Development of an oligonucleotide-based SNP detection method on lateral flow strips using hexapet tages

Detection of point mutations or single nucleotide polymorphisms (SNPs) is important in relation to disease susceptibility or detection in pathogens of mutations determining drug resistance or host range. There is an emergent need for rapid detection methods amenable to point-of-care applications. The purpose of this study was to reduce to practice a novel method for SNP detection and to demonstrate that this technology can be used downstream of nucleic acid amplification. The authors used a model system to develop an oligonucleotide-based SNP detection system on nitrocellulose lateral flow strips. To optimize the assay they used cloned sequences of the herpes simplex virus-1 (HSV-1) DNA polymerase gene into which they introduced a point mutation. The assay system uses chimeric polymerase chain reaction (PCR) primers that incorporate hexameric repeat tags ("hexapet tags"). The chimeric sequences allow capture of amplified products to predefined positions on a lateral flow strip. These "hexapet" sequences have minimal cross-reactivity and allow specific hybridization-based capture of the PCR products at room temperature onto lateral flow strips that have been striped with complementary hexapet tags. The allele-specific amplification was carried out with both mutant and wild-type primer sets present in the PCR mix ("competitive" format). The resulting PCR products carried a hexapet tag that corresponded with either a wild-type or mutant sequence. The lateral flow strips are dropped into the PCR reaction tube, and mutant sequence and wild-type sequences diffuse along the strip and are captured at the corresponding position on the strip. A red line indicative of a positive reaction is visible after 1 minute. Unlike other systems that require separate reactions and strips for each target sequence, this system allows multiplex PCR reactions and multiplex detection on a single strip or other suitable substrates. Unambiguous visual discrimination of a point mutation under room temperature hybridization conditions was achieved with this model system in 10 minutes after PCR. The authors have developed a capture-based hybridization method for the detection and discrimination of HSV-1 DNA polymerase genes that contain a single nucleotide change. It has been demonstrated that the hexapet oligonucleotides can be adapted for hybridization on the lateral flow strip platform for discrimination of SNPs. This is the first step in demonstrating SNP detection on lateral flow using the hexapet oligonucleotide capture system. It is anticipated that this novel system can be widely used in point-of-care settings.

Testing term structure estimation methods:evidence from the UK STRIPs market

Prices and yields of UK government zero-coupon bonds are used to test alternative yield curve estimation models. Zero-coupon bonds permit a more pure comparison, as the models are providing only the interpolation service and also not making estimation feasible. It is found that better yield curves estimates are obtained by fitting to the yield curve directly rather than fitting first to the discount function. A simple procedure to set the smoothness of the fitted curves is developed, and a positive relationship between oversmoothness and the fitting error is identified. A cubic spline function fitted directly to the yield curve provides the best overall balance of fitting error and smoothness, both along the yield curve and within local maturity regions.

Rapid serodiagnosis of Staphylococcus aureus surgical site infection following median sternotomy

Objectives: To determine the sensitivity and specificity of a novel ELISA for the serodiagnosis of surgical site infection (SSI) due to staphylococci following median sternotomy. Methods: Twelve patients with a superficial sternal SSI and 19 with a deep sternal SSI due to Staphylococcus aureus were compared with 37 control patients who also underwent median sternotomy for cardiac surgery but exhibited no microbiological or clinical symptoms of infection. A further five patients with sternal SSI due to coagulase-negative (CoNS) staphylococci were studied. An ELISA incorporating a recently recognised exocellular short chain form of lipoteichoic acid (lipid S) recovered from CoNS, was used to determine serum levels of anti-lipid S IgG in all patient groups. Results: Serum anti-lipid S IgG titres of patients with sternal SSI due to S. aureus were significantly higher than the control patients (P<0.0001). In addition, patients with deep sternal SSI had significantly higher serum anti-lipid S IgG titres than patients with superficial sternal SSI (P=0.03). Serum anti-lipid S IgG titres of patients with sternal SSI due to CoNS were significantly higher than the control patients (P=0.001). Conclusion: The lipid S ELISA may facilitate the diagnosis of sternal SSI due to S. aureus and could also be of value with infection due to CoNS. © 2005 Published by Elsevier Ltd. on behalf of The Bristish Infection Society.

Local-Median Method of Forecasting for Regression Time Series under Outliers

2002 Mathematics Subject Classification: 62M20, 62-07, 62J05, 62P20.

Far field of binary phase gratings with errors in the height of the strips

Diffraction gratings are not always ideal but, due to the fabrication process, several errors can be produced. In this work we show that when the strips of a binary phase diffraction grating present certain randomness in their height, the intensity of the diffraction orders varies with respect to that obtained with a perfect grating. To show this, we perform an analysis of the mutual coherence function and then, the intensity distribution at the far field is obtained. In addition to the far field diffraction orders, a "halo" that surrounds the diffraction order is found, which is due to the randomness of the strips height.

Computing the Oja Median in R : The Package OjaNP

Acknowledgements The work of Klaus Nordhausen was supported by the Academy of Finland (grant 268703). Oleksii Pokotylo is supported by the Cologne Graduate School of Management, Economics and Social Sciences. The work of Daniel Vogel was supported by the DFG collaborate research grant SFB 823

Modelling the effectiveness of grass buffer strips in managing muddy floods under a changing climate

Muddy floods occur when rainfall generates runoff on agricultural land, detaching and transporting sediment into the surrounding natural and built environment. In the Belgian Loess Belt, muddy floods occur regularly and lead to considerable economic costs associated with damage to property and infrastructure. Mitigation measures designed to manage the problem have been tested in a pilot area within Flanders and were found to be cost-effective within three years. This study assesses whether these mitigation measures will remain effective under a changing climate. To test this, the Water Erosion Prediction Project (WEPP) model was used to examine muddy flooding diagnostics (precipitation, runoff, soil loss and sediment yield) for a case study hillslope in Flanders where grass buffer strips are currently used as a mitigation measure. The model was run for present day conditions and then under 33 future site-specific climate scenarios. These future scenarios were generated from three earth system models driven by four representative concentration pathways and downscaled using quantile mapping and the weather generator CLIGEN. Results reveal that under the majority of future scenarios, muddy flooding diagnostics are projected to increase, mostly as a consequence of large scale precipitation events rather than mean changes. The magnitude of muddy flood events for a given return period is also generally projected to increase. These findings indicate that present day mitigation measures may have a reduced capacity to manage muddy flooding given the changes imposed by a warming climate with an enhanced hydrological cycle. Revisions to the design of existing mitigation measures within existing policy frameworks are considered the most effective way to account for the impacts of climate change in future mitigation planning. 

Mucosal modulation of contractility in bladder strips from normal and overactive rat models and the effect of botulinum toxin A on overactive bladder strips

AIMS: To investigate the local, regulatory role of the mucosa on bladder strip contractility from normal and overactive bladders and to examine the effect of botulinum toxin A (BoNT-A).

METHODS: Bladder strips from spontaneously hyperactive rat (SHR) or normal rats (Sprague Dawley, SD) were dissected for myography as intact or mucosa-free preparations. Spontaneous, neurogenic and agonist-evoked contractions were investigated. SHR strips were incubated in BoNT-A (3 h) to assess effects on contractility.

RESULTS: Spontaneous contraction amplitude, force-integral or frequency were not significantly different in SHR mucosa-free strips compared with intacts. In contrast, spontaneous contraction amplitude and force-integral were smaller in SD mucosa-free strips than in intacts; frequency was not affected by the mucosa. Frequency of spontaneous contractions in SHR strips was significantly greater than in SD strips. Neurogenic contractions in mucosa-free SHR and SD strips at higher frequencies were smaller than in intact strips. The mucosa did not affect carbachol-evoked contractions in intact versus mucosa-free strips from SHR or SD bladders. BoNT-A reduced spontaneous contractions in SHR intact strips; this trend was also observed in mucosa-free strips but was not significant. Neurogenic and carbachol-evoked contractions were reduced by BoNT-A in mucosa-free but not intact strips. Depolarisation-induced contractions were smaller in BoNT-A-treated mucosa-free strips.

CONCLUSIONS: The mucosal layer positively modulates spontaneous contractions in strips from normal SD but not overactive SHR bladder strips. The novel finding of BoNT-A reduction of contractions in SHR mucosa-free strips indicates actions on the detrusor, independent of its classical action on neuronal SNARE complexes.

Sosiaalisen median yksilöbrändin merkitys työnhaussa ja yritysten näkökanta työntekijän sosiaalisen median käyttäytymiselle

Työn tavoitteena oli tutkia, kuinka yksilön brändi muodostuu sosiaalisessa mediassa ja mitä sosiaalisen median kanavia suositaan työnhakijoiden ja yritysten keskuudessa. Haettiin myös alueellisilta yrityksiltä vastausta siihen, perehdyttävätkö he uusia työntekijöitä sosiaalisen median käyttäytymisessä. Tietolähteinä käytettiin brändin luomiseen ja sosiaalisen median strategiaan keskittyvää kirjallisuutta sekä yrityksien ja opiskelijoiden haastatteluja. Työn tuloksina todettiin suosituimmiksi kanaviksi itsensä markkinointiin verkostoitumispalvelu LinkedIn. Yritykset korostivat omien projektien merkitystä osaamisen näyttämisessä työnhaussa ja hyvin viestittyä persoonallisuutta hakemuksissa arvostettiin.

Least Median Of Squares Estimation In Power Systems

Static state estimators currently in use in power systems are prone to masking by multiple bad data. This is mainly because the power system regression model contains many leverage points; typically they have a cluster pattern. As reported recently in the statistical literature, only high breakdown point estimators are robust enough to cope with gross errors corrupting such a model. This paper deals with one such estimator, the least median of squares estimator, developed by Rousseeuw in 1984. The robustness of this method is assessed while applying it to power systems. Resampling methods are developed, and simulation results for IEEE test systems discussed. © 1991 IEEE.

Urheiluviestinnän murroksessa. Superpesis-seurojen sosiaalisen median käyttö

Urheiluseurojen viestintä on murroksen keskellä. Sosiaalisen median menestyksen myötä seuroista on tullut eräänlaisia omia uutistoimistojaan, joilta odotetaan ammattimaista ja ennen kaikkea nopeaa viestintää edustusjoukkueen ja sen pelaajien kuulumisista ja ottelutuloksista. Sosiaalinen media on myös itsessään muodostunut tärkeäksi tekijäksi urheiluseurojen viestinnän ja markkinoinnin tehokkuudessa sekä brändin muodostumisessa ja näkyvyydessä. Kaikilla urheiluseuroilla ei kuitenkaan ole tarvittavia resursseja menestyvän brändin luomiseksi sosiaalisen median kanavia käyttäen. Esimerkkinä tässä tutkimuksessa toimivat Superpesis-sarjan pesäpalloseurat, joiden sisältä miesten ja naisten sarjoista löytyy suuria eroavaisuuksia saatavilla olevissa resursseissa ja toteutetun viestinnän laadussa, mieleenpainuvuudessa ja tehokkuudessa. Tutkimukseni primaariaineistoina toimivat Superpesis-seuroille toteutettu sosiaalisen median käyttöä koskeva kyselyaineisto ja naisten Superpesis-seura Pesäkarhujen sosiaalisen median ja kotisivujen tilastot vuosilta 2013–2016. Kyselyyn vastasi 25 mahdollisesta Superpesis-seurasta 22 seuraa, joten vastaajajoukko on edustava kertomaan siitä, miten huipputason pesäpalloseurat tällä hetkellä viestivät. Saamieni tutkimustulosten perusteella listasin näille seuroille sosiaalisen median käytön suosituksia, joiden kautta seurojen on mahdollista kehittää viestintäänsä.

Urheiluviestinnän murroksessa. Superpesis-seurojen sosiaalisen median käyttö.

Urheiluseurojen viestintä on murroksen keskellä. Sosiaalisen median menestyksen myötä seuroista on tullut eräänlaisia omia uutistoimistojaan, joilta odotetaan ammattimaista ja ennen kaikkea nopeaa viestintää edustusjoukkueen ja sen pelaajien kuulumisista ja ottelutuloksista. Sosiaalinen media on myös itsessään muodostunut tärkeäksi tekijäksi urheiluseurojen viestinnän ja markkinoinnin tehokkuudessa sekä brändin muodostumisessa ja näkyvyydessä. Kaikilla urheiluseuroilla ei kuitenkaan ole tarvittavia resursseja menestyvän brändin luomiseksi sosiaalisen median kanavia käyttäen. Esimerkkinä tässä tutkimuksessa toimivat Superpesis-sarjan pesäpalloseurat, joiden sisältä miesten ja naisten sarjoista löytyy suuria eroavaisuuksia saatavilla olevissa resursseissa ja toteutetun viestinnän laadussa, mieleenpainuvuudessa ja tehokkuudessa. Tutkimukseni primaariaineistoina toimivat Superpesis-seuroille toteutettu sosiaalisen median käyttöä koskeva kyselyaineisto ja naisten Superpesis-seura Pesäkarhujen sosiaalisen median ja kotisivujen tilastot vuosilta 2013–2016. Kyselyyn vastasi 25 mahdollisesta Superpesis-seurasta 22 seuraa, joten vastaajajoukko on edustava kertomaan siitä, miten huipputason pesäpalloseurat tällä hetkellä viestivät. Saamieni tutkimustulosten perusteella listasin näille seuroille sosiaalisen median käytön suosituksia, joiden kautta seurojen on mahdollista kehittää viestintäänsä.