14 research outputs found
PLoS One
No full textNeisseria meningitidis (Nm), Haemophilus influenzae (Hi), and Streptococcus pneumoniae (Sp) are the lead causes of bacterial meningitis. Detection of these pathogens from clinical specimens using traditional real-time PCR (rt-PCR) requires DNA extraction to remove the PCR inhibitors prior to testing, which is time consuming and labor intensive. In this study, five species-specific (Nm-sodC and -ctrA, Hi-hpd#1 and -hpd#3 and Sp-lytA) and six serogroup-specific rt-PCR tests (A, B, C, W, X, Y) targeting Nm capsular genes were evaluated in the two direct rt-PCR methods using PerfeCTa and 5x Omni that do not require DNA extraction. The sensitivity and specify of the two direct rt-PCR methods were compared to TaqMan traditional rt-PCR, the current standard rt-PCR method for the detection of meningitis pathogens. The LLD for all 11 rt-PCR tests ranged from 6,227 to 272,229 CFU/ml for TaqMan, 1,824-135,982 for 5x Omni, and 168-6,836 CFU/ml for PerfeCTa. The diagnostic sensitivity using TaqMan ranged from 89.2%-99.6%, except for NmB-csb, which was 69.7%. For 5x Omni, the sensitivity varied from 67.1% to 99.8%, with three tests below 90%. The sensitivity of these tests using PerfeCTa varied from 89.4% to 99.8%. The specificity ranges of the 11 tests were 98.0-99.9%, 97.5-99.9%, and 92.9-99.9% for TaqMan, 5x Omni, and PerfeCTa, respectively. PerfeCTa direct rt-PCR demonstrated similar or better sensitivity compared to 5x Omni direct rt-PCR or TaqMan traditional rt-PCR. Since the direct rt-PCR method does not require DNA extraction, it reduces the time and cost for processing CSF specimens, increases testing throughput, decreases the risk of cross-contamination, and conserves precious CSF. The direct rt-PCR method will be beneficial to laboratories with high testing volume.201626829233PMC47355091023
Evaluations of the Environmental Effects of Controlled Tile Drainage on Watershed and River Using the Improved SWAT and the QUAL2Kw Under Current and Future Climate Regimes
No full textIn agriculture-dominated areas, water pollution resulting from nutrients migrating from farms to water bodies is a major concern. The migration is further exacerbated by traditional tile drain known as Uncontrolled Tile Drainage (UCTD), which removes excess water from areas to keep the water table low enough for crops to grow. UCTD, commonly used in Ontario, Canada, is believed to contribute to water quality issues, whereas Controlled Tile Drainage (CTD) is an alternative technique in which a structure controls the outlets of the drains so that water only leaves a field when the water table level exceeds a desired threshold. Considered as a Best Management Practice (BMP), CTD has been documented as an efficient practice preventing nutrients from migrating out of agricultural fields. This thesis aims to improve our understanding of the environmental benefits of replacing UCTD with CTD. Three significant contributions were achieved.
The first contribution of the thesis is the improvements of the algorithm for calculating nitrates in tile flows in the Soil and Water Assessment Tool (SWAT) model. Researchers have simulated CTD by dynamically changing tile depth to mimic the operation of outlet structure gates, but it has been demonstrated that doing so results in inaccuracies, and so the algorithm in the model has been improved subsequently. The current author proposed and tested a new algorithm for calculating nitrates in tile flows that better represents the dynamics of water and nutrients in soil layers for the SWAT model. A model for the South Nation watershed, located in Ontario, Canada, was then developed and successfully calibrated using the improved SWAT model.
The second contribution was the extension of the SWAT model to simulate riverine hydraulic and water quality processes by coupling it with the QUAL2Kw model. In this thesis, a procedure is developed to couple the SWAT model and the QUAL2Kw model to enable continuous simulations of 13 water quality parameters in the South Nation River system. The coupled model was calibrated and verified at various observed locations along the river during the five seasons of growth from 2006 to 2010. The simulation results suggested that CTD also improved the water quality of the river by lowering biologically available N levels of NO2--N, and NO3--N, thereby impeding phytoplankton growth in the river.
The third contribution is the verification of the benefits of replacing UCTD with CTD in the future climates. The confirmation was done using the SWAT model alone, and then the coupled SWAT/QUAL2K models, using a matrix of climate change experiments performed with several Global Climate Models and Regional Climate Models. The results suggest that nutrient loading from the watershed will increase in the 2021–2050 period compared to the 1985–2006 period. Thus, pollution from agricultural fields will worsen with the current UCTD approach, while the results also show that CTD would perform effectively and stably in future climate scenarios and could counterbalance the effects of climate change on water quality.
To the author’s knowledge, this study is the first attempt to date to assess the environmental effects of CTD on a watershed and river by coupling the SWAT and QUAL2Kw models. The findings expand the current scope of knowledge on the environmental effects of CTD on watersheds and rivers under current and future climate change regimes. Long periods of continuous simulation and a matrix of climate change scenarios also make this study stand out from other studies. It laid a foundation for future investigations
Lancet Infect Dis
No full textBackgroundTo combat Neisseria meningitidis serogroup A epidemics in the meningitis belt of sub-Saharan Africa, a meningococcal serogroup A conjugate vaccine (MACV) has been progressively rolled out since 2010. We report the first meningitis epidemic in Niger since the nationwide introduction of MACV.MethodsWe compiled and analysed nationwide case-based meningitis surveillance data in Niger. Cases were confirmed by culture or direct real-time PCR, or both, of cerebrospinal fluid specimens, and whole-genome sequencing was used to characterise isolates. Information on vaccination campaigns was collected by the Niger Ministry of Health and WHO.FindingsFrom Jan 1 to June 30, 2015, 9367 suspected meningitis cases and 549 deaths were reported in Niger. Among 4301 cerebrospinal fluid specimens tested, 1603 (37\ub73%) were positive for a bacterial pathogen, including 1147 (71\ub75%) that were positive for N meningitidis serogroup C (NmC). Whole-genome sequencing of 77 NmC isolates revealed the strain to be ST-10217. Although vaccination campaigns were limited in scope because of a global vaccine shortage, 1\ub74 million people were vaccinated from March to June, 2015.InterpretationThis epidemic represents the largest global NmC outbreak so far and shows the continued threat of N meningitidis in sub-Saharan Africa. The risk of further regional expansion of this novel clone highlights the need for continued strengthening of case-based surveillance. The availability of an affordable, multivalent conjugate vaccine may be important in future epidemic response.CC999999/Intramural CDC HHS/United State
J Infect Dis
No full textBackground.In 2010, Niger and other meningitis belt countries introduced a meningococcal serogroup A conjugate vaccine (MACV). We describe the epidemiology of bacterial meningitis in Niger from 2010 to 2018.Methods.Suspected and confirmed meningitis cases from January 1, 2010 to July 15, 2018 were obtained from national aggregate and laboratory surveillance. Cerebrospinal fluid specimens were analyzed by culture and/or polymerase chain reaction. Annual incidence was calculated as cases per 100 000 population. Selected isolates obtained during 2016\u20132017 were characterized by whole-genome sequencing.Results.Of the 21 142 suspected cases of meningitis, 5590 were confirmed: Neisseria meningitidis ([Nm] 85%), Streptococcus pneumoniae ([Sp] 13%), and Haemophilus influenzae ([Hi] 2%). No NmA cases occurred after 2011. Annual incidence per 100 000 population was more dynamic for Nm (0.06\u20137.71) than for Sp (0.18\u20130.70) and Hi (0.01\u20130.23). The predominant Nm serogroups varied over time (NmW in 2010\u20132011, NmC in 2015\u20132018, and both NmC and NmX in 2017\u20132018). Meningococcal meningitis incidence was highest in the regions of Niamey, Tillabery, Dosso, Tahoua, and Maradi. The NmW isolates were clonal complex (CC)11, NmX were CC181, and NmC were CC10217.Conclusions.After MACV introduction, we observed an absence of NmA, the emergence and continuing burden of NmC, and an increase in NmX. Niger\u2019s dynamic Nm serogroup distribution highlights the need for strong surveillance programs to inform vaccine policy.001/WHO_/World Health Organization/InternationalCC999999/ImCDC/Intramural CDC HHS/United States2021-01-15T00:00:00Z31671439PMC7808897896
The 'Synopsis Chronike' and its place in the Byzantine chronicle tradition: its sources (Creation – 1081 CE)
No full textThe subject of this thesis is the Synopsis Chronike (or Synopsis Sathas), a Byzantine chronicle of the thirteenth century that conveys the history of the world, starting from Adam and concluding with the recapture of Constantinople in 1261. The study focuses on the first part of the text (Adam – Nikephoros Botaneiates), and more specifically on the comprehensive presentation and analysis of the whole corpus of its sources, passage by passage, in order to reconstruct the background of the chronicle and to determine its place in the Byzantine chronicle tradition.
Following the introductory first chapter, which sets out the aims of the thesis and establishes its methodology, chapter two offers an overview of the chronicle itself, and a first discussion of the main issues it presents: the key characteristics of its narrative structure, its manuscript tradition, and – mainly – the problem of its authorship, with special reference to the commonly supposed author, Theodore Skoutariotes, bishop of Kyzikos. Chapter three conveys a detailed presentation of the results of our research; following the discussion of the sources and influences of the proem, it attempts to place each passage of the Synopsis Chronike in the context of any related texts, which are then identified as 'main sources', 'other sources' and 'parallel passages', depending on their link to the Synopsis Chronike. Chapter four discusses individually each text that appears as a source of the Synopsis Chronike, and locates its place amongst the whole corpus of the sources. Furthermore, it examines the passages for which we were not able to identify a main source, and suggests possible sources that have not survived. Finally, the concluding chapter of the thesis summarises the earlier discussion, and attempts to combine the different pieces of information, and to provide an overall picture of the background of the Synopsis Chronike in order to establish – to the degree that it is possible – its position in the Byzantine chronicle tradition
Development of Real-Time PCR Methods for the Detection of Bacterial Meningitis Pathogens without DNA Extraction.
No full textNeisseria meningitidis (Nm), Haemophilus influenzae (Hi), and Streptococcus pneumoniae (Sp) are the lead causes of bacterial meningitis. Detection of these pathogens from clinical specimens using traditional real-time PCR (rt-PCR) requires DNA extraction to remove the PCR inhibitors prior to testing, which is time consuming and labor intensive. In this study, five species-specific (Nm-sodC and -ctrA, Hi-hpd#1 and -hpd#3 and Sp-lytA) and six serogroup-specific rt-PCR tests (A, B, C, W, X, Y) targeting Nm capsular genes were evaluated in the two direct rt-PCR methods using PerfeCTa and 5x Omni that do not require DNA extraction. The sensitivity and specify of the two direct rt-PCR methods were compared to TaqMan traditional rt-PCR, the current standard rt-PCR method for the detection of meningitis pathogens. The LLD for all 11 rt-PCR tests ranged from 6,227 to 272,229 CFU/ml for TaqMan, 1,824-135,982 for 5x Omni, and 168-6,836 CFU/ml for PerfeCTa. The diagnostic sensitivity using TaqMan ranged from 89.2%-99.6%, except for NmB-csb, which was 69.7%. For 5x Omni, the sensitivity varied from 67.1% to 99.8%, with three tests below 90%. The sensitivity of these tests using PerfeCTa varied from 89.4% to 99.8%. The specificity ranges of the 11 tests were 98.0-99.9%, 97.5-99.9%, and 92.9-99.9% for TaqMan, 5x Omni, and PerfeCTa, respectively. PerfeCTa direct rt-PCR demonstrated similar or better sensitivity compared to 5x Omni direct rt-PCR or TaqMan traditional rt-PCR. Since the direct rt-PCR method does not require DNA extraction, it reduces the time and cost for processing CSF specimens, increases testing throughput, decreases the risk of cross-contamination, and conserves precious CSF. The direct rt-PCR method will be beneficial to laboratories with high testing volume
認知心理学的知見を踏まえた国語教科書「書くこと」教材の分析 : 小学校学習指導要領改訂による変化を中心に
No full text2011-03-31本研究の目的は、小学校国語教科書の「書くこと」教材を認知心理学的視点から分析し、その特徴を明らかにすることである。平成10(1998)年版学習指導要領が反映された平成17(2005)年度版教科書と平成20(2008)年版学習指導要領が反映された平成23(2011)年度版教科書（光村図書、東京書籍、教育出版）を対象にして調査した結果、平成17年度版から平成23年度版への変化として、(1)子どもに考えさせるための問いが設定されている、(2)文章の「型」や具体的観点等の手がかりが示されている、(3)プランニングや下書き中の子どもの思考が可視化されている、という点が示され、子どもの認知的負担を軽減する効果が期待できることが伺われた。その一方、平成17年度版と平成23年度版で、（1）読み手を意識させるための具体的活動が設定されていない、（2）下書きや推敲の扱いが少なく、書くことが再帰的プロセスであることが示されていない、という点に変化が見られず、認知心理学的な研究知見が十分に生かされていないことも示され、今後改善していく必要があることが明らかとなった。The purpose of this study was to examine the teaching units for writing within Japanese language textbooks for elementary schools from the perspective of cognitive psychology. The author surveyed textbooks that were published in Heisei 17 (2005) and Heisei 23 (2011) by three publishing companies （Mitsumura Tosho, Tokyo Shoseki, and Kyoiku Shuppan). Textbooks published in Heisei 17 were reflected the National Curriculum Standards for Elementary Schools notified in Heisei 10 (1998) , while textbooks published in Heisei 23 were reflected the National Curriculum Standards for Elementary Schools notified in Heisei 20 (2008). The results indicated that textbooks published in Heisei 23 (1) contained many questions facilitated children's thinking, (2) showed text structures and various hints, and (3) made children's thoughts while planning and drafting visible. These characteristics were expected to help to lighten children's cognitive burden. Meanwhile, both textbooks published in Heisei 17 and ones in Heisei 23 (1) did not contain activities to make children aware of readers, and (2) did not show that writing was a recursive process and writers should make many drafts and revise. Therefore, textbooks did not reflect the knowledge of cognitive psychology well and needed to be improved immediately.departmental bulletin pape
Diagnostic sensitivity and specificity for the real-time PCR tests by latent class analysis.
No full textDiagnostic sensitivity and specificity for the real-time PCR tests by latent class analysis.</p
