gebhart/patrepeval huggingface dataset:
A Sample Purification Method for Rugged and High-Performance DNA Sequencing by Capillary Electrophoresis Using Replaceable Polymer Solutions. B. Quantitative Determination of the Role of Sample Matrix Components on Sequencing Analysis (1998)

In the previous paper, a sample cleanup procedure for DNA sequencing reaction products was developed, in which template DNA was removed by ultrafiltration and the total concentration of salts (chloride and di- and deoxynucleotides) was decreased below 10 microM using gel filtration. In this paper, a quantitative study of the effects of these sample solution components on the injected amount and separation efficiency of the sequencing fragments in capillary electrophoresis is presented. The presence of chloride and deoxynucleotides in a total concentration above 10 microM in the sample solution significantly decreased the amount of DNA sequencing fragments injected into the capillary column. However, the separation efficiency was not affected upon increasing the amount of salt. On the other hand, in the presence of only 0.1 microgram of template in the sample (one-third of the lowest quantity recommended in cycle sequencing) and at very low chloride concentration (approximately 5 microM), the separation efficiency decreased by 70%, and the injected amount of DNA sequencing fragments was 40% lower compared to the sample cleaned by the new purification method. The deleterious effect of template DNA on the separation of sequencing fragments was suppressed in the presence of salt in a concentration above 100 microM in the sample solution. Separately, it was found that both the electric field strength and duration of injection affected the resolution of DNA sequencing fragments when the cleaned up sample solution was used. Separation efficiencies of 15 x 10(6) theoretical plates/m were achieved when the sample was loaded at low electric field, e.g., 25 V/cm for 80 s or less. The results demonstrate that the sample solution components (chloride, deoxynucleotides, template DNA) and injection conditions must be controlled to achieve high performance and rugged DNA sequencing analysis.
Elasticity and antiferromagnetism of metallic antiferromagnetics (1959)

If an antiferromagnetic is spontaneously deformed on cooling through the Néel temperature, then the application of an external stress results in a redistribution of domain vectors, e.g. they may rotate or antiferromagnetic domain walls may move. This causes an additional strain component which will be apparent as an anomalous variation of the Young's modulus with the temperature. The results of measurements of the temperature dependence of Young's modulus for antiferromagnetic γ-CuMn alloys and mixed phase (α + γ) CuMn alloys are reported. The (α + y) alloys show (a) a Young's modulus variation of the expected form which is due to the contained α-Mn, (b) a Young's modulus anomaly at about 130 °K associated with the precipitated γ-CuMn (containing 40 atomic percent Mn). It is shown that the latter phase below 130 °K exhibits ferromagnetic characteristics. A smooth temperature variation of Young's modulus has been obtained for Pd which is consistent with the assumption that Pd is not antiferromagnetic at low temperatures.
T-cell specific avian TdT: characterization of the cDNA and recombinant enzyme (1995)

A cDNA clone coding for avian terminal deoxynucleotidyl transferase (TdT) has been isolated and sequenced. The size of this cDNA was 2545 bp with an open reading frame of 1521 bp and a predicted translation product of 58 kDa. Comparison of this TdT sequence with other known TdT sequences has revealed a very high degree of homology at both the DNA and predicted amino acid levels. The chicken TdT cDNA was expressed in a bacterial system and the protein was purified by affinity chromatography. The purified recombinant enzyme, with a specific activity of approximately 1700 U/mg protein, was significantly less active than TdTs from mammalian species. This finding correlates with the observation that TdT isolated from avian thymus has lower activity than that isolated from any mammalian thymus source. Northern blot hybridization analyses and reverse transcription PCR of RNA preparations were carried out with the chicken cDNA. The data generated from these experiments revealed that the TdT RNA was only expressed in the thymus and not in the bone marrow or the bursa of Fabricius during pre- and post hatching chicken development. These data suggest that while TdT is probably involved in N region addition in chicken T-cell receptor genes, it is unlikely to play a role in diversification of immunoglobulin genes.
From sequences to shapes and back: a case study in RNA secondary structures (1994)

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that sequences sharing the same structure are distributed randomly over sequence space. All common structures can be accessed from an arbitrary sequence by a number of mutations much smaller than the chain length. The sequence space is percolated by extensive neutral networks connecting nearest neighbours folding into identical structures. Implications for evolutionary adaptation and for applied molecular evolution are evident: finding a particular structure by mutation and selection is much simpler than expected and, even if catalytic activity should turn out to be sparse of RNA structures, it can hardly be missed by evolutionary processes.
AVP2, a Sequence-Divergent, K+-Insensitive H+-Translocating Inorganic Pyrophosphatase from Arabidopsis (2000)

Plant vacuolar H(+)-translocating inorganic pyrophosphatases (V-PPases; EC 3.6.1.1) have been considered to constitute a family of functionally and structurally monotonous intrinsic membrane proteins. Typified by AVP1 (V. Sarafian, Y. Kim, R.J. Poole, P.A. Rea [1992] Proc Natl Acad Sci USA 89: 1775-1779) from Arabidopsis, all characterized plant V-PPases share greater than 84% sequence identity and catalyze K(+)-stimulated H(+) translocation. Here we describe the molecular and biochemical characterization of AVP2 (accession no. AF182813), a sequence-divergent (36% identical) K(+)-insensitive, Ca(2+)-hypersensitive V-PPase active in both inorganic pyrophosphate hydrolysis and H(+) translocation. The differences between AVP2 and AVP1 provide the first indication that plant V-PPases from the same organism fall into two distinct categories. Phylogenetic analyses of these and other V-PPase sequences extend this principle by showing that AVP2, rather than being an isoform of AVP1, is but one representative of a novel category of AVP2-like (type II) V-PPases that coexist with AVP1-like (type I) V-PPases not only in plants, but also in apicomplexan protists such as the malarial parasite Plasmodium falciparum.
Use of Silicone in the Treatment of Intestinal Gas and Bloating (1960)

Silicone defoamers have been used successfully to eliminate the mucuscovered bubbles which obstruct a gastroscopist's view of the stomach. This led to their trial in treating patients complaining of flatulence and distention. Two hundred patients, aged 23 to 84 years, were given methyl polysiloxane, a physiologically inert silicone, for four weeks to three and a half years. Although other measures had not relieved symptoms, 40 mg. of methyl polysiloxane taken orally 4 times daily produced excellent or good results in 151 patients. In a control group of 20 patients who had had excellent or good results from the methyl polysiloxane, the substitution of a lactose placebo was followed by renewed complaints within 24 hours in 18 patients.
Design, Synthesis, and Vasorelaxant and Platelet Antiaggregatory Activities of Coumarin—Resveratrol Hybrids. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
18-OXOCORTISOL, A NATURALLY OCCURRING MINERALOCORTICOID AGONIST. (1983)

Two C-18-oxygenated corticosteroids, 18-hydroxy- and 18-oxocortisol, have recently been isolated from the urine of patients with primary and genetic (dexamethasone-suppressible) aldosteronism and from adrenal tissue. The relevance of these steroids to the manifestations of mineralocorticoid excess in these disorders was investigated by measuring their affinity to rat renal corticosteroid receptors. 18-0xocortisol showed greater affinity than the 18-hydroxy derivative for both mineralocorticoid and the glucocorticoid receptors and was accordingly assayed in vivo for mineralocorticoid activity. The 18-oxo derivative was found to be an agonist with a sodium-retaining and kaliuretic action qualitatively similar to that of aldosterone. Although 18-oxocortisol was one-third as active as 11-deoxycorticosterone in this assay, it was a more potent mineralocorticoid at the same total plasma concentration because of its lower affinity for corticosteroid-binding globulin.
Exposure of Candida albicans to antifungal agents affects expression of SAP2 and SAP9 secreted proteinase genes (2005)

Antifungal agents with three different mechanisms of action similarly generate a rise in expression of SAP2 and activity of the secreted Sap2 gene product, a known virulence factor, in most isolates of C. albicans. One isolate of the fungus showed an opposite response.
DeepSTCL: A Deep Spatio-temporal ConvLSTM for Travel Demand Prediction (2018)

Urban resource scheduling is an important part of the development of a smart city, and transportation resources are the main components of urban resources. Currently, a series of problems with transportation resources such as unbalanced distribution and road congestion disrupt the scheduling discipline. Therefore, it is significant to predict travel demand for urban resource dispatching. Previously, the traditional time series models were used to forecast travel demand, such as AR, ARIMA and so on. However, the prediction efficiency of these methods is poor and the training time is too long. In order to improve the performance, deep learning is used to assist prediction. But most of the deep learning methods only utilize temporal dependence or spatial dependence of data in the forecasting process. To address these limitations, a novel deep learning traffic demand forecasting framework which based on Deep Spatio-Temporal ConvLSTM is proposed in this paper. In order to evaluate the performance of the framework, an end-to- end deep learning system is designed and a real dataset is used. Furthermore, the proposed method can capture temporal dependence and spatial dependence simultaneously. The closeness, period and trend components of spatio-temporal data are used in three predicted branches. These branches have the same network structures, but do not share weights. Then a linear fusion method is used to get the final result. Finally, the experimental results on DIDI order dataset of Chengdu demonstrate that our method outperforms traditional models with accuracy and speed.
Mechanism of activation of protein kinase C: roles of diolein and phosphatidylserine (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of activation of protein kinase C: roles of diolein and phosphatidylserineMarian Mosior and Richard M. EpandCite this: Biochemistry 1993, 32, 1, 66–75Publication Date (Print):January 12, 1993Publication History Published online1 May 2002Published inissue 12 January 1993https://pubs.acs.org/doi/10.1021/bi00052a010https://doi.org/10.1021/bi00052a010research-articleACS PublicationsRequest reuse permissionsArticle Views188Altmetric-Citations69LEARN 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
Using XHMM Software to Detect Copy Number Variation in Whole‐Exome Sequencing Data (2014)

Copy number variation (CNV) has emerged as an important genetic component in human diseases, which are increasingly being studied for large numbers of samples by sequencing the coding regions of the genome, i.e., exome sequencing. Nonetheless, detecting this variation from such targeted sequencing data is a difficult task, involving sorting out signal from noise, for which we have recently developed a set of statistical and computational tools called XHMM. In this unit, we give detailed instructions on how to run XHMM and how to use the resulting CNV calls in biological analyses.
CD44 expression in the developing and growing rat intervertebral disc (2000)

CD44 has been identified at the time of extracellular matrix formation and expansion in several sites of the developing embryo (Wheatley et al. [1993] Development 119:295-306). The nucleus pulposus, consisting of a hydrated extracellular matrix tissue at birth, not previously closely analyzed, was examined for expression of CD44 in the developing and aging rat intervertebral disc. CD44 was identified solely on notochordal cells from the first onset of intervertebral disc formation (day 15 embryo) through the loss of notochordal cells from the nucleus pulposus (12-24 months of age). No CD44 expression was found in the notochordal cells prior to disc formation or in any cells other than the notochordal cells in the annulus fibrosus or nucleus pulposus of the intervertebral disc. Using reverse transcriptase-polymerase chain reaction methodology, the single 365 amino acid CD44 standard, CD44s, open reading frame was amplified from notochordal cells isolated from the nucleus pulposus. Western blot analysis of a cultured nucleus pulposus notochordal cells total protein extract identified a single CD44 species devoid of chondroitin sulfate with a mass of approximately 85 kDa, characteristic of CD44s. Cell surface detection for CD44 was co-localized with hyaluronan and proteoglycans at first appearance of disc formation in the nucleus pulposus.
Detection of Unknown Anomalies in Streaming Videos with Generative Energy-based Boltzmann Models (2018)

Abnormal event detection is one of the important objectives in research and practical applications of video surveillance. However, there are still three challenging problems for most anomaly detection systems in practical setting: limited labeled data, ambiguous definition of "abnormal" and expensive feature engineering steps. This paper introduces a unified detection framework to handle these challenges using energy-based models, which are powerful tools for unsupervised representation learning. Our proposed models are firstly trained on unlabeled raw pixels of image frames from an input video rather than hand-crafted visual features; and then identify the locations of abnormal objects based on the errors between the input video and its reconstruction produced by the models. To handle video stream, we develop an online version of our framework, wherein the model parameters are updated incrementally with the image frames arriving on the fly. Our experiments show that our detectors, using Restricted Boltzmann Machines (RBMs) and Deep Boltzmann Machines (DBMs) as core modules, achieve superior anomaly detection performance to unsupervised baselines and obtain accuracy comparable with the state-of-the-art approaches when evaluating at the pixel-level. More importantly, we discover that our system trained with DBMs is able to simultaneously perform scene clustering and scene reconstruction. This capacity not only distinguishes our method from other existing detectors but also offers a unique tool to investigate and understand how the model works.
A Practical Route to Quinolines from Anilines (2001)

A practical route to quinoline from anilines through acid-mediated cyclization of 3-(N-aryl-N-sulfonylamino)propionaldehydes has been developed.Treatment of the cyclization products, dihydroquinoline intermediates with KOH in DMSO leads to substituted quinolines.
Electrodeposition of Metals from Organic Solutions (1957)

The electrodeposition of Be from nonaqueous media was studied. Be compounds used as solutes were the hydride, aluminohydride, borohydride, halides, alkyls, and aryls. Their preparation, chemical properties, and electrochemical properties in nonaqueous media were investigated. Electrodeposits of Be (95% pure) and Be alloys, such as Be‐B and Be‐Al, were obtained from organic solutions. It is believed that these represent the first metallic deposits consisting essentially of Be that have been obtained from organic baths.
Insulin Regulates Glucagon-Like Peptide-1 Secretion from the Enteroendocrine L Cell (2008)

Insulin resistance and type 2 diabetes mellitus are associated with impaired postprandial secretion of glucagon-like peptide-1 (GLP-1), a potent insulinotropic hormone. The direct effects of insulin and insulin resistance on the L cell are unknown. We therefore hypothesized that the L cell is responsive to insulin and that insulin resistance impairs GLP-1 secretion. The effects of insulin and insulin resistance were examined in well-characterized L cell models: murine GLUTag, human NCI-H716, and fetal rat intestinal cells. MKR mice, a model of chronic hyperinsulinemia, were used to assess the function of the L cell in vivo. In all cells, insulin activated the phosphatidylinositol 3 kinase-Akt and MAPK kinase (MEK)-ERK1/2 pathways and stimulated GLP-1 secretion by up to 275 +/- 58%. Insulin resistance was induced by 24 h pretreatment with 10(-7) m insulin, causing a marked reduction in activation of Akt and ERK1/2. Furthermore, both insulin-induced GLP-1 release and secretion in response to glucose-dependent insulinotropic peptide and phorbol-12-myristate-13-acetate were significantly attenuated. Whereas inhibition of phosphatidylinositol 3 kinase with LY294002 potentiated insulin-induced GLP-1 release, secretion was abrogated by inhibiting the MEK-ERK1/2 pathway with PD98059 or by overexpression of a kinase-dead MEK1-ERK2 fusion protein. Compared with controls, MKR mice were insulin resistant and displayed significantly higher fasting plasma insulin levels. Furthermore, they had significantly higher basal GLP-1 levels but displayed impaired GLP-1 secretion after an oral glucose challenge. These findings indicate that the intestinal L cell is responsive to insulin and that insulin resistance in vitro and in vivo is associated with impaired GLP-1 secretion.
Retarding field energy analyzer for the Saskatchewan Torus–Modified plasma boundary (2009)

The retarding field energy analyzer (RFA) is a simple and reliable diagnostic technique to measure the ion temperature in the scrape-off layer and edge of magnetic fusion devices. Design and operation features of a single-sided (facing the ion flow) RFA for ion temperature measurements in the Saskatchewan Torus-Modified (STOR-M) tokamak are described. Its compact size (21 x 15 x 20 mm3) allows RFA measurements without perturbing plasma significantly. Both ion and electron temperature have been measured by RFA in the STOR-M tokamak. A method is proposed to correct the effects of ion flow on the ion temperature using the simultaneously measured Mach number. The measured electron temperature is consistent with the previously reported Langmuir probe data. Abnormal behavior of the RFA has been observed in both ion and electron modes when RFA is inserted deep into the plasma.
Personalized Medicine in Psoriasis: Concept and Applications (2010)

Personalized medicine is a new treatment modality where patients are the center of interest. Thus, one drug does not fit all; rather we look for a drug which fits the individual patients' disease. Treatment is moving towards molecular medicine driven by the growing knowledge and understanding of pharmacogenetics. Psoriasis is a common dermatological disease characterized by genetic polymorphism. The association of biomarkers and psoriasis is helpful to evaluate susceptibility to the disease, its severity and its progression. Additionally, the response to treatment will be anticipated. The growing expenses of health care systems worldwide are primarily due to increasing costs of chronic disease management. Hence, activation of preventive medicine will minimize treatment costs. A revolution in treatment modalities is expected to start at the level of pharmaceutical companies, as personalization of medicine will decrease the cost of clinical trials by minimizing the number of subjects required. In turn, this will decrease the cost of developing new medications. My vision for the future is that personalized medicine will mandate special physicians capable of understanding molecular medicine and using genetics and biomarkers for diagnosis, evaluation of the effect of drugs and overall prognosis. This new therapeutic modality will need special training.
Rewarding Effects of Optical Stimulation of Ventral Tegmental Area Glutamatergic Neurons (2015)

Ventral tegmental area (VTA) neurons play roles in reward and aversion. The VTA has three major neuronal phenotypes: dopaminergic, GABAergic, and glutamatergic. VTA glutamatergic neurons--expressing vesicular glutamate transporter-2 (VGluT2)--project to limbic and cortical regions, but also excite neighboring dopaminergic neurons. Here, we test whether local photoactivation of VTA VGluT2 neurons expressing Channelrhodopsin-2 (ChR2) under the VGluT2 promoter causes place preference and supports operant responding for the stimulation. By using a Cre-dependent viral vector, ChR2 (tethered to mCherry) was expressed in VTA glutamatergic neurons of VGluT2::Cre mice. The mCherry distribution was evaluated by immunolabeling. By confocal microscopy, we detected expression of mCherry in VTA cell bodies and local processes. In contrast, VGluT2 expression was restricted to varicosities, some of them coexpressing mCherry. By electron microscopy, we determined that mCherry-VGluT2 varicosities correspond to axon terminals, forming asymmetric synapses on neighboring dopaminergic neurons. These findings indicate that ChR2 was present in terminals containing glutamatergic synaptic vesicles and involved in local synaptic connections. Photoactivation of VTA slices from ChR2-expressing mice induced AMPA/NMDA receptor-dependent firing of dopaminergic neurons projecting to the nucleus accumbens. VTA photoactivation of ChR2-expressing mice reinforced instrumental behavior and established place preferences. VTA injections of AMPA or NMDA receptor antagonists blocked optical self-stimulation and place preference. These findings suggest a role in reward function for VTA glutamatergic neurons through local excitatory synapses on mesoaccumbens dopaminergic neurons.