiology does not add to clinical assessment. As a consequence radiological imaging is unnecessary and can be omitted.

Non-restorative surgery for rectal cancer: indications in 2003.

BACKGROUND: Although the majority of patients with low rectal tumours can now be offered restorative surgery, a subset of patients with very distal, locally extensive tumours, or excessive comorbidity, continue to require abdominoperineal resection or a Hartmann's procedure. The Clinical Standards Board for Scotland (CSBS) recommends that the permanent stoma rate for patients with rectal cancer should be no more than 40%. The aim of this study was to determine the proportion of patients not suitable for restorative surgery and to explore the remaining indications for non-restorative surgery. MATERIALS AND METHODS: Data pertaining to the management of 100 consecutive patients treated for a rectal adenocarcinoma were extracted from a prospective database. RESULTS: Eighty-one patients underwent primary restorative surgery; 12 patients, 9 of whom had received neoadjuvant therapy, had abdominoperineal excision for low rectal or anorectal tumours. Seven patients with locally extensive disease underwent an unplanned Hartmann's procedure rather than high anterior resection. Two of these resections were incomplete and two patients had metastatic disease not detected on staging. CONCLUSION: Not all patients with rectal cancer can avoid the formation of a stoma, but our results show that more than 80% of patients can be offered primary restorative surgery. The CSBS guidelines do not reflect acceptable contemporary practice and should be revised. This is particularly pertinent with the likely introduction of population screening for colorectal cancer.