Systematic comparison of the human saliva and plasma proteomes

The proteome of human salivary fluid has the potential to open new doors for disease biomarker discovery. A recent study to comprehensively identify and catalog the human ductal salivary proteome led to the compilation of 1166 proteins. The protein complexity of both saliva and plasma is large, suggesting that a comparison of these two proteomes will provide valuable insight into their physiological significance and an understanding of the unique and overlapping disease diagnostic potential that each fluid provides. To create a more comprehensive catalog of human salivary proteins, we have first compiled an extensive list of proteins from whole saliva (WS) identified through MS experiments. The WS list is thereafter combined with the proteins identified from the ductal parotid, and submandibular and sublingual (parotid/SMSL) salivas. In parallel, a core dataset of the human plasma proteome with 3020 protein identifications was recently released. A total of 1939 nonredundant salivary proteins were compiled from a total of 19 14474 unique peptide sequences identified from whole and ductal salivas[semi] 740 out of the total 1939 salivary proteins were identified in both whole and ductal saliva. A total of 597 of the salivary proteins have been observed in plasma. Gene ontology (GO) analysis showed similarities in the distributions of the saliva and plasma proteomes with regard to cellular localization, biological processes, and molecular function, but revealed differences which may be related to the different physiological functions of saliva and plasma. The comprehensive catalog of the salivary proteome and its comparison to the plasma proteome provides insights useful for future study, such as exploration of potential biomarkers for disease diagnostics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61527/1/prca_200800140_sm_miscellaneous_information.pd

Une réinterprétation de l’acte de foi face aux défis de nouveaux athées

Artykuł traktuje o potrzebie odnowienia rozumienia rzeczywistości wiary w kontekście wyzwań, które nowy ateizm stawia przed osobami wierzącymi. Wśród poruszanych wątków pojawiły się też problem niewiary w ogólności czy obojętności. Istotne w reformie odczytywania współcześnie natury wiary jest to, by wiarę rozpatrywać w zgodzie z rozumem, odpowiedzialnością, wolnością i jej posłannictwem. Z przeprowadzonych rozważań wynika możliwość i potrzeba współpracy wiary i rozumu, która jest najlepszą formą reakcji na opinie nowych ateistów. Widać, że często ateizm w wydaniu klasycznym jest formą zniewolenia umysłu, a w formie współczesnej stanowi zniewolenie woli. Jednakże źle realizowana wiara, oderwana od swoich korzeni, wynaturzona i pozbawiona racjonalności stanowi dokładnie to samo zniewolenie i staje się tak samo niebezpieczna jak ateizm. Kryzys wiary pojawia się tam, gdzie brakuje racjonalności. Jeśli wiara boi się rozumu, to znaczy, że czegoś jej brakuje. Być może brakuje jej zakorzenienia w prawdzie, odwagi do podjęcia decyzji i wzięcia odpowiedzialności. Być może boi się wątpliwości, wciąż postrzegając je jako wadę, zamiast widzieć w nich szansę. Być może boi się pytań, na które nie ma łatwych odpowiedzi; pytań, na które odpowiedzi szuka się latami albo i przez całe życie. Jeśli rozum boi się wiary, to znaczy, że brakuje mu krytycyzmu i pokory – samoświadomości. Jeśli rozum boi się wiary, to znaczy, że boi się, że może nie być samowystarczalny. Być może boi się nadprzyrodzoności, bo ona stawia przed człowiekiem kolejne wyzwania. Być może boi się, że przygoda z wiarą zaskoczy go na tyle, że będzie musiał zreorganizować całe swoje myślenie. Być może boi się, że dotąd błądził i będzie musiał rozpocząć poszukiwania od nowa. Ratunkiem dla wiary jest skazanie jej na racjonalność. Nie chodzi tu o to, by nie docenić wiary jako takiej, a przecenić rozum. Wręcz przeciwnie, chodzi o zachowanie zdrowych relacji między nimi, tak by rozum wspierał człowieka na drodze do Boga, pozwalając tajemnicą nazywać to, co faktycznie nią jest, a nie to, czego jeszcze człowiek nie zdołał odkryć.The theme of this article is Reinterpretation the act of faith to the challenges of the new atheists. The first part is dedicated to the new atheism, the definition of this trend, its characteristics, the main representatives and their demands. The second point of the work is a response to the challenges the new atheists to the people of believers. The article discusses the need to renew the understanding of the reality of the faith in the context of the challenges the new atheism. Among the topics discussed there were also a problem of unbelief and indifference in general. The conducted considerations that possibility and need for cooperation between faith and reason, which is the best form of response to the views of the new atheists. It is noted that often with the release of the classic atheism is a form of enslavement of the mind, in the form of modern slavery is the will. However, poorly implemented faith, detached from their roots, unnatural and devoid of rationality is exactly the same as slavery and becomes as dangerous as atheism. The crisis of faith occurs where lack of rationality. The point is not to underestimate the faith as such and overestimate reason. On the contrary, to preserve a healthy relationship between them, so as to support human mind on the way to God, letting the mystery call it what it really is, and not what else man was able to discover

Green Urban Drainage Infrastructure : Hydrology and Modelling of Grass Swales

The management of urban runoff has evolved along with the advancement of understanding of runoff environmental impacts. Besides the impacts on water quality in the receiving waters, the impacts on the urban hydrologic regime include reduced infiltration by the sealing of pervious land, reduced evapotranspiration by removal of vegetation, and the resulting increase of stormwater runoff peaks and volumes causing flooding, and ultimately degradation of receiving waters. In such considerations, urban stormwater management benefits from the implementation of Green Infrastructure which includes decentralized vegetative controls that capture and infiltrates rain where it falls and thus reduces and improves stormwater runoff. An example of small scale elements of Green Infrastructure are traditional grass swales. Through shallow depressions with mild side slopes grass swales collect and infiltrate stormwater from parking lots and roads, while runoff flows are attenuated and further conveyed depending on the hydraulic loading. Grass swales usually operate reliably and their maintenance needs are well understood. Their hydrological performance is, beside their dimensions and the contributing area, determined mainly by hydraulic and soil-related hydrological parameters that change with the intensity of the storm. Yet, because swales discharge to downstream drainage elements, either to the conventional sewer system or to other stormwater management facilities, the knowledge of the underlying inter-related processes and influential factors that govern the hydraulic and hydrological performance of grass swales is required. Against this background, this thesis is devoted to such questions as (i) what are the differences in the hydraulic and hydrological performance of the studied swales, (ii) how do soil characteristics, including the antecedent soil moisture, influence the swale water balance for various hydraulic loadings; and (iii) how can the related hydrological processes be simulated in high-resolution and reliably predicted using a grid-based, distributed model. For this purpose, full-scale studies were performed in three 30-m grass swale sections in Luleå, Northern Sweden, by collecting hydraulic and hydrological data based on routine storm events mimicking block-rainfall storm events of 2 months and 3 years recurrence. The resulting runoff and soil moisture data were used to calculate the swale water balance, to derive event hydrographs and to obtain calibration and validation data for model simulations. The experimental results showed that the relative swale flow volume reduction decreased with an increasing soil moisture and indicated the transition in dominating swale functions: at low initial SWC, runoff was highly attenuated (up to 74%), but for high SWC, the conveyance function dominated (with attenuation as low as 17%). Runoff flow peaks were reduced, proportionally to the volume reductions. Swale outflow hydrograph lag times varied between 5 to 15 minutes and decreased with increasing soil moisture. The swale wetness affected runoff formation, attenuation and subsequent outlet discharge and, for the short-duration events tested, only the top soil layer contributed to these findings. In the three swales tested, soils, initial soil water content, saturated hydraulic conductivity and topography varied spatially significantly. Double-ring infiltrometer measurements resulted in values of 1.78, 4.04 and 9.41 cm/hr (n=9) in the three swales tested and deviated from estimates from averages of spatially integrated infiltration rates. However, with regard to spatial variability, only the topography, described as irregularities in the swale bottom slopes affected the swale runoff dissipation and conveyance in the early phase of the events. Together with estimates of the water stored in the top soil layer, 4-32% of runoff volumes from the mimicked 2-month storm were temporarily stored. The distributed model Mike SHE was found capable of simulating swale drainage processes, when properly calibrated. Close agreement (NSE>0.8) was found not only for the measured and simulated swale outlet hydrographs, but also for the changes of the soil moisture in the top soil layer, which shows rapid increase up to the saturated soil water content, but minor or no progression in depths of 0.2 m. The model output was little sensitive to the initial soil water content, especially for low inflow which resulted in larger residuals in simulated runoff peak flows and volumes. As in field measurements, spatial variability of the initial soil water content had no effect on the swale outflow, but the accuracy of the topographical representation. The thesis findings include several implications regarding effects of the assessed parameters in the application of the model for swale flow simulation and eventually the design of grass swales.Urban dagvattenhantering har utvecklats parallellt med en ökad förståelse för dagvattnets allmänna miljöpåver­kan. Utöver ytvattenkvalitén i recipientvatten påverkas även den hydrologiska regimen genom reducerad infilt­rationsförmåga i mark orsakad av allt tätare ytskikt samt reducerad evapotranspiration orsakad av minskad vegetationsutbredning. Detta ger både förhöjda toppflöden och avrinningsvolymer, vilket kan resultera i över­svämning och slutligen en försämrad ytvattenkvalité i recipienterna. Dagens urbana dagvattensystem förändras mot en högre grad av grön infrastruktur som en central systemkomponent. Decentraliserad omhändertagning av dagvatten såsom svackdiken utjämnar och för bort dagvattensflöden, samtidigt som de fungerar tillförlitligt och deras underhållsåtgärder är välkända. Uppbyggda med små svackor och låglutande slänter samlar svackdiken in och infiltrerar dagvatten från parkeringsytor och vägar. Dessa svackdikens hydrologiska funktion bestäms av en rad faktorer, utöver teknisk dimensionering och avrinningsområdets storlek och hydrologi, även av hydraulik och jordartsrelaterad hydrologi som förändras beroende på respektive nederbördstillfälles intensitet och varak­tighet. Eftersom svackdikens utflöde passerar nedströms liggande dagvattentekniker/anordningar, antingen konventionella ledningssystem eller andra teknologier, krävs full förståelse och kunskap om de faktorer som styr svackdikens hydraulik och hydrologi. Mot denna bakgrund fokuserar avhandlingen på frågorna (i) vilka skillnader finns med avseende på hydraulisk och hydrologisk prestanda för de studerade svackdiken, (ii) i vilken mån påverkar markartsförhållanden, inklu­sive ingående markfuktighet, svackdikens vattenbalans vid varierande hydraulisk belastning; samt (iii) hur och i vilken mån kan ovanstående simuleras högupplöst och förutsägbart, via den rutnätsbaserade distribuerade mo­dellen Mike SHE. Därför har fullskaliga studier bedrivits i två 30 m långa svackdiken i Luleå kommuns södra stadsområde, där hydrauliska och hydrologiska data insamlats baserat på standardiserade nederbördsförlopp, återskapande blockregn med 2 månaders och 3 års återkomsttid. Data för avrinning och markfukthalter använ­des för att beräkna svackdikenas vattenbalans, nederbördförloppens hydrografer samt erhålla kalibrering- och valideringsdata för modellsimuleringar. Resultaten från experimenten visade att den volymetriska flödesre­duktionen minskade relativt sett med ökande markfukthalt, indikerande en övergång för svackdikets domine­rande funktionalitet: vid låga initiala SWC var avrinningen tydligt dämpad (upp till 74%), medan för höga SWC innebar att transportfunktionen dominerade (med dämpningsgrad ner mot 17%). Avrinnande momentana topp­flöden reducerades proportionellt mot volymreduktionen. Laggtiden för svackdikets utflödeshydrograf varierade mellan 5 och 15 minuter och reducerades med ökande markfukthalt. Fuktförhållandena i svackdiket påverkade avrinningsförloppet, flödesdämpning och efterföljande utsläpp, och enbart svackdikets översta markskikt berör­des under de kortvariga bevattningscyklerna. I de tre testade svackdikena varierade jordart, initial markfukthalt, mättad hydraulisk konduktivitet och topografi signifikant. Mätningar med dubbelrings infiltrometrar gav föl­jande resultat, 1.78, 4.04 samt 9.41 cm/h (n=9), vilket avvek från medelvärdesbaserat estimat från spatialt inte­grerade infiltrationshastigheter. Med avseende på spatial variabilitet påverkade endast svackdikenas topografi, i form av ojämnheter i och nära dikesbotten, avrinningsförloppen och bortledning under den inledande fasen av regnhändelsen. Sammantaget med uppskattningar av den lagrat vatten i marklagrets toppskikt, bedöms 4-32% av svackdikets ytavrinning från ett simulerade nederbördtillfälle med 2 månaders återkomststid kunna lagras tillfälligt. Mike SHE befanns kapabel att med god noggrannhet kunna reproducera naturbundna dräneringsför­lopp och flöden i svackdiken, förutsatt tillbörlig kalibrering. God överensstämmelse (NSE>0.8) framkom inte bara mellan uppmätta och simulerade utgående hydrografer, utan också beträffande ändring av markfukthalt i ytligt marklager med snabb höjning av fukthalt upp emot full vattenmättnad. Däremot framkom endast mindre (eller total frånvaro av) överensstämmelse vad gäller markdjup av 0.2 m. Modellens output uppvisade låg käns­lighet för ursprunglig markfukthalt, speciellt gällande lågt flöde vilket resulterade i större residualer för simule­rade toppflöden och avrinningsvolymer. För fältförsöken framkom att den initiala markfukthaltens spatiala variabilitet inte påverkade utflödet från svackdiket – i motsats till noggrannheten i dikets topografiska repre­sentation. Denna uppsats belyser samband och följdverkningar beträffande påverkan från undersökta parametrar på en modell för flödes- och vattenföring i ett svackdike och framledes framtida design av svackdiken

Comparison of spatial interpolation methods for soil moisture in Green Stormwater Infrastructure

Knowledge about soil-physical variables of Green Stormwater Infrastructure (GSI) like soil moisture (θ) isessential to understanding their hydrologic and treatment performance. θ depends on many local factorsand is subject to high spatial and temporal variability (Takagi and Lin, 2012; Yao et al. 2013; Nasta et al. 2018).Information about the spatially continuous data of θ can help to understand the hydrologic response andprovide an input for initial conditions to improve hydrologic modelling results. A number of deterministic andprobabilistic interpolation methods and tools are available today to model the spatial distribution ofenvironmental parameters such as θ (Li and Heap 2011; Yao et al. 2013). The quality of the spatialinterpolation, however, depends on sample size, sample distribution and correlation to various other factors,for example terrain profile or vegetation coverage and makes the selection of the appropriate methoddifficult. Six methods commonly applied to soil characteristics have been selected to interpolate data thathas been retrieved from 16 time-domain reflectometers measuring θ in the upper 30 cm of a GSI-site ́ssurface. As θ changes at each sampling point also vary over time and therefore change the coefficients ofsome interpolation methods, estimates were compared for each hour of a 24-hour rainfall event. This isespecially relevant as GSI soils are not only subjected to rainfall but also to distinct lateral inflows fromimpervious areas. Cross-validation and common error calculations were used to assess the statisticalperformance of the results and identify a method with least errors. (15) (PDF) Comparison of spatial interpolation methods for soil moisture in Green Stormwater Infrastructure. Available from:

Comparison of spatial interpolation methods for soil moisture in Green Stormwater Infrastructure

Knowledge about soil-physical variables of Green Stormwater Infrastructure (GSI) like soil moisture (θ) isessential to understanding their hydrologic and treatment performance. θ depends on many local factorsand is subject to high spatial and temporal variability (Takagi and Lin, 2012; Yao et al. 2013; Nasta et al. 2018).Information about the spatially continuous data of θ can help to understand the hydrologic response andprovide an input for initial conditions to improve hydrologic modelling results. A number of deterministic andprobabilistic interpolation methods and tools are available today to model the spatial distribution ofenvironmental parameters such as θ (Li and Heap 2011; Yao et al. 2013). The quality of the spatialinterpolation, however, depends on sample size, sample distribution and correlation to various other factors,for example terrain profile or vegetation coverage and makes the selection of the appropriate methoddifficult. Six methods commonly applied to soil characteristics have been selected to interpolate data thathas been retrieved from 16 time-domain reflectometers measuring θ in the upper 30 cm of a GSI-site ́ssurface. As θ changes at each sampling point also vary over time and therefore change the coefficients ofsome interpolation methods, estimates were compared for each hour of a 24-hour rainfall event. This isespecially relevant as GSI soils are not only subjected to rainfall but also to distinct lateral inflows fromimpervious areas. Cross-validation and common error calculations were used to assess the statisticalperformance of the results and identify a method with least errors. (15) (PDF) Comparison of spatial interpolation methods for soil moisture in Green Stormwater Infrastructure. Available from:

Green infrastructure drainage of a commercial plaza without directly connected impervious areas: a case study

A paired-catchment study of two adjacent commercial areas in northern Sweden, one with Green Infrastructure (GI) storm drainage and the other with a conventional storm sewer system, served to evaluate the hydrological performance of both drainage systems and demonstrate advantages of GI. The GI catchment avoided directly-connected impervious areas by diverting runoff from a parking lot to a cascade of three infiltration features, a fractured rock strip draining onto a sloping infiltration area, followed by a collector swale. Both catchments were monitored over 4 years by measuring rainfall, runoff and, in the vicinity of the swale, soil water content and groundwater levels. For frequent storms, the median GI efficiencies in reducing runoff volumes and peak flows, and extending peak flow lags, were 96, 99 and 60%, respectively, compared to conventional drainage The storm rainfall depth, initial soil water content, increases in intra-event soil water storage and groundwater levels, had statistically significant effects on either runoff volume or peak flow reductions. No effects were found for storm rainfall intensity and duration, antecedent dry days, and initial groundwater levels. The study demonstrated that GI drainage can be successfully applied even in the challenging environment of a subarctic climate.Validerad;2023;Nivå 2;2023-02-10 (joosat);Licens fulltext: CC BY License</p