gebhart/patrepeval huggingface dataset:
Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (2010)

DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and show that each technique operates in a different domain of the CpG density landscape. We explored the effect of whole-genome amplification and illustrate that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. By using MBDCap, we compare and contrast microarray- and sequencing-based readouts and highlight the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed, and consideration must be made in light of the GC content, the extent of DNA amplification, and the copy number.
Detection of Escherichia coli O157:H7 by multiplex PCR (1995)

In order to develop a PCR assay for Escherichia coli O157:H7, a portion of the 60-MDa plasmid harbored by enterohemorrhagic E. coli (EHEC) was sequenced and PCR primers were designed. A multiplex PCR method was then designed by employing primers specific for the EHEC eaeA gene, conserved sequences of Shiga-like toxins I (SLT-I) and II (SLT-II), and the 60-MDa plasmid. PCR products of 1,087 bp (eaeA), 227 and/or 224 bp (SLT-I and/or SLT-II), and 166 bp (plasmid) were successfully amplified simultaneously in a single reaction. The multiplex PCR method can be used to specifically identify EHEC of serogroup O157.
REDUCED CEREBRAL INFECTION OF NEOSPORA CANINUMI--INFECTED MICE AFTER VACCINATION WITH RECOMBINANT MICRONEME PROTEIN NCMIC3 AND (2003)

C57BL/6 mice were vaccinated with a bacterially expressed and purified polyhistidine-tagged full-length version of the microneme protein NcMIC3 (recNcMIC3) emulsified in Ribi Adjuvant System (RAS). Subsequently, they were challenged by intraperitoneal inoculation of 2 X 106 live Neospora caninum tachyzoites. As controls, groups of mice received phosphate- buffered saline (PBS)-RAS alone (adjuvant control) or were treated with PBS before infection (infection control). The protective effect of vaccination was assessed by Neospora-specific polymerase chain reaction (PCR), immunohistochemical investigation of brain tissue, and serological means (enzyme-linked immunosorbent assay). Assessment by PCR performed on DNA from different organs revealed that in all treatment groups parasite DNA could only be detected in brain tissue. According to the PCR results, the recNcMIC3 vaccine conferred protection to 75% of mice (n = 16 in 2 independent experiments), whereas application of PBS-RAS and of PBS alone resulted in protection of 12.5% and 0% of mice, respectively (n = 16 as above). Mice in the PBS-treated infection control group were affected by evident clinical signs of neosporosis starting on day 6 postinfection (p.i.). Conversely, none of the animals treated with either PBS-RAS or recNcMIC3 exhibited any symptoms until day 21 p.i. Immu- nohistochemical staining of paraffin-embedded brain tissue sections confirmed the protective effect of recNcMIC3 vaccination. Quantitative Neospora-specific real-time PCR revealed that infection intensities were lower in the brain tissues of recNcMIC3- vaccinated mice compared with PBS-RAS-treated adjuvant control mice. Serological analysis showed that the protective effect observed in recNcMIC3-vaccinated mice was associated with a Th2-type IgG 1 antibody response directed against native NcMIC3 and a mixed IgG1-IgG2a antibody response directed against the recombinant antigen itself. Taken together, these results dem- onstrated that recombinant NcMIC3 vaccine confers a significant protectivity against experimentally induced cerebral neosporosis in mice.
Chemical synthesis of proteins in solution (1999)

Development of a novel strategy suitable for the solution synthesis of proteins is described, wherein the entire molecule is assembled from fully protected segments in the size range of about 10 residues. Each segment is designed so as to have a common structure of Boc-peptide-OPac (Pac: phenacyl) and all of the side-chain functional groups are protected by Bzl-based groups. New types of solvent systems are described for dissolving fully protected segments in which the segment condensation reactions in solution can be carried out smoothly. After removal of the Boc or Pac group, the segments are coupled together to obtain the entire sequence using the 1-ethyl-3-(3'-dimethylaminopropyl)-carbodiimide/3, 4-dihydro-3-hydroxy-4-oxo-1,2,3-benzotriazine method. The side-chain protecting groups are then removed by HF and the liberated peptide is subjected to folding reactions to obtain the native conformation. Applying the strategy, the 123-residue human angiogenin, the 121-residue human midkine, the 136-residue human pleiotrophin, and the 238-residue Aequoria green fluorescent protein were synthesized successfully.
Bayesian Compression for Deep Learning (2017)

Compression and computational efficiency in deep learning have become a problem of great significance. In this work, we argue that the most principled and effective way to attack this problem is by adopting a Bayesian point of view, where through sparsity inducing priors we prune large parts of the network. We introduce two novelties in this paper: 1) we use hierarchical priors to prune nodes instead of individual weights, and 2) we use the posterior uncertainties to determine the optimal fixed point precision to encode the weights. Both factors significantly contribute to achieving the state of the art in terms of compression rates, while still staying competitive with methods designed to optimize for speed or energy efficiency.
International Prognostic Scoring System–independent cytogenetic risk categorization in primary myelofibrosis (2009)

Among 200 patients with primary myelofibrosis, karyotype at diagnosis was abnormal in 83 (42%). To assess their individual prognostic impact, specific cytogenetic abnormalities with more than or equal to 5 informative cases were identified and the rest grouped separately as "other abnormalities." Median survival in patients with sole +9 (n = 6), sole 20q- (n = 21), sole 13q- (n = 8), normal karyotype (n = 117), "other abnormalities" (n = 28), complex karyotype (n = 13), and sole +8 (n = 7) were "not reached," 112, 105, 80, 46, 34, and 28 months, respectively (P = .01). Accordingly, 4 cytogenetic risk groups were considered: (1) favorable (sole +9, 20q-, or 13q-), (2) normal, (3) unfavorable (complex karyotype or sole +8), and (4) "other abnormalities." Multivariable analysis confirmed the International Prognostic Scoring System (IPSS)-independent prognostic value of both 4-way and 2-way (ie, favorable/normal vs unfavorable/other abnormalities; IPSS-adjusted hazard ratio = 0.37; 95% confidence interval, 0.24-0.58) cytogenetic risk categorization (P < .01). The ability to prognostically dissect a specific IPSS category has major therapeutic implications.
[Expression of prostaglandin transporter in colorectal cancer tissues and its relationship with clinicopathological features]. (2015)

Expression levels of PGT mRNA and protein in colorectal cancer tissue are significantly down-regulation. PGT expression is associated with invasion depth and late stages.
Optimizing Electrode Placement Using Finite-Element Models in Radiofrequency Ablation Treatment Planning (2008)

Conventional radiofrequency ablation (RFA) planning methods for identifying suitable electrode placements typically use geometric shapes to model ablation outcomes. A method is presented for searching electrode placements that couples finite-element models (FEMs) of RFA together with a novel optimization strategy. The method was designed to reduce the need for model solutions per local search step. The optimization strategy was tested against scenarios requiring single and multiple ablations. In particular, for a scenario requiring multiple ablations, a domain decomposition strategy was described to minimize the complexity of simultaneously searching multiple electrode placements. The effects of nearby vasculature on optimal electrode placement were also studied. Compared with geometric planning approaches, FEMs could potentially deliver electrode placement plans that provide more physically meaningful predictions of therapeutic outcomes.
D-Homosteroids. I. 3β-Hydroxy-17a,17a-dimethyl-D-homoandrostane-17-one and Related Compounds1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTD-Homosteroids. I. 3β-Hydroxy-17a,17a-dimethyl-D-homoandrostane-17-one and Related Compounds1Milan Uskoković, Marcel Gut, and Ralph I. DorfmanCite this: J. Am. Chem. Soc. 1959, 81, 17, 4561–4566Publication Date (Print):September 1, 1959Publication History Published online1 May 2002Published inissue 1 September 1959https://pubs.acs.org/doi/10.1021/ja01526a030https://doi.org/10.1021/ja01526a030research-articleACS PublicationsRequest reuse permissionsArticle Views111Altmetric-Citations7LEARN 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
Back to the future (1995)

Article Back to the future: pen and paper technology supports complex group coordination Share on Authors: Steve Whittaker Lotus Development Corporation, One Rogers St, Cambridge MA Lotus Development Corporation, One Rogers St, Cambridge MAView Profile , Heinrich Schwarz Science, Technology, Society Program, Massachusetts Institute of Technology, Cambridge, MA Science, Technology, Society Program, Massachusetts Institute of Technology, Cambridge, MAView Profile Authors Info & Claims CHI '95: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsMay 1995 Pages 495–502https://doi.org/10.1145/223904.223971Online:01 May 1995Publication History 17citation560DownloadsMetricsTotal Citations17Total Downloads560Last 12 Months14Last 6 weeks0 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 SiteGet Access
Query Optimization for XML (1999)

XML is an emerging standard for data representation and exchange on the World-Wide Web. Due to the nature of information on the Web and the inherent flexibility of XML, we expect that much of the data encoded in XML will be semistructured:the data may be irregular or incomplete, and its structure may change rapidly or unpredictably. This paper describes the query processor of Lore,aDBMS for XML-based data supporting an expressive query language. We focus primarily on Lore&amp;apos;s cost-based query optimizer. While all of the usual problems associated with cost-based query optimization apply to XML-based query languages, a number of additional problems arise, such as new kinds of indexing, more complicated notions of database statistics, and vastly different query execution strategies for different databases. We define appropriate logical and physical query plans, database statistics, and a cost model, and we describe plan enumeration including heuristics for reducing the large search space. Our optimizer is fully implemented in Lore and preliminary performance results are reported.
Genome-wide target profiling of piggyBac and Tol2in HEK 293: pros and cons for gene discovery and gene therapy (2011)

The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting.
Gender in psychotherapy: controversies, impacts and healing (2006)

Issues related to gender have enormous impact on every facet of human existence and relationship. Psychotherapy could be defined as the co-enquiry into the experience of human existence and relationship, and as such is massively affected by gender difference and the allied and inseparable issue of sexuality. My personal experience has been that gender issues have been central in every aspect of psychotherapy through being a client, in training and in working as a therapist. At times, however, this was unclear and confusing. The territory often went unexplored and unspoken because of taboos and sensitivities. Issues of gender have felt unworkable because they constellate a filter through which all experience passes in a deeply held unconscious and numinous manner, almost too close to bring into focus. Gender is like a blackboard onto which our experience is scored.
A multi-band RF CMOS LC bandpass filter with continuous frequency tuning design (2010)

In this paper, a 2nd order tunable RF CMOS LC bandpass filter with the on-chip inductor is presented. Q-enhancement and tuning are also considered. The Q-tuning is implemented through an adjustable negative conductance generator circuit. The simulated results show that the center frequency of the filter using a 0.18µm CMOS process can be operated from 1.90GHz to 2.42GHz frequency band under 3.3V supply by a set of capacitor array and the varactors that achieve the coarse and exact tuning respectively
The beta-lactam biosynthesis genes for isopenicillin N epimerase and deacetoxycephalosporin C synthetase are expressed from a single transcript in Streptomyces clavuligerus (1990)

Isopenicillin N isomerase (epimerase) has been purified from Streptomyces clavuligerus, and the amino acid sequence of the N-terminus has been determined. By using single oligonucleotide probes based on high GC codon bias ("guessmers"), the translation start codons were determined for two successive genes in the beta-lactam-biosynthetic pathway and mapped within a 3.6-kilobase-pair KpnI restriction fragment. The epimerase gene (cefD) was located immediately upstream of the deacetoxycephalosporin C synthetase (expandase) gene (cefE) that was characterized previously. cefD was sequenced and expressed in Escherichia coli; the resulting cell extracts contained epimerase activity. Western immunoblots demonstrated that a protein comigrated with purified S. clavuligerus epimerase at 44 kilodaltons. cefD and cefE were separated by an 81-base-pair segment. The DNA sequence upstream of the epimerase gene had a high AT content, suggestive of a promoter region. Primer extension analysis of S. clavuligerus mRNA showed that the start of transcription occurred approximately 130 base pairs upstream of the epimerase translation start site; Northern (RNA blot) analysis revealed a hybridization signal large enough to code for both epimerase and expandase, and nuclease S1 protection assays showed that a single message may code for epimerase, expandase, and another unknown protein. When cefD and cefE were placed in an expression vector, concomitant synthesis of both epimerase and expandase occurred in E. coli.
High Current Generation Coupled to Caustic Production Using a Lamellar Bioelectrochemical System (2010)

Recently, bioelectrochemical systems (BESs) have emerged as a promising technology for energy and product recovery from wastewaters. To become economically viable, BESs need to (i) reach sufficient turnover rates at scale and (ii) generate a product that offsets the investment costs within a reasonable time frame. Here we used a liter scale, lamellar BES to produce a caustic solution at the cathode. The reactor was operated as a three-electrode system, in which the anode potential was fixed and power was supplied over the reactor to allow spontaneous anodic current generation. In laboratory conditions, with acetate as electron donor in the anode, the system generated up to 1.05 A (at 1.77 V applied cell voltage, 1015 A m(-3) anode volume), and allowed for the production of caustic to 3.4 wt %, at an acetate to caustic efficiency of 61%. The reactor was subsequently operated on a brewery site, directly using effluent from the brewing process. Currents of up to 0.38 A were achieved within a six-week time frame. Considerable fluctuations over weekly periods were observed, due to operational parameter changes. This study is the first to demonstrate effective production of caustic at liter scale, using BESs both in laboratory and field conditions. It also shows that input of power can easily be justified by product value.
Incorporation of a Bioactive Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis To Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D 1H NMR (2011)

By use of a solid-phase synthetic approach, a bioactive reverse turn heterocycle was incorporated into a cyclic peptide template to probe melanocortin receptor potency and ligand structural conformations. The five melanocortin receptor isoforms (MC1R-MC5R) are G-protein-coupled receptors (GPCRs) that are regulated by endogenous agonists and antagonists. This pathway is involved in pigmentation, weight, and energy homeostasis. Herein, we report novel analogues of the chimeric AGRP-melanocortin peptide template integrated with a small molecule moiety to probe the structural and functional consequences of the core His-Phe-Arg-Trp peptide domain using a reverse-turn heterocycle. A series of six compounds are reported that result in inactive to full agonists with nanomolar potency. Biophysical structural analysis [2D (1)H NMR and computer-assisted molecular modeling (CAMM)] were performed on selected analogues, resulting in the identification that these peptide-small molecule hybrids possessed increased flexibility and fewer discrete conformational families compared to the reference peptide and result in a novel template for further structure-function studies.
Classical transmitters in the CNS (1984)

I. General features of chemically identified neurons (F.E. Bloom). II. Catecholamines, serotonin, acetylcholine, and gamma-aminobutyric acid in the rat brain: biochemical studies (M.J. Brownstein and M. Palkovits). III. Dopamine-containing systems in the CNS (A. Bjorklund and O. Lindvall). IV. Noradrenaline-containing neuron systems (R.Y. Moore and J.P. Card). V. Central catecholamine neurons as revealed by immunohistochemistry with special reference to adrenaline neurons (T. Hokfelt, O. Johansson and M. Goldstein). VI. Distributional maps of tyrosine-hydroxlase-immunoreactive neurons in the rat brain (T. Hokfelt, R. Martensson, A. Bjorklund, S. Kleinau and M. Goldstein). VII. Low power photography in the fluorescence microscope using an automatic dark-field condenser-scanner (R. Martensson and A. Bjorklund). VIII. Immunocytochemical localization of aromatic-L-aminoacid decarboxylase (C.B. Jaeger, D.A. Ruggiero, V.R. Albert, T.H. Joh and D.J. Reis). IX. Comparative anatomy of central monoaminergic systems (A. Parent, D. Poitras and L. Dube). Subject index.
Insects groom their antennae to enhance olfactory acuity (2013)

Grooming, a common behavior in animals, serves the important function of removing foreign materials from body surfaces. When antennal grooming was prevented in the American cockroach, Periplaneta americana, field emission gun scanning electron microscopy images revealed that an unstructured substance accumulated on nongroomed antennae, covering sensillar pores, but not on groomed antennae of the same individuals. Gas chromatography analysis of antennal extracts showed that over a 24-h period nongroomed antennae accumulated three to four times more cuticular hydrocarbons than groomed antennae. Moreover, nongroomed antennae accumulated significantly more environmental contaminants from surfaces (stearic acid) and from air (geranyl acetate) than groomed antennae. We hypothesized that the accumulation of excess native cuticular hydrocarbons on the antennae would impair olfactory reception. Electroantennogram experiments and single-sensillum recordings supported this hypothesis: antennae that were prevented from being groomed were significantly less responsive than groomed antennae to the sex pheromone component periplanone-B, as well as to the general odorants geranyl acetate and hexanol. We therefore conclude that antennal grooming removes excess native cuticular lipids and foreign chemicals that physically and/or chemically interfere with olfaction, and thus maintains the olfactory acuity of the antennae. Similar experimental manipulations of the German cockroach (Blattella germanica), carpenter ant (Camponotus pennsylvanicus), and the housefly (Musca domestica), which use different modes of antennal grooming, support the hypothesis that antennal grooming serves a similar function in a wide range of insect taxa.
MAX1andMAX2control shoot lateral branching inArabidopsis (2002)

Plant shoots elaborate their adult form by selective control over the growth of both their primary shoot apical meristem and their axillary shoot meristems. We describe recessive mutations at two loci in Arabidopsis, MAX1 and MAX2, that affect the selective repression of axillary shoots. All the first order (but not higher order) axillary shoots initiated by mutant plants remain active, resulting in bushier shoots than those of wild type. In vegetative plants where axillary shoots develop in a basal to apical sequence, the mutations do not clearly alter node distance, from the shoot apex, at which axillary shoot meristems initiate but shorten the distance at which the first axillary leaf primordium is produced by the axillary shoot meristem. A small number of mutant axillary shoot meristems is enlarged and, later in development, a low proportion of mutant lateral shoots is fasciated. Together, this suggests that MAX1 and MAX2 do not control the timing of axillary meristem initiation but repress primordia formation by the axillary meristem. In addition to shoot branching, mutations at both loci affect leaf shape. The mutations at MAX2 cause increased hypocotyl and petiole elongation in light-grown seedlings. Positional cloning identifies MAX2 as a member of the F-box leucine-rich repeat family of proteins. MAX2 is identical to ORE9, a proposed regulator of leaf senescence ( Woo, H. R., Chung, K. M., Park, J.-H., Oh, S. A., Ahn, T., Hong, S. H., Jang, S. K. and Nam, H. G. (2001) Plant Cell 13, 1779-1790). Our results suggest that selective repression of axillary shoots involves ubiquitin-mediated degradation of as yet unidentified proteins that activate axillary growth.