LabView Interface for School-Network DAQ Card

A low-cost DAQ card has been developed for school-network cosmic ray detector projects, providing digitized data from photomultiplier tubes via a standard serial interface. To facilitate analysis of these data and to provide students with a starting point for custom readout systems, a model interface has been developed using the National Instruments LabVIEW(R) system. This user-friendly interface allows one to initialize the trigger coincidence conditions for data-taking runs and to monitor incoming or pre-recorded data sets with updating singles- and coincidence-rate plots and other user-selectable histograms.Comment: 4 pages, 6 figures. Presented as Paper NS26-119 at IEEE-NSS 2003, Portland, OR, by R. J. Wilke

Rapid and sensitive insulated isothermal PCR for point-of-need feline leukaemia virus detection

Objectives: Feline leukaemia virus (FeLV), a gamma retrovirus, causes diseases of the feline haematopoietic system that are invariably fatal. Rapid and accurate testing at the point-of-need (PON) supports prevention of virus spread and management of clinical disease. This study evaluated the performance of an insulated isothermal PCR (iiPCR) that detects proviral DNA, and a reverse transcription (RT)-iiPCR that detects both viral RNA and proviral DNA, for FeLV detection at the PON. Methods: Mycoplasma haemofelis, feline coronavirus, feline herpesvirus, feline calicivirus and feline immunodeficiency virus were used to test analytical specificity. In vitro transcribed RNA, artificial plasmid, FeLV strain American Type Culture Collection VR-719 and a clinical FeLV isolate were used in the analytical sensitivity assays. A retrospective study including 116 clinical plasma and serum samples that had been tested with virus isolation, real-time PCR and ELISA, and a prospective study including 150 clinical plasma and serum samples were implemented to evaluate the clinical performances of the iiPCR-based methods for FeLV detection. Results: Ninety-five percent assay limit of detection was calculated to be 16 RNA and five DNA copies for the RT-iiPCR, and six DNA copies for the iiPCR. Both reactions had analytical sensitivity comparable to a reference real-time PCR (qPCR) and did not detect five non-target feline pathogens. The clinical performance of the RT-iiPCR and iiPCR had 98.82% agreement (kappa[κ] = 0.97) and 100% agreement (κ = 1.0), respectively, with the qPCR (n = 85). The agreement between an automatic nucleic extraction/RT-iiPCR system and virus isolation to detect FeLV in plasma or serum was 95.69% (κ = 0.95) and 98.67% (κ = 0.85) in a retrospective (n = 116) and a prospective (n = 150) study, respectively. Conclusions and relevance: These results suggested that both RT-iiPCR and iiPCR assays can serve as reliable tools for PON FeLV detection

A survey of bariatric surgical and reproductive health professionals' knowledge and provision of contraception to reproductive-aged bariatric surgical patients

BACKGROUND: Over 80 % of bariatric surgical patients are women with obesity in their reproductive years. Obesity adversely affects fertility; the rapid weight loss following bariatric surgery can increase fecundity. Current guidelines recommend avoiding pregnancy for up to 24 months following surgery, but little is known about current contraceptive care of women who undergo bariatric surgery. Two surveys were undertaken with bariatric surgical and contraceptive practitioners in England to establish current contraceptive practices in both groups. METHODS: Two anonymous on-line surveys were sent to all 382 members of the British Obesity and Metabolic Surgery Society (BOMSS) and an estimated 300 contraceptive practitioners in the North East of England. RESULTS: The BOMSS survey elicited a response rate of 17 % (n = 65), mainly from bariatric surgeons (n = 24 (36 %)). Most respondents (97 %) acknowledged the need to educate patients, but contraceptive information was only provided by 7 % (n = 4) of respondents in bariatric surgical clinics. Less than half of respondents were confident discussing contraception, and the majority requested further training, guidance and communication with contraceptive practitioners. The majority of respondents to the contraceptive practitioner survey were general practitioners (28 %, n = 20). Three quarters of respondents reported little knowledge of bariatric surgery, and many reported not seeing women with obesity requiring contraception before (66 %, n = 45) or after surgery (71 %, n = 49). CONCLUSIONS: There is a need to increase knowledge levels of contraception within bariatric surgical teams and to understand why, despite increasing levels of bariatric surgery, women do not seem to be appearing for advice in contraceptive settings

60dB high-extinction auto-configured Mach-Zehnder interferometer

Imperfections in integrated photonics manufacturing have a detrimental effect on the maximal achievable visibility in interferometric architectures. These limits have profound implications for further photonics technological developments and in particular for quantum photonics technologies. Active optimisation approaches, together with reconfigurable photonics, have been proposed as a solution to overcome this. In this paper, we demonstrate an ultra-high (>60 dB) extinction ratio in a silicon photonic device consisting of cascaded Mach-Zehnder interferometers, in which additional interferometers function as variable beamsplitters. The imperfections of fabricated beamsplitters are compensated using an automated progressive optimization algorithm with no requirement for pre-calibration. This work shows the possibility of integrating and accurately controlling linear-optical components for large-scale quantum information processing and other applications.Comment: 4 pages, 3 figure

Genome-wide and protein kinase-focused RNAi screens reveal conserved and novel damage response pathways in Trypanosoma brucei

All cells are subject to structural damage that must be addressed for continued growth. A wide range of damage affects the genome, meaning multiple pathways have evolved to repair or bypass the resulting DNA lesions. Though many repair pathways are conserved, their presence or function can reflect the life style of individual organisms. To identify genome maintenance pathways in a divergent eukaryote and important parasite, Trypanosoma brucei, we performed RNAi screens to identify genes important for survival following exposure to the alkylating agent methyl methanesulphonate. Amongst a cohort of broadly conserved and, therefore, early evolved repair pathways, we reveal multiple activities not so far examined functionally in T. brucei, including DNA polymerases, DNA helicases and chromatin factors. In addition, the screens reveal Trypanosoma- or kinetoplastid-specific repair-associated activities. We also provide focused analyses of repair-associated protein kinases and show that loss of at least nine, and potentially as many as 30 protein kinases, including a nuclear aurora kinase, sensitises T. brucei to alkylation damage. Our results demonstrate the potential for synthetic lethal genome-wide screening of gene function in T. brucei and provide an evolutionary perspective on the repair pathways that underpin effective responses to damage, with particular relevance for related kinetoplastid pathogens. By revealing that a large number of diverse T. brucei protein kinases act in the response to damage, we expand the range of eukaryotic signalling factors implicated in genome maintenance activities

The Performance of Alternative Livelihood Initiatives on Local Livelihoods and Forest Conservation Management - A Case Study in Talai Commune, Dong Nai Province, Vietnam

Protected forest areas worldwide are located close to forest dependent communities that continue to use forest resources for their livelihoods to varying extents. With these areas designated as protected areas it prevents local people from practising their traditional income-generating or subsistence activities that rely on access to forest areas. Although governments view protected areas as a measure for forest conservation, they pose a number of key challenges to local people's livelihoods. In a number of developing countries, including Vietnam, the use of forest resources in protected areas have presented a threat to forest conservation outcomes. A satisfactory resolution to the tension between livelihoods and biodiversity conservation objectives in protected areas is an ongoing challenge for governments and local people living near protected areas. Cat Tien National Park, a protected area in Dong Nai Province, Vietnam is well-known for its diversity of flora and fauna and offers a noteworthy case study. One of the issues in Cat Tien National Park is the practice of collecting non-timber forest products that is considered widespread, despite it being illegal under the protected status of the Park. Achieving forest conservation goals under these circumstances, even if extraction levels were low, appears to be a challenging task. In order to address livelihood challenges, governmental agencies, and non-governmental organisations have attempted to engage local people in alternative livelihood initiatives. These initiatives commonly seek to provide new income sources as a substitute for earnings from traditional livelihood practices, thereby reducing extraction pressures on the Park. These livelihood initiatives have been active in the last thirteen years. The aim of this thesis is therefore to examine the performance of two alternative livelihood initiatives (the Talai Ecotourism Venture and the Forest Protection Team (FPT)) on local livelihoods for those ethnic groups living in close proximity to the Park and associated effects on forest conservation management goals. The research provided insights into the participation of local people in decisions about the management and conservation of forest resources in their role as FPT members. It also attempts to draw lessons that can be applied to alternative livelihood initiatives elsewhere in Vietnam and other developing countries. A case study approach with a mixed method has been employed in this study. Household surveys (n=150) of three ethnic groups (Chau Ma, Stieng and Kinh) and key informant interviews (n=36) were conducted to collect data on a range of aspects, including: household demographics, forest usage, and local views on the impact of the two alternative livelihood initiatives on their livelihood and perception of forest conservation. The key informants were interviewed at length about their roles, responsibilities, the quality of the local participation, and evaluation of the effectiveness of the two alternative livelihood initiatives on local livelihood and forest conservation. Field research findings were supplemented and triangulated with participant observation activities to gain insight into the physical, social, cultural, and economic aspects of the case context. About one third of Chau Ma and Stieng households had a high reliance on NTFPs, while Kinh households had no reliance on NTFPs for their livelihood. The dependence on NTFPs for Chau Ma and Stieng people was a result of limited opportunities for other livelihood options due to relinquishing agricultural land and low education levels. For Chau Ma and Stieng people struggling to adjust from a subsistence forest-based livelihood to living outside the forest, around 41% continued to visit the forest for cultural reasons, but at low to moderate levels (63%). A significant finding of the study is that the benefits of the alternative livelihood initiatives did not extend to the whole community and were focused largely on those ethnic minorities of Chau Ma and Stieng directly involved in the initiatives. Further, for the two alternative livelihood initiatives, the direct participants gained the greatest benefits either through employment, access to Village Development Fund, or greater access to NTFPs. The study has also found that current livelihood initiatives have not been effective due to limited local participation in decision-making processes, and minimal interaction with local people outside the initiatives. Specifically, the governance of these initiatives was not aligned with communitybased principles. The one-way information sharing, and top-down decision-making led to the ethnic minorities assuming only a passive role in the process for the two alternative livelihood initiatives. In addition, local members of both livelihood initiatives did not receive the training or support they required to effectively carry out their responsibilities. The results of the case studies also showed that there was a lack of responsiveness from key governing authorities such as the Private Company, Talai Forest Station, Park Board to variations in ethnic groups' socio-economic status, and levels of literacy. As a whole, such deficient governance arrangements and processes prevented the initiatives from achieving their goals and engaging with the broader community. In addition, evidence suggests that the Talai Ecotourism Venture and the Forest Protection Team initiatives have not led to a substantial change in local people's awareness of the importance of forest conservation and lessening the pressure on forest resource extraction as expected. These findings demonstrate the need for better governance, which provide stakeholders with the ability to demonstrate their understanding and fulfil their responsibilities independently. A greater level of accountability and transparency in benefit sharing mechanisms such as Village Development Fund (Talai Ecotourism Venture), and Forest Protection Team reporting is also required for ensuring greater community participation and empowerment. Another important implication of improved accountability is for a more effective relationship between government, private enterprise and local people in decision making and empowering them in their roles. Finally, the findings also highlight the significance of capacity building for various stakeholders so that they can develop skills and knowledge required to carry out decision-making responsibilities in ecotourism and forest management. Most importantly, alternative livelihood initiatives need to be designed and implemented with sensitivity to the local cultures otherwise; they can limit potential equality and increase obstacles to local people's participation and decision-making. Thus, it is recommended that Indigenous knowledge should be recognized and incorporated into initiatives for protecting and managing forest resources

Composite Quasar Spectra From the Sloan Digital Sky Survey

We have created a variety of composite quasar spectra using a homogeneous data set of over 2200 spectra from the Sloan Digital Sky Survey (SDSS). The quasar sample spans a redshift range of 0.044 <= z <= 4.789, and an absolute r' magnitude range of -18.0 to -26.5. The median composite covers a rest wavelength range from 800 - 8555A, and reaches a peak signal-to-noise ratio of over 300 per 1A resolution element in the rest frame. We have identified over 80 emission line features in the spectrum. Emission line peak velocity shifts of the broad permitted and semi-forbidden lines are strongly correlated with ionization energy, as previously suggested, but we find that the narrow forbidden lines are also shifted by amounts which are strongly correlated with ionization energy. The magnitude of the forbidden line shifts is < 100 km/s, compared to shifts of up to 550 km/s for some of the permitted and semi-forbidden lines. At wavelengths longer than the Ly-a emission, the continuum of the geometric mean composite is well-fit by two power-laws, with a break at approximately 5000A. The frequency power law index, alpha_nu, is -0.44 from 1300 - 5000A, and -2.45 redward of about 5000A. The abrupt change in slope can be accounted for partly by host galaxy contamination at low redshift. Stellar absorption lines, including higher-order Balmer lines, seen in the composites suggest that young or intermediate age stars make a significant contribution to the light of the host galaxies. An electronic table of the median quasar template is available.Comment: 40 pages, including 11 postscript figures, accepted by AJ; for the full version of table 1, see: ftp://sdss.fnal.gov/pub/danvb/qsocomposite/sdss_qso_median.tab

The Chandra COSMOS Survey: III. Optical and Infrared Identification of X-ray Point Sources

The Chandra COSMOS Survey (C-COSMOS) is a large, 1.8 Ms, Chandra program that has imaged the central 0.9 deg^2 of the COSMOS field down to limiting depths of 1.9 10^-16 erg cm^-2 s-1 in the 0.5-2 keV band, 7.3 10^-16 erg cm^-2 s^-1 in the 2-10 keV band, and 5.7 10^-16 erg cm^-2 s-1 in the 0.5-10 keV band. In this paper we report the i, K and 3.6micron identifications of the 1761 X-ray point sources. We use the likelihood ratio technique to derive the association of optical/infrared counterparts for 97% of the X-ray sources. For most of the remaining 3%, the presence of multiple counterparts or the faintness of the possible counterpart prevented a unique association. For only 10 X-ray sources we were not able to associate a counterpart, mostly due to the presence of a very bright field source close by. Only 2 sources are truly empty fields. Making use of the large number of X-ray sources, we update the "classic locus" of AGN and define a new locus containing 90% of the AGN in the survey with full band luminosity >10^42 erg/s. We present the linear fit between the total i band magnitude and the X-ray flux in the soft and hard band, drawn over 2 orders of magnitude in X-ray flux, obtained using the combined C-COSMOS and XMM-COSMOS samples. We focus on the X-ray to optical flux ratio (X/O) and we test its known correlation with redshift and luminosity, and a recently introduced anti-correlation with the concentration index (C). We find a strong anti-correlation (though the dispersion is of the order of 0.5 dex) between C and X/O, computed in the hard band, and that 90% of the obscured AGN in the sample with morphological information live in galaxies with regular morphology (bulgy and disky/spiral), suggesting that secular processes govern a significant fraction of the BH growth at X-ray luminosities of 10^43- 10^44.5 erg/s.Comment: 21 pages, 17 figures, 4 tables; accepted for publication in ApJS. The catalog is available at the urls listed in the pape

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses