154,373 research outputs found
Primer1: Primer design Web service for Tetra-Primer ARMS-PCR
No full textTetra-primer ARMS-PCR is used extensively as a low cost, single PCR assay requiring no post-PCR manipulation. The design of successful primers depends on a number of variables such as melting temperatures, GC content, complementarity and selection of mismatch bases. The optimal selection of primers can be achieved in an automated way using a program which evaluates candidate primers for a given sequence. The Primer1 software was developed originally for use in the context of restriction fragment length polymorphism analysis using gel electrophoresis. However, recent applications have been more diverse, reviewed here, and we present an overview of the Primer1 software for primer design and web-service. We have updated the Primer1 program, and provide more complete details of the implementation. We also provide test data and output. The program is now available on a new, efficient, LAMP web service for users at: http://primer1.soton.ac.uk/primer1.htm
Neuropsychological constraints to human data production on a global scale
No full textWhich are the factors underlying human information production on a global level? In order to gain an insight into this question we study a corpus of 252–633 mil. publicly available data files on the Internet corresponding to an overall storage volume of 284–675 Terabytes. Analyzing the file size distribution for several distinct data types we find indications that the neuropsychological capacity of the human brain to process and record information may constitute the dominant limiting factor for the overall growth of globally stored information, with real-world economic constraints having only a negligible influence. This supposition draws support from the observation that the files size distributions follow a power law for data without a time component, like images, and a log-normal distribution for multimedia files, for which time is a defining qualia.
Author summary: The generation of new information is limited by two key factors, by the incurring economic costs and by the capacity of the human brain to process and store data and information; the controlling agent needs to retain an overall understanding even when data is generated by semiautomatic processes. These processes are reflected in the statistical properties of the data files publicly available on the Internet. Collecting a corpus of 252–633 mil. files we find that the statistics of the file size distribution are consistent with the supposition that data production on a global level is shaped and limited by the neuropsychological information processing capacity of the brain, with economic and hardware constraints having a negligible influence
Letter, [Author unclear] to Paulina T. Merritt
No full textHandwritten letter to Paulina Merritt from an unknown author, October 1, 1876.
GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags
No full textThe availability of sequenced genomes has generated a need for experimental approaches that allow the simultaneous analysis of large, or even complete, sets of genes. To facilitate such analyses, we have developed GST-PRIME, a software package for retrieving and assembling gene sequences, even from complex genomes, using the NCBI public database, and then designing sets of primer pairs for use in gene amplification. Primers were designed by the program for the direct amplification of gene sequence tags (GSTs) from either genomic DNA or cDNA. Test runs of GST-PRIME on 2000 randomly selected Arabidopsis and Drosophila genes demonstrate that 93 and 88% of resulting GSTs, respectively, fulfilled imposed length criteria. GST-PRIME primer pairs were tested on a set of 1900 Arabidopsis genes coding for chloroplast-targeted proteins: 95% of the primer pairs used in PCRs with genomic DNA generated the correct amplicons. GST-PRIME can thus be reliably used for large-scale or specific amplification of intron-containing genes of multicellular eukaryotes
MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling
No full textBackground
Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm.
Results
After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively.
Conclusions
MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base
Mellékvesekéreg szcintigráfia SPECT/CT kvantitatív értékelése primer hyperaldosteronismusban
No full textA primer mellékvesekéreg túlműködés differenciál-diagnosztikája világos, alaposan irodalmazott és használt téma. A mellékvesekéreg szcintigráfia egy planáris leképzéstechnika, mely bizonyítottan idejétmúlt. A jelen vizsgálatunkkal a steroid szuppresszióban végzett mellékvesekéreg SPECT/CT lehetőségeit vizsgáltuk primer hyperaldosteronismusban szenvedő betegeken. A vizsgálatba azokat a betegeket vontuk be, akik vállalták a műtétet, amennyiben egyoldali mellékvese kéreg adenoma derül ki, a laborparamétereiből egyértelműen magas szérum aldoszteron, és alacsony renin szintet mérhetünk, valamint a aldoszteron/renin hányadosuk több, mint 30. A radiofarmakon (131I-Norcholesterol) injektálása előtt 5 nappal és a végső leképzésig dexamethason szuppressziót, valamint 3 nappal a radiofarmakon injektálása előtt pajzsmirigy védő szert alkalmaztunk. Az elkészült SPECT/CT képeken a májra egy 6cm-es VOI-t, a mellékvese régiókra 2, 2,5, 3, 3,5, 4, 4,5 és 5cm-es VOI-kat helyeztünk és mértük az összbeütést és az 1 voxelre eső maximális beütést. 30 beteget választottunk be a vizsgálatba. Azt találtunk, ahogy a máj összaktivitás/mellékvese összaktivitás nem különíti el jól az egyoldali mellékvese kéreg adenomát a kétoldali mellékvesekéreg hyperplasiától. Amennyiben a mellékvesék aktivitásarányát vizsgáltuk, úgy mind az összaktivitásarány, mind a maximumarány jól elkülönítette a két betegcsoportot. A VOI-k méretében a 3cm-es VOI-t találtuk a legjobbnak. A vizsgálatunkkal bebizonyítottuk, hogy a dexamethason szuppresszióban végzett mellékvese kéreg SPECT/CT-nek helye van a rutin diagnosztikában, jó találti pontossággal különítette a kétoldali mellékvese kéreg hyperplasiát az egyoldali mellékvese adenomától. Javaslatot tettünk a módszer elhelyezésére a diagnosztikai sorban.általános orvosnappalimagyaregységes, osztatla
Is a primer needed for orthodontic bonding? A randomised controlled trial
No full textIs a primer needed for orthodontic bonding? A Randomised
controlled trial
Objective: To evaluate the clinical performance of APC Victory IITM (3M Unitek) brackets in direct orthodontic bonding with and without the use of primer.
Design: A single operator two centre prospective randomised controlled clinical trial.
Setting: The orthodontic departments at the Leeds Dental Institute and St.Luke’s hospital, Bradford.
Subjects and methods: 92 patients requiring orthodontic treatment with fixed appliances. 46 Patients randomly allocated to control (with primer) or test (without primer). Patients bonded using a standardised procedure.
Main outcome measures: Number of bracket failures, time to bond-up appliances and the adhesive remnant index (ARI) when bracket failure occurred, over a six month period
Results: Failure rate with primer 8.8%, without primer 13.8%, no statistically significant difference- P value 0.051. Mean difference in bondup time per bracket was 0.068 minutes which was not statistically significant (P =0.402). Statistically significant difference in the ARI – ARI 0
with primer 55.9%, no primer 81.5%, (P= 8.1622e-008).
Conclusion: There is no statistically significant difference in the bracket failure rate with or without primer when bonding APC Victory IITM (P=0.051). No significant difference in bond-up times. Statistically significant difference in the ARI, bonding without primer providing a lower ARI
Primer siliyer diskinezi tanısında transmisyon elektron mikroskopi
No full textPrimer siliyer diskinezi (PSD), siliya fonksiyon bozukluğunun neden olduğu, çoğunlukla otozomal resesif geçişli, klinik ve genetik olarak heterojen bir hastalıktır. PSD klinik fenotipi değişkendir. Üst ve alt solunum sistemi, üreme organları, kalp ve siliyaların bulunduğu diğer sistemleri tutar. Zamanında doğan PSD'li bebeklerin yaklaşık %80'i, doğum sonrası 24 saat içinde solunum sıkıntısı kliniği gösterir ve oksijen desteği gerektirir. Sonraki dönemde tekrarlayan pnömoni veya bronşit yaygın görülür. Kronik, efüzyonlu tekrarlayan orta kulak iltihabı, özellikle yaşamın ilk yılında, PSD'li çocukların en az %80'ini etkiler. Hastaların yaklaşık %80'inde yıl boyu devam eden burun tıkanıklığı ve kronik sinüzit vardır. Situs inversus totalis daha sık olmak üzere bir dizi organ lateralite kusuru görülür. Erkeklerde infertilite, kadınlarda ektopik gebelik sıktır. Bazı durumlarda, PSD'nin polikistik böbrek, hidrosefali, polispleni gibi nadir ve olağandışı bozukluklarla ilişkili olduğu gösterilmiştir. Son zamanlarda genetik çalışmaların hızlanmasıyla yapılan çalışmalar, farklı genlerdeki mutasyonların değişken fenotiplere yol açtığını göstermektedir. Bununla ilgili vaka serileri mevcuttur.Primary ciliary dyskinesia (PSD) is mostly autosomal recessive clinically and genetically heterogeneous disease caused by cilia dysfunction. It affects the upper and lower respiratory system, reproductive organs, heart, and other systems where the cilia are located. Approximately 80% of term babies with PSD show respiratory distress within 24 hours of birth and require oxygen support. In addition, recurrent pneumonia or bronchitis is common. Chronic, recurrent otitis media with effusion affects at least 80% of children with PSD, particularly in the first year of life. About 80% of patients have yearround nasal congestion and chronic sinusitis. Several organ laterality defects are seen, with the situs inversus totalis being more common. Infertility in men and ectopic pregnancy in women are common. In some cases, PSD is associated with rare and unusual disorders such as polycystic kidney, hydrocephalus, and polysplenia. In addition, recent genetic studies show that mutations in different genes lead to variable phenotypes. There are case series related to this
Swelling and shrinking kinetics of a lamellar gel phase
No full textWe investigate the swelling and shrinking of L lamellar gel phases composed of surfactant and fatty alcohol after contact with aqueous poly(ethyleneglycol) solutions. The height change Δh(t) is diffusionlike with a swelling coefficient S: Δh=S√t. On increasing polymer concentration, we observe sequentially slower swelling, absence of swelling, and finally shrinking of the lamellar phase. This behavior is summarized in a nonequilibrium diagram and the composition dependence of S quantitatively described by a generic model. We find a diffusion coefficient, the only free parameter, consistent with previous measurements
Handwritten biographical information on Paulina T. McClung Merritt
No full textA handwritten biography of Paulina T. McClung Merritt by an unknown author, 1892.
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