gebhart/patrepeval huggingface dataset:
Denaturing high-performance liquid chromatography: A review (2001)

Denaturing high-performance liquid chromatography (DHPLC) compares two or more chromosomes as a mixture of denatured and reannealed PCR amplicons, revealing the presence of a mutation by the differential retention of homo- and heteroduplex DNA on reversed-phase chromatography supports under partial denaturation. Temperature determines sensitivity, and its optimum can be predicted by computation. Single-nucleotide substitutions, deletions, and insertions have been detected successfully by on-line UV or fluorescence monitoring within 2-3 minutes in unpurified amplicons as large as 1.5 Kb. Sensitivity and specificity of DHPLC consistently exceed 96%. These features and its low cost make DHPLC one of the most powerful tools for the re-sequencing of the human and other genomes. Aside from its application to the mutational analysis of candidate genes, DHPLC has proven instrumental in elucidating human evolution and in the mapping of genes. Employing completely denaturing conditions, the utility of DHPLC has been extended to the genotyping of known polymorphisms by utilizing the ability of poly(styrene-divinylbenzene) to resolve single-stranded DNA molecules of identical size that differ in a single base. Under completely denaturing conditions, it is thus possible to resolve all possible base substitutions with the single exception of C-->G transversions. Improvements in throughput became feasible with the recent introduction of monolithic poly(styrene-divinylbenzene) capillaries that lend themselves to the fabrication of arrays connected to a multi-color laser induced fluorescence scanner or a mass spectrometer.
Information capacity of a multipath mobile communication channel with large number of receiving antennas (2002)

The expression for stationary channel information capacity of a mobile communication channel with a large number of receiving antennas in the presence of multipath signal propagation is shown. It has been shown that the capacity is approaching information capacity of the orthogonal Gaussian channel with no interference. The system with adaptive linear MMSE receivers and adaptive interference cancellation is presented as a possible low computational complexity solution achieving the theoretical capacity.
Handbook of Print Media (2004)

Based on a virtual network that collects and connects a large number of the molecules known to be involved in a disease, one can simulate the effects of controlling molecules, allowing for the observation of how this affects the rest of the network. This is important to mimic the effect of a drug, but also to be aware of -and possibly control- its side effects. Using this approach in RA research we have been able to contribute to the field by suggesting molecules to be targeted in new therapies and more importantly, to warrant efficacy, to hypothesise novel recommendations on existing drugs currently under test.
조선시대 봉수체제와 입지에 관한 연구 - 강원도를 중심으로 - (2001)

烽燧란 횃불과 연기로 변경의 급한 보고를 중앙에 전하는 고대의 통신방법으로 정치·행정적인 기능을 담당했던 驛院制와는 달리 군사적 기능을 담당한 상향식 연락체계였다. 우리 나라의 봉수제는 삼국시대부터 존속되었고 고려시대의 확립기를 거쳐 조선시대에 구체화되어 경국대전 에 규정으로 확정되었다. 임진왜란 이후 봉수제가 폐지되었다가 숙종시 다시 파발제와 함께 운영되다 갑오개혁 이후 근대적인 우편제도의 도입으로 폐지되었다. 조선시대 봉수제도에는 봉수의 관장 및 종류, 전보요령, 봉수대 시설, 근무요원 및 근무태만에 대한 벌칙이 규정되어 있었고, 전국에는 5炬의 봉수망이 조직되어 모두 서울로 연결되고 있었다. 강원도는 크게 제 1炬 봉수인 직봉과 동해안의 간봉으로 구성되고 봉수대의 갯수도 15·16C에는 48개, 18C에는 31개, 19C에는 간봉이 폐쇄되고 11개의 직봉만이 존속하였다. 강원도 봉수대의 입지는 해안지역의 경우는 육지가 바다로 돌출한 串이나 봉서대간 상통이 유리한 저산성 산지가 대부분으로 고도는 100m이내이다. 내륙 지역에는 높은 고산 준령을 피하고 오르내리기에 어렵지 않은 고도 200∼900m의 산들이다. 강원도 봉수로는 역로와 근대적 교통수단이 지나는 노선과 유사한 노선을 택하고 있다. 이는 함경·강원도에서 백두대간을 넘어 서울을 잇는 가장 빠르고 효율적인 교통·통신망으로 추가령 구조곡을 따르는 입지적 특성을 보인다.
Effect of Transcranial Brain Stimulation for the Treatment of Alzheimer Disease: A Review (2011)

Available pharmacological treatments for Alzheimer disease (AD) have limited effectiveness, are expensive, and sometimes induce side effects. Therefore, alternative or complementary adjuvant therapeutic strategies have gained increasing attention. The development of novel noninvasive methods of brain stimulation has increased the interest in neuromodulatory techniques as potential therapeutic tool for cognitive rehabilitation in AD. In particular, repetitive transcranial magnetic stimulation (rTMS) and transcranial direct current stimulation (tDCS) are noninvasive approaches that induce prolonged functional changes in the cerebral cortex. Several studies have begun to therapeutically use rTMS or tDCS to improve cognitive performances in patients with AD. However, most of them induced short-duration beneficial effects and were not adequately powered to establish evidence for therapeutic efficacy. Therefore, TMS and tDCS approaches, seeking to enhance cognitive function, have to be considered still very preliminary. In future studies, multiple rTMS or tDCS sessions might also interact, and metaplasticity effects could affect the outcome.
Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1 (1997)

Sphingomonas yanoikuyae B1 is able to grow on a wide variety of aromatic compounds including biphenyl, naphthalene,phenanthrene, toluene, m-, and p-xylene. In addition, the initial enzymes for degradation of biphenyl have the ability to metabolize a wide variety of different polycyclic aromatic hydrocarbons. The catabolic pathways for the degradation of both the monocyclic and polycyclic aromatic hydrocarbons are intertwined, joining together at the level of (methyl)benzoate and catechol. Both upper branches of the catabolic pathways are induced when S. yanoikuyae B1 is grown on either class of compound. An analysis of the genes involved in the degradation of these aromatic compounds reveals that at least six operons are involved. The genes are not arranged in discrete pathway units but are combined in groups with genes for the degradation of both classes of compounds in the same operon.Genes for multiple dioxygenases are present perhaps explaining the ability of S. yanoikuyae B1 to grow on a wide variety of aromatic compounds.
Quantitative Analysis of Her-2/neu (ERBB2) Gene Expression Using Reverse Transcriptase Polymerase Chain Reaction (1993)

Inappropriate expression of Her-2/neu (ERBB2) gene has been associated with impaired breast cancer prognosis, suggesting a functional role in tumor progression. Herein we describe a quantitative method for analysis of Her-2/neu gene messenger RNA (mRNA), which employs reverse transcriptase polymerase chain reaction (RT-PCR) on a 10-microns cryostat section. The technique combines modified RNA extraction with complementary DNA (cDNA) synthesis to achieve a high level of sensitivity. Utilizing this PCR-based gene expression assay, we were able to quantitate variable amounts of Her-2/neu mRNA in cell lines with established levels of gene expression and in clinical human breast cancer specimens. In clinical samples, mRNA levels correlated with intensity of immunoperoxidase staining for corresponding oncoprotein. We conclude that PCR-based mRNA quantitation can be applied to quantitative analysis of Her-2/neu gene expression, and potentially many other genes, in samples of limited size.
Exonucleolytic Proofreading during Replication of Repetitive DNA (1996)

We are attempting to understand the processes required to accurately replicate the repetitive DNA sequences whose instability is associated with several human diseases. Here we test the hypothesis that the contribution of exonucleolytic proofreading to frameshift fidelity during replication of repetitive DNA sequences diminishes as the number of repeats in the sequence increases. The error rates of proofreading-proficient T7, T4, and Pyrococcus furiosis DNA polymerases are compared to their exonuclease-deficient derivatives, for +1 and -1 base errors in homopolymeric repeat sequences of three to eight base pairs. All three exonuclease-deficient polymerases produce frameshift errors during synthesis at rates that increase as a function of run length, suggesting the involvement of misaligned intermediates. Their wild-type counterparts are all much more accurate, suggesting that the majority of the intermediates are corrected by proofreading. However, the contribution of the exonuclease to fidelity decreases substantially as the length of the homopolymeric run increases. For example, the exonuclease enhances the frameshift fidelity of T7 DNA polymerase in a run of three A.T base pairs by 160-fold, similar to its contribution to base substitution fidelity. However, in a run of eight consecutive A.T base pairs, the exonuclease only enhances frameshift fidelity by 7-fold. A similar pattern was observed with T4 and Pfu DNA polymerases. Thus, both polymerase selectivity and exonucleolytic proofreading efficiency are diminished during replication of repetitive sequences. This may place an increased relative burden on post-replication repair processes to reduce rates of addition and deletion mutations in organisms whose genome contains abundant simple repeat DNA sequences.
Computer-generated floral ornament (1998)

Article Free Access Share on Computer-generated floral ornament Authors: Michael T. Wong Univ. of Washington, Seattle Univ. of Washington, SeattleView Profile , Douglas E. Zongker Univ. of Washington, Seattle Univ. of Washington, SeattleView Profile , David H. Salesin Univ. of Washington, Seattle Univ. of Washington, SeattleView Profile Authors Info & Claims SIGGRAPH '98: Proceedings of the 25th annual conference on Computer graphics and interactive techniquesJuly 1998 Pages 423–434https://doi.org/10.1145/280814.280948Published:24 July 1998Publication History 52citation1,319DownloadsMetricsTotal Citations52Total Downloads1,319Last 12 Months103Last 6 weeks15 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Early and Late Recurrence After Liver Resection for Hepatocellular Carcinoma (2006)

Early and late recurrences are linked to different predictive factors. The modality of presentation of the recurrence together with the feasibility of a radical treatment are the best determinants for the prognosis.
Learning Image Representations Tied to Ego-Motion (2015)

Understanding how images of objects and scenes behave in response to specific ego-motions is a crucial aspect of proper visual development, yet existing visual learning methods are conspicuously disconnected from the physical source of their images. We propose to exploit proprioceptive motor signals to provide unsupervised regularization in convolutional neural networks to learn visual representations from egocentric video. Specifically, we enforce that our learned features exhibit equivariance, i.e, they respond predictably to transformations associated with distinct ego-motions. With three datasets, we show that our unsupervised feature learning approach significantly outperforms previous approaches on visual recognition and next-best-view prediction tasks. In the most challenging test, we show that features learned from video captured on an autonomous driving platform improve large-scale scene recognition in static images from a disjoint domain.
Critical Evaluation of Urine-Based PCR Assay for Diagnosis of Lyme Borreliosis (2005)

Many approaches were made in recent years to establish urine PCR as a diagnostic tool for Lyme borreliosis, but results are contradictory. In the present study, a standardized protocol spiking urine from healthy donors with a defined amount of whole Borrelia or Borrelia DNA was established. The development of a nested real-time PCR targeting ospA enabled a highly sensitive and quantitative analysis of these samples. We show the following. (i) Storage of spiked urine samples for up to 6 months at--20 degrees C had no negative effect on spike recovery. (ii) Centrifugation of 10 ml of urine at 40,000 x g for 30 min resulted in a concentration of both spikes, i.e., whole Borrelia and DNA. (iii) The inhibition of DNA spike recovery in 48% (11 of 23 samples) of urine samples tested could be attributed to nuclease activity. This was abrogated by alkalizing the urine or by working with the samples on ice. Despite optimized conditions, analysis of urine samples of 12 patients with erythema migrans, the clinical stage considered to be associated with the highest bacterial load, revealed a positive result in only one sample. All 12 samples were negative by an alternative PCR targeting flagellin. The results of our study support doubts that urine is a suitable material for diagnosis of Lyme borreliosis.
The C9orf72 GGGGCC Repeat Is Translated into Aggregating Dipeptide-Repeat Proteins in FTLD/ALS (2013)

Expansion of a GGGGCC hexanucleotide repeat upstream of the C9orf72 coding region is the most common cause of familial frontotemporal lobar degeneration and amyotrophic lateral sclerosis (FTLD/ALS), but the pathomechanisms involved are unknown. As in other FTLD/ALS variants, characteristic intracellular inclusions of misfolded proteins define C9orf72 pathology, but the core proteins of the majority of inclusions are still unknown. Here, we found that most of these characteristic inclusions contain poly-(Gly-Ala) and, to a lesser extent, poly-(Gly-Pro) and poly-(Gly-Arg) dipeptide-repeat proteins presumably generated by non-ATG-initiated translation from the expanded GGGGCC repeat in three reading frames. These findings directly link the FTLD/ALS-associated genetic mutation to the predominant pathology in patients with C9orf72 hexanucleotide expansion.
Shape-Driven Gabor Jets for Face Description and Authentication (2007)

This paper proposes, through the combination of concepts and tools from different fields within the computer vision community, an alternative path to the selection of key points in face images. The classical way of attempting to solve the face recognition problem using algorithms which encode local information is to localize a predefined set of points in the image, extract features from the regions surrounding those locations, and choose a measure of similarity (or distance) between correspondent features. Our approach, namely shape-driven Gabor jets, aims at selecting an own set of points and features for a given client. After applying a ridges and valleys detector to a face image, characteristic lines are extracted and a set of points is automatically sampled from these lines where Gabor features (jets) are calculated. So each face is depicted by R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> points and their respective jets. Once two sets of points from face images have been extracted, a shape-matching algorithm is used to solve the correspondence problem (i.e., map each point from the first image to a point within the second image) so that the system is able to compare shape-matched jets. As a byproduct of the matching process, geometrical measures are computed and compiled into the final dissimilarity function. Experiments on the AR face database confirm good performance of the method against expression and, mainly, lighting changes. Moreover, results on the XM2VTS and BANCA databases show that our algorithm achieves better performance than implementations of the elastic bunch graph matching approach and other related techniques.
Pilot study of the effect of individualised homeopathy on the pruritus associated with atopic dermatitis in dogs (2009)

Twenty dogs with confirmed atopic dermatitis were treated with homeopathy. In the first phase of this pilot study, all of the dogs were treated by a veterinary homeopath with individualised remedies prescribed on the basis of the dog's cutaneous signs and constitutional characteristics. The response to treatment was assessed by scoring the severity of pruritus from 0 to 10 on a validated scale. The dogs were evaluated at monthly intervals for at least two months. In 15 cases, the owners reported no improvement following homeopathic treatment. In the other five cases, the owners believed that the homeopathic treatment was associated with a substantial improvement, and reported reductions in pruritus scores ranging from 64 to 100 per cent. These five dogs were selected for the second phase of the study, in which homeopathic remedies were tested against placebos in a randomised and blinded trial. In one of these dogs, atopic dermatitis resolved completely and so this dog could not participate in phase 2; another dog was euthanased because of status epilepticus before phase 2 could be started. In the remaining three cases, the owners correctly distinguished between the placebo and homeopathic remedies, and reported reductions in the pruritus score of 0, 0.2 and 0.8 following placebo treatment and 4.3, 2.4 and 3.0, respectively, following the remedy.
Effect of Treatment With Low Doses of Hydrocortisone and Fludrocortisone on Mortality in Patients With Septic Shock (2002)

In our trial, a 7-day treatment with low doses of hydrocortisone and fludrocortisone significantly reduced the risk of death in patients with septic shock and relative adrenal insufficiency without increasing adverse events.
Organonitrogen derivatives of metal carbonyls. VIII. Reactions of metal carbonyl anions with .alpha.-chloroenamines (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganonitrogen derivatives of metal carbonyls. VIII. Reactions of metal carbonyl anions with .alpha.-chloroenaminesR. B. King and K. C. HodgesCite this: J. Am. Chem. Soc. 1975, 97, 10, 2702–2712Publication Date (Print):May 1, 1975Publication History Published online1 May 2002Published inissue 1 May 1975https://pubs.acs.org/doi/10.1021/ja00843a020https://doi.org/10.1021/ja00843a020research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Etch Stop Barriers in Silicon Produced by Ion Implantation of Electrically Non‐Active Species (1992)

Silicon layers implanted with silicon, germanium, and carbon ions at doses between 1E14 and 3E16 ions/cm2 and energies between 35 and 200 keV were tested as etch stop barriers in an ethylenediamine‐pyrocatechol‐water solution. The decrease in the etch stop effect with annealing temperature was measured. The results obtained indicate that the effectiveness of the etch stop is influenced by both the implantation damage and the chemical interaction between the implanted ions and the defective crystal.
Pulse Width Programming in Spinal CordStimulation: A Clinical Study (2010)

Variable PW programming in SCS appears to have clinical value, demonstrated by some patients improving their paresthesia-pain overlap, as well as the ability to increase and even 'steer' paresthesia coverage.
A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. (1994)

We have determined that 10Sa RNA (one of the small stable RNAs found in Escherichia coli) has an interesting structural feature: the 5' end and the 3' end of 10Sa RNA can be arranged in a structure that is equivalent to a half-molecule (acceptor stem and TFC stem-loop) of alanine tRNA of E. coli. Primer-extension analysis of 10Sa RNA extracted from a bacterial mutant with temperature-sensitive RNase P function revealed that the precursor to 10Sa RNA (pre-10Sa RNA) is folded into a pre-tRNA-like structure in vivo such that it can be cleaved by RNase P to generate the 5' end of the mature 10Sa RNA. The purified 10Sa RNA can be charged with alanine in vitro. Disruption of the gene encoding 10Sa RNA (ssrA) caused a reduction in the rate of cell growth, which was especially apparent at 45 degrees C, and a reduction in motility on semisolid agar. These phenotypic characteristics of the deletion strain (delta ssrA) allowed us to investigate the effects of some mutations in 10Sa RNA in vivo, although the exact function of 10Sa RNA still remains unclear. When the G.U pair (G3.U357) in 10Sa RNA, which may be equivalent to the determinant G.U pair of alanine tRNA, was changed to a G.A or G.C pair, the ability to complement the phenotypic mutations of the delta ssrA strain was lost. Furthermore, this inability to complement the mutant phenotypes that was caused by the substitution of the determinant bases by a G.A pair could be overcome by the introduction of a gene encoding alanyl-tRNA synthetase (alaS) on a multicopy plasmid. The evidence suggests that the proposed structural features of 10Sa RNA are indeed manifested in vivo.
A major outer membrane protein of Moraxella catarrhalis is a target for antibodies that enhance pulmonary clearance of the pathogen in an animal model (1993)

A murine immunoglobulin G monoclonal antibody (MAb) raised against outer membrane vesicles of Moraxella catarrhalis 035E was shown to bind to a surface-exposed epitope of a major outer membrane protein of this organism. This outer membrane protein, which had an apparent molecular weight of approximately 80,000 in sodium dodecyl sulfate-polyacrylamide gels, was designated CopB. MAb 10F3, reactive with CopB, bound to a majority (70%) of M. catarrhalis strains tested. More importantly, mice passively immunized with MAb 10F3 exhibited an enhanced ability to clear a bolus challenge of M. catarrhalis from their lungs, a result which suggested that CopB might have potential as a vaccine candidate. The M. catarrhalis gene encoding CopB was cloned in Escherichia coli, and nucleotide sequence analysis of the copB gene indicated that the CopB protein was synthesized with a leader peptide, a finding confirmed by N-terminal amino acid sequence analysis of the mature CopB protein purified from M. catarrhalis 035E. Southern blot analysis showed that chromosomal DNA from seven different M. catarrhalis strains hybridized with a probe comprising the majority of the copB structural gene from strain 035E. Additional data emphasizing the extent of conservation of the CopB protein among M. catarrhalis strains were obtained from Western immunoblot analyses with polyclonal antisera raised against CopB proteins from different M. catarrhalis strains used to probe the recombinant form of the CopB protein from strain 035E. The ability of the CopB protein to function as a target for biologically active antibodies and its apparent conservation among M. catarrhalis strains warrant further investigation of this outer membrane protein as a potential vaccine candidate.