gebhart/patrepeval huggingface dataset:
Crystal Structure and Photodynamic Behavior of the Blue Emission Variant Y66H/Y145F of Green Fluorescent Protein (1997)

The crystal structure of a blue emission variant (Y66H/Y145F) of the Aequorea victoria green fluorescent protein has been determined by molecular replacement and the model refined. The crystallographic R-factor is 18.1% for all data from 20 to 2.1 A, and the model geometry is excellent. The chromophore is non-native and is autocatalytically generated from the internal tripeptide Ser65-His66-Gly67. The final electron density maps indicate that the formation of the chromophore is complete, including 1,2 dehydration of His66 as indicated by the planarity of the chromophore. The chromophore is in the cis conformation, with no evidence for any substantial fraction of the trans configuration or uncyclized apoprotein, and is well-shielded from bulk solvent by the folded protein. These characteristics indicate that the machinery for production of the chromophore from a buried tripeptide unit is not only intact but also highly efficient in spite of a major change in chromophore chemical structure. Nevertheless, there are significant rearrangements in the hydrogen bond configuration around the chromophore as compared to wild-type, indicating flexibility of the active site. pH titration of the intact protein and the chromopeptide (pKa1 = 4.9 +/- 0.1, pKa2 = 12.0 +/- 0.1) suggests that the predominant form of the chromophore in the intact protein is electrically neutral. In contrast to the wild-type protein [Chattoraj, M., King, B. A., Bublitz, G. U., & Boxer, S. G. (1996) Proc. Natl. Acad. Sci. U.S.A., 8362-8367], femtosecond fluorescence up-conversion spectroscopy of the intact protein and a partially deuterated form strongly suggests that excited-state proton transfer is not coupled to fluorescence emission.
Inflammatory bowel disease-like enteritis and caecitis in a senescence accelerated mouse P1/Yit strain (1998)

Enteric inflammation in the ileum and caecum developed in the SAMP1/Yit strain. The pathophysiological characteristics of the disease in this mouse have some similarities to those of human inflammatory bowel disease (IBD). This mouse strain should be a useful model system for elucidating the interaction between the pathogenesis of IBD and the gut microflora.
Scalable Person Re-identification: A Benchmark (2015)

This paper contributes a new high quality dataset for person re-identification, named "Market-1501". Generally, current datasets: 1) are limited in scale, 2) consist of hand-drawn bboxes, which are unavailable under realistic settings, 3) have only one ground truth and one query image for each identity (close environment). To tackle these problems, the proposed Market-1501 dataset is featured in three aspects. First, it contains over 32,000 annotated bboxes, plus a distractor set of over 500K images, making it the largest person re-id dataset to date. Second, images in Market-1501 dataset are produced using the Deformable Part Model (DPM) as pedestrian detector. Third, our dataset is collected in an open system, where each identity has multiple images under each camera. As a minor contribution, inspired by recent advances in large-scale image search, this paper proposes an unsupervised Bag-of-Words descriptor. We view person re-identification as a special task of image search. In experiment, we show that the proposed descriptor yields competitive accuracy on VIPeR, CUHK03, and Market-1501 datasets, and is scalable on the large-scale 500k dataset.
First Row Divalent Transition Metal Complexes of Aryl-Appended Tris((pyridyl)methyl)amine Ligands:  Syntheses, Structures, Electrochemistry, and Hydroxamate Binding Properties (2003)

Divalent manganese, cobalt, nickel, and zinc complexes of 6-Ph(2)TPA (N,N-bis((6-phenyl-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine; [(6-Ph(2)TPA)Mn(CH(3)OH)(3)](ClO(4))(2) (1), [(6-Ph(2)TPA)Co(CH(3)CN)](ClO(4))(2) (2), [(6-Ph(2)TPA)Ni(CH(3)CN)(CH(3)OH)](ClO(4))(2) (3), [(6-Ph(2)TPA)Zn(CH(3)CN)](ClO(4))(2) (4)) and 6-(Me(2)Ph)(2)TPA (N,N-bis((6-(3,5-dimethyl)phenyl-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine; [(6-(Me(2)Ph)(2)TPA)Ni(CH(3)CN)(2)](ClO(4))(2) (5) and [(6-(Me(2)Ph)(2)TPA)Zn(CH(3)CN)](ClO(4))(2) (6)) have been prepared and characterized. X-ray crystallographic characterization of 1A.CH(3)()OH and 1B.2CH(3)()OH (differing solvates of 1), 2.2CH(3)()CN, 3.CH(3)()OH, 4.2CH(3)()CN, and 6.2.5CH(3)()CN revealed mononuclear cations with one to three coordinated solvent molecules. In 1A.CH(3)()OH and 1B.2CH(3)()OH, one phenyl-substituted pyridyl arm is not coordinated and forms a secondary hydrogen-bonding interaction with a manganese bound methanol molecule. In 2.2CH(3)()CN, 3.CH(3)()OH, 4.2CH(3)()CN, and 6.2.5CH(3)()CN, all pyridyl donors of the 6-Ph(2)TPA and 6-(Me(2)Ph)(2)TPA ligands are coordinated to the divalent metal center. In the cobalt, nickel, and zinc derivatives, CH/pi interactions are found between a bound acetonitrile molecule and the aryl appendages of the 6-Ph(2)TPA and 6-(Me(2)Ph)(2)TPA ligands. (1)H NMR spectra of 4 and 6 in CD(3)NO(2) solution indicate the presence of CH/pi interactions, as an upfield-shifted methyl resonance for a bound acetonitrile molecule is present. Examination of the cyclic voltammetry of 1-3 and 5 revealed no oxidative (M(II)/M(III)) couples. Admixture of equimolar amounts of 6-Ph(2)TPA, M(ClO(4))(2).6H(2)O, and Me(4)NOH.5H(2)O, followed by the addition of an equimolar amount of acetohydroxamic acid, yielded the acetohydroxamate complexes [((6-Ph(2)TPA)Mn)(2)(micro-ONHC(O)CH(3))(2)](ClO(4))(2) (8), [(6-Ph(2)TPA)Co(ONHC(O)CH(3))](ClO(4))(2) (9), [(6-Ph(2)TPA)Ni(ONHC(O)CH(3))](ClO(4))(2) (10), and [(6-Ph(2)TPA)Zn(ONHC(O)CH(3))](ClO(4))(2) (11), all of which were characterized by X-ray crystallography. The Mn(II) complex 8.0.75CH(3)()CN.0.75Et(2)()O exhibits a dinuclear structure with bridging hydroxamate ligands, whereas the Co(II), Ni(II), and Zn(II) derivatives all exhibit mononuclear six-coordinate structures with a chelating hydroxamate ligand.
Concept discovery from text (2002)

Broad-coverage lexical resources such as WordNet are extremely useful. However, they often include many rare senses while missing domain-specific senses. We present a clustering algorithm called CBC (Clustering By Committee) that automatically discovers concepts from text. It initially discovers a set of tight clusters called committees that are well scattered in the similarity space. The centroid of the members of a committee is used as the feature vector of the cluster. We proceed by assigning elements to their most similar cluster. Evaluating cluster quality has always been a difficult task. We present a new evaluation methodology that is based on the editing distance between output clusters and classes extracted from WordNet (the answer key). Our experiments show that CBC outperforms several well-known clustering algorithms in cluster quality.
Displacement of the nitro group of substituted nitrobenzenes-a synthetically useful process (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDisplacement of the nitro group of substituted nitrobenzenes-a synthetically useful processNathan Kornblum, Leung Cheng, Robert C. Kerber, Melvin M. Kestner, Barry N. Newton, Harold W. Pinnick, Ronald G. Smith, and Peter A. WadeCite this: J. Org. Chem. 1976, 41, 9, 1560–1564Publication Date (Print):April 1, 1976Publication History Published online1 May 2002Published inissue 1 April 1976https://pubs.acs.org/doi/10.1021/jo00871a016https://doi.org/10.1021/jo00871a016research-articleACS PublicationsRequest reuse permissionsArticle Views1306Altmetric-Citations107LEARN 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
CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. (1989)

In mammals and other vertebrates, cytosine methylation in CpG sites is often negatively correlated with gene activity. Because methylation of the promoter region is most crucial for this effect, the simplest hypothesis is that CpG methylation interferes with the binding of specific transcription factors. We have examined this hypothesis with two different transcription factor-binding sites that contain a CpG dinucleotide, namely the cAMP-responsive element (CRE; 5'-TGACGTCA) and the Sp1-binding site (5'-GTGAGGCGGTGAGACT). We have reported previously that CpG methylation of the Sp1-binding site affected neither factor binding nor transcription in HeLa cells, which may be related to the fact that Sp1 is typically associated with promoters of housekeeping genes. In contrast, CREs are often associated with promoters of cell type-specific genes. A synthetic oligonucleotide containing two tandem CREs derived from the gene encoding the human glycoprotein hormone alpha-subunit was cloned upstream of a reporter gene. Transcription of this gene was dependent on the CRE sequences in both PC12 and HeLa cells. Bandshift and methylation interference assays show that similar, if not the same, factor(s) bind to the CRE in both cell lines, even though induction by cAMP was only observed in PC12 cells. CpG methylation of the CRE consensus sequences (TGACGTCA) resulted in loss of specific factor binding, as well as loss of transcriptional activity in vitro and in vivo, in both cell types. This suggests that the inactivity of methylated promoters can, at least in some cases, be explained by their inability to bind specific transcription factors.
Identification of Novel Biomarker Candidates for the Immunohistochemical Diagnosis of Cholangiocellular Carcinoma (2014)

The aim of this study was the identification of novel biomarker candidates for the diagnosis of cholangiocellular carcinoma (CCC) and its immunohistochemical differentiation from benign liver and bile duct cells. CCC is a primary cancer that arises from the epithelial cells of bile ducts and is characterized by high mortality rates due to its late clinical presentation and limited treatment options. Tumorous tissue and adjacent non-tumorous liver tissue from eight CCC patients were analyzed by means of two-dimensional differential in-gel electrophoresis and mass-spectrometry-based label-free proteomics. After data analysis and statistical evaluation of the proteins found to be differentially regulated between the two experimental groups (fold change ≥ 1.5; p value ≤ 0.05), 14 candidate proteins were chosen for determination of the cell-type-specific expression profile via immunohistochemistry in a cohort of 14 patients. This confirmed the significant up-regulation of serpin H1, 14-3-3 protein sigma, and stress-induced phosphoprotein 1 in tumorous cholangiocytes relative to normal hepatocytes and non-tumorous cholangiocytes, whereas some proteins were detectable specifically in hepatocytes. Because stress-induced phosphoprotein 1 exhibited both sensitivity and specificity of 100%, an immunohistochemical verification examining tissue sections of 60 CCC patients was performed. This resulted in a specificity of 98% and a sensitivity of 64%. We therefore conclude that this protein should be considered as a potential diagnostic biomarker for CCC in an immunohistochemical application, possibly in combination with other candidates from this study in the form of a biomarker panel. This could improve the differential diagnosis of CCC and benign bile duct diseases, as well as metastatic malignancies in the liver.
OTO-104 (2010)

OTO-104 is a novel proprietary therapeutic delivery system that can achieve prolonged, sustained release of dexamethasone within the inner ear fluids. The administration of this clinical candidate formulation via intratympanic injection is expected to be well tolerated both locally and systemically.
Naming and registration for IBM distributed systems (1992)

Today's trends toward interconnection of networks expose limitations and deficiencies of traditional identification schemes. The need arises for a uniform naming solution that can accommodate the size and heterogeneity of worldwide domains, while still remaining understandable, usable, and manageable by human users. This paper describes a proposatol name objects and resources in distributed environments; each object or resource cabne located, accessed, communicated with, operated on, managed, or secured using the same, unique name. The solution proposed here includes registration mechanisms necessary to ensure name uniqueness. The schemeis based on existing standards, mainly Open Systems Interconnection (OSI) Distinguished Names; whenever standards disagree, the preference goesto the alternative that offers the widest usage acrosasll protocols. Clear, consistent naming guidelineasr e given that would enable ISM customers who have purchased IBM networking and system management products to name their resourcesso that their administrative processes and IBM's products and protocols can support those resources effectively. A method is suggested to encompass existing name spaces in a single, worldwide namings pace, and a migration pathis sketched. The interoperation of different protocols across network boundariesu sing the same naming constructs is shown by means of several scenarios. The naming and addressing scheme proposed here requires nothing new or different from the already defined standards, but allows interoperation among them by using a subset of each.
The Medical Cost of Undiagnosed Sleep Apnea (1999)

Obstructive sleep apnea is an under-diagnosed, but common disorder with serious adverse consequences. Cost data from the year prior to the diagnosis of sleep-disordered breathing in a consecutive series of 238 cases were used to estimate the potential medical cost of undiagnosed sleep apnea and to determine the relationship between the severity of sleep-disordered breathing and the magnitude of medical costs. Among cases, mean annual medical cost prior to diagnosis was $2720 versus $1384 for age and gender matched controls (p<0.01). Regression analysis showed that the reciprocal of the apnea hypopnea index among cases was significantly related to log-transformed annual medical costs after adjusting for age, gender, and body mass index (p<0.05). We conclude that patients with undiagnosed sleep apnea had considerably higher medical costs than age and sex matched individuals and that the severity of sleep-disordered breathing was associated with the magnitude of medical costs. Using available data on the prevalence of undiagnosed moderate to severe sleep apnea in middle-aged adults, we estimate that untreated sleep apnea may cause $3.4 billion in additional medical costs in the U.S. Whether medical cost savings occur with treatment of sleep apnea remains to be determined.
Molecular Cloning of the Chicken Progesterone Receptor (1986)

To define the functional domains of the progesterone receptor required for gene regulation, complementary DNA (cDNA) clones encoding the chicken progesterone receptor have been isolated from a chicken oviduct lambda gt11 cDNA expression library. Positive clones expressed antigenic determinants that cross-reacted with six monospecific antibodies derived from two independent sources. A 36-amino acid peptide sequence obtained by microsequencing of purified progesterone receptor was encoded by nucleotide sequences in the longest cDNA clone. Analysis of the amino acid sequence of the progesterone receptor deduced from the cDNA clones revealed a cysteine-rich region that was homologous to a region found in the estrogen and glucocorticoid receptors and to the avian erythroblastosis virus gag-erb-A fusion protein. Northern blot analysis with chicken progesterone receptor cDNA's indicated the existence of at least three messenger RNA species. These messages were found only in oviduct and could be induced by estrogens.
Meta-Analysis of the Effects of Soy Protein Intake on Serum Lipids (1995)

In this meta-analysis we found that the consumption of soy protein rather than animal protein significantly decreased serum concentrations of total cholesterol, LDL cholesterol, and triglycerides without significantly affecting serum HDL cholesterol concentrations.
Joint data and channel estimation using blind trellis search techniques (1994)

A novel method of maximum likelihood sequence estimation is proposed for data that are transmitted over unknown linear channels. This procedure does not require a startup sequence for estimating the channel impulse response. Rather, the data and the channel are simultaneously estimated. It is implemented without any loss of optimality by a trellis search algorithm which searches for the best data sequence from among a number of hypothesized trellises which are constructed from the observed sequence. The number of states in each trellis and the number of trellises grow exponentially with the channel memory. A suboptimal trellis search algorithm is proposed whose complexity at best is slightly higher than that of the adaptive Viterbi algorithm operating with a known channel response. A simplified channel estimation algorithm when the number of data alphabets is greater than 2 is also proposed. Fast convergence of the algorithm in estimating the channel is demonstrated for binary pulse amplitude modulation over a variety of channels. Convergence over a wide range of SNR occurs within 100 symbols. The channel estimation algorithm for multi-level signals converges within 500-1000 symbols. We finally present an application of this algorithm to the problem of sequence estimation in the presence of rapidly time-varying intersymbol interference. The algorithm provides reliable zero-delay decisions which results in a better channel tracking algorithm when compared to previously proposed schemes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recent Developments in the Detection of Fetal Single Gene Differences in Maternal Plasma and the Role of Size Fractionation (2006)

The presence of cell-free fetal DNA in maternal plasma allowed noninvasive prenatal diagnosis of fetal loci completely absent from the maternal genome, such as SRY gene and RhD gene. However, the detection of fetal point mutations is hindered by the predominance of maternal DNA sequences. Recent studies have shown that cell-free fetal DNA exists in maternal plasma in small fragments. Thus, cell-free fetal DNA can be enriched by size fractionation, which improves detection of fetal gene mutations. Furthermore, it has been shown that Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) mass spectrometry also permits the detection of fetal SNPs from maternal plasma. These two new developments are discussed.
High sensitivity quantification of RNA from gels and autoradiograms with affordable optical scanning. (1992)

To increase sensitivity and to improve normalization of RNA levels in Northern blot analysis, a comparatively inexpensive optical scanner was utilized for digitizing photonegatives of ethidium bromide stained gels and autoradiograms. The optical scanner captures the image with a maximum resolution of 300 dots per inch by assigning one of 256 gray levels (8-bit) to each dot in the image. With the use of the public domain NIH Image program (requires a Macintosh II and an 8-bit video card), gel or autoradiogram bands in the digitized image are selected and their average gray scale density measured. We found that the digitized image of a photonegative of a TAE (Tris-acetate/EDTA) agarose gel, loaded incrementally with 50-1500 ng total RNA, produced a linear response over a 4-fold range down to 100 ng (R2 greater than 0.950). In utilizing "quantification" gels like this, RNA samples that are too dilute or too small for traditional spectrophotometric techniques can be normalized and loaded uniformly onto subsequent Northern gels. Results from autoradiogram scans demonstrate highly linear gray scale responses over a 4-fold range of total RNA (R2 greater than 0.950) that are reproducible with different blots and probe types (e.g., riboprobe, cDNA and oligonucleotide). In addition, we describe a normalization technique using a 30-mer oligonucleotide probe for rat 28S ribosomal RNA as a measure of total RNA loaded per gel lane. Altogether, this scanning, ribosomal RNA normalization system allows the measurement of relative changes between 20% and 400% using standard autoradiographic methods.
Skeletal Effects of Calcitonin in Ovariectomized Rats* (1991)

Although calcitonin (CT) has been shown to be effective for the prevention of bone loss in early postmenopausal women, the skeletal effects of the hormone specifically during the early stages of estrogen deficiency have not been characterized histomorphometrically to date. The current study involves use of the ovariectomized (OVX) rat as an animal model for early postmenopausal bone loss to perform such a histomorphometric analysis. One group of OVX rats was injected sc with salmon CT on alternate days for a 6-week period. Additional groups of OVX and sham-operated control rats were treated with vehicle alone. In comparison to control rats, the proximal tibia of vehicle-treated OVX rats were characterized by a 3-fold decrease in cancellous bone volume and significant increases in osteoblast surface (+200%), osteoclast surface (+143%), mineralizing surface (+111%), mineral apposition rate (+36%), bone formation rate (+181%), and longitudinal bone growth (+38%). In contrast, treatment of OVX rats with CT normalized tibial cancellous bone volume and significantly decreased all of the above cellular- and fluorochrome-based indices of bone turnover to near control levels. The results indicate that CT treatment depresses bone turnover and prevents the development of osteopenia in OVX rats. These findings are consistent with the bone protective effect of CT in early postmenopausal women and further support the OVX rat as an animal model for the preclinical evaluation of prophylactic treatments for postmenopausal bone loss.
Essential oils of Phlomis species growing in Greece: chemical composition and antimicrobial activity (2004)

Abstract The essential oils obtained from the aerial parts of Phlomis fruticosa , P. cretica and P. samia , growing in Greece, were analysed by GC and GC–MS. From the 72 identiﬁed constituents, representing 84.3%, 90.4% and 67.4% of the oils, respectively, α ‐pinene, limonene, β ‐caryophyllene, linalool, ( E )‐ β ‐farnesene, germacrene D, ( Z )‐ γ ‐bisabolene and cis ‐ β ‐ocimene were the major components. Furthermore, all the oils exhibited an interesting antimicrobial proﬁle after they were tested against two Gram‐positive and four Gram‐negative bacteria and three pathogenic fungi. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Evaluation of the substrate noise effect on analog circuits in mixed-signal designs (2002)

This paper describes an approach used to simulate the bulk in such a way that we can evaluate the substrate noise effect on analog designs. For these simulations a simple model is used in order to reduce the time needed for the simulations. In this model we take into account the effect of the bonding wire and the bulk resistance. This simulation technique was applied to a sample and hold circuit.