gebhart/patrepeval huggingface dataset:
Limitations of Serum Creatinine Level and Creatinine Clearance as Filtration Markers in Cirrhosis (1994)

Our results indicate that renal failure is greatly underestimated on the basis of serum creatinine level and Ccr in cirrhotic patients. Clinical implications of this observation include excessive dosage of potentially nephrotoxic drugs and failure to recognize renal impairment induced by such medical treatments as diuretic therapy or paracentesis.
JPEG-HDR: A Backwards-Compatible, High Dynamic Range Extension to JPEG (2005)

The transition from traditional 24-bit RGB to high dynamic range (HDR) images is hindered by excessively large file formats with no backwards compatibility. In this paper, we demonstrate a simple approach to HDR encoding that parallels the evolution of color television from its grayscale beginnings. A tone-mapped version of each HDR original is accompanied by restorative information carried in a subband of a standard output-referred image. This subband contains a compressed ratio image, which when multiplied by the tone-mapped foreground, recovers the HDR original. The tone-mapped image data is also compressed, and the composite is delivered in a standard JPEG wrapper. To na&#xEF;ve software, the image looks like any other, and displays as a tone-mapped version of the original. To HDR-enabled software, the foreground image is merely a tone-mapping suggestion, as the original pixel data are available by decoding the information in the subband. Our method further extends the color range to encompass the visible gamut, enabling a new generation of display devices that are just beginning to enter the market.
Electron‐immunocytochemical studies of perivascular nerves of mesenteric and renal arteries of golden hamsters during and after arousal from hibernation (1999)

Electron immunocytochemistry was used to examine perivascular nerves of hamster mesenteric and renal arteries during hibernation and 2 h after arousal from hibernation. Vessels from cold-exposed but nonhibernating, and normothermic control hamsters were also examined. During hibernation the percentage of axon profiles in mesenteric and renal arteries that were immunopositive for markers of sympathetic nerves, tyrosine hydroxylase (TH) and neuropeptide Y (NPY), were increased 2-3 fold compared with normothermic and cold control animals. This increase was reduced markedly only 2 h after arousal from hibernation. The small percentage of nitric oxide synthase-1-positive axon profiles found in mesenteric (but not renal) arteries was also increased during hibernation and returned towards control values after arousal. In contrast, the percentage of perivascular axons immunostaining for vasoactive intestinal polypeptide (VIP), a marker for parasympathetic nerves, was reduced in mesenteric arteries during hibernation. There was no labelling of perivascular nerves for substance P in either mesenteric or renal arteries. It is suggested that the increase in percentage of TH- and NPY-immunostained perivascular nerves may account for the increased vasoconstriction associated with high vascular resistance that is known to occur during hibernation. The reduction in the percentage of axons positive for VIP in hibernating animals would contribute to this mechanism since this neuropeptide is a vasodilator.
Condensation of tetraaldehydes with pyrrole. Direct synthesis of capped porphyrins (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCondensation of tetraaldehydes with pyrrole. Direct synthesis of capped porphyrinsJoseph Almog, Jack E. Baldwin, Robert L. Dyer, and Mary PetersCite this: J. Am. Chem. Soc. 1975, 97, 1, 226–227Publication Date (Print):January 1, 1975Publication History Published online1 May 2002Published inissue 1 January 1975https://pubs.acs.org/doi/10.1021/ja00834a059https://doi.org/10.1021/ja00834a059research-articleACS PublicationsRequest reuse permissionsArticle Views542Altmetric-Citations94LEARN 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
Acidic Mammalian Chitinase in Asthmatic Th2 Inflammation and IL-13 Pathway Activation (2004)

Chitin is a surface component of parasites and insects, and chitinases are induced in lower life forms during infections with these agents. Although chitin itself does not exist in humans, chitinases are present in the human genome. We show here that acidic mammalian chitinase (AMCase) is induced via a T helper-2 (Th2)-specific, interleukin-13 (IL-13)-mediated pathway in epithelial cells and macrophages in an aeroallergen asthma model and expressed in exaggerated quantities in human asthma. AMCase neutralization ameliorated Th2 inflammation and airway hyperresponsiveness, in part by inhibiting IL-13 pathway activation and chemokine induction. AMCase may thus be an important mediator of IL-13-induced responses in Th2-dominated disorders such as asthma.
Recent advances in inducible gene expression systems (1998)

A means of controlling the level and timing of expression of specific genes in cultured cells or in animals would have broad applications. There has been recent progress in two very promising systems: problems due to the high background expression from tetracycline-responsive promoters have been solved by constructing tetracycline-sensitive transcriptional repressors; and new rapamycin analogues have been isolated that are capable of activating the FK506-inducible system but lack the cytostatic side effects of the original inducers. Both systems now provide opportunities for expressing toxic genes, growth arrest genes, and therapeutic products in a regulated fashion previously not possible.
Calcimimetics as an Adjuvant Treatment for Familial Hypophosphatemic Rickets (2008)

Traditional therapy of XLH with phosphate and calcitriol elevates FGF23 and has the potential to stimulate PTH. Short-term treatment with cinacalcet suppresses PTH, leading to increase in TP/GFR and serum phosphate. Thus, long-term clinical studies are needed to investigate whether cinacalcet may be a useful adjuvant in the treatment of XLH, allowing the use of lower doses of phosphate and calcitriol.
Affect extraction using aural, visual and linguistic features from multimedia documents (2012)

This work attempts to extract a viewer’s emotion from the three modalities of a movie: audio, visual and text. A major obstacle for emotion research has been the lack of appropriately annotated databases, limiting the potential of supervised algorithms. To that end we develop and present a database of movie affect, annotated in continuous time, on a continuous valence-arousal scale. Supervised learning methods are proposed to model the continuous affective response using hidden Markov Models and low-level audio-visual features and classify each video frame into one of seven discrete categories (in each dimension); the discrete-valued curves are then converted to continuous values via spline interpolation. A variety of audio-visual features are investigated and an optimal feature set is selected. The potential of the method is verified on twelve 30-minute movie clips with good precision at a macroscopic level. This method proves not suitable to process subtitle information, so we explore the creation of a textual affective model, starting with a fully automated algorithm for expanding an affective lexicon with new entries. Continuous valence ratings are estimated for unseen words under the assumption that semantic similarity implies affective similarity. Starting from a set of manually annotated words, a linear model is trained using the least mean squares algorithm. The semantic similarity between the selected features and the unseen words is computed with various similarity metrics, and used to compute the valence of unseen words. The proposed algorithm performs very well on reproducing the valence ratings of the Affective Norms for English Words (ANEW) and General Inquirer datasets. We then use three simple fusion schemes to combine lexical valence scores into sentence-level scores, producing state-of-the-art results on the sentence rating task of the SemEval 2007 corpus.
Engineering aspects and applications of the new Raman instrumentation (2005)

Raman instrumentation design has improved radically in efficiency and ease of use over the past 15 years. New technologies made this possible with introduction of the first commercial high-efficiency (high speed) Raman systems incorporating low power lasers. Systems were introduced for the first time on production and process lines. Higher efficiency systems have continued to evolve, as a result of novel engineering solutions. Raman-near field optical systems and Raman-SEM (scanning electron microscopy) combinations have created a new area of nanoscale spectroscopic measurements. New application areas are: (a) semiconductor processing; (b) pharmaceutical drug processing; (c) gemology; (d) narcotic and explosives forensic detection; (e) coatings on computer hard disks and read heads; (f) endoscopic and Raman detection of oesophageal and other types of cancer. Comparisons are made with competing optical and alternative instrumentation techniques for general Raman work and the applications.
Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry (2001)

A new method combining chemical modification and affinity purification is described for the characterization of serine and threonine phosphopeptides in proteins. The method is based on the conversion of phosphoserine and phosphothreonine residues to S-(2-mercaptoethyl)cysteinyl or beta-methyl-S-(2-mercaptoethyl)cysteinyl residues by beta-elimination/1,2-ethanedithiol addition, followed by reversible biotinylation of the modified proteins. After trypsin digestion, the biotinylated peptides were affinity-isolated and enriched, and subsequently subjected to structural characterization by liquid chromatography/tandem mass spectrometry (LC/MS/MS). Database searching allowed for automated identification of modified residues that were originally phosphorylated. The applicability of the method is demonstrated by the identification of all known phosphorylation sites in a mixture of alpha-casein, beta-casein, and ovalbumin. The technique has potential for adaptations to proteome-wide analysis of protein phosphorylation.
Discovery of a Class of Novel Tankyrase Inhibitors that Bind to Both the Nicotinamide Pocket and the Induced Pocket (2013)

Potent and selective inhibitors of tankyrases have recently been characterized to bind to an induced pocket. Here we report the identification of a novel potent and selective tankyrase inhibitor that binds to both the nicotinamide pocket and the induced pocket. The crystal structure of human TNKS1 in complex with this "dual-binder" provides a molecular basis for their strong and specific interactions and suggests clues for the further development of tankyrase inhibitors.
The interaction of human bone marrow cells with nanotopographical features in three dimensional constructs (2006)

Until now, nanotopography has been considered in 2D construct designs. This has been due to fabrication limitations with traditional lithographic processes relying on the ability to focus radiation that will expose a radiation sensitive resist (e.g. photolithography and electron beam lithography). More recently, alternative methods that offer rapid and cheap nanofabrication have been developed; such methods include polymer demixing and colloidal lithography. Polymer demixing in 2D has relied on spin casting of polymer blends-such as polystyrene and polybromostyrene in a solvent such as toluene. As the solvent evaporates, the polymers phase separate and form nanoislands. In this study, the polymer blend solution has been blown through fine tubes and allowed to demix, thus providing 3D constructs for cell biology. The ability to fabricate in tubes may be useful in many applications, for example stents, conduits, and bone repair (when considering structures such as Haversian tubes and Volkmann's canals). As proof of concept, human osteoprogenitor cells have been used to test the cell response to the nanopatterned tubes. The results show that nanofeatures of size X, diameter Y, and spacing Z decrease cell spreading, reduce cytoskeletal organization, and increase endocytotic activity within the cells.
P-selectin glycoprotein ligand-1 mediates rolling of human neutrophils on P-selectin. (1995)

Neutrophils roll on P-selectin expressed by activated platelets or endothelial cells under the shear stresses in the microcirculation. P-selectin glycoprotein ligand-1 (PSGL-1) is a high affinity ligand for P-selectin on myeloid cells. However, it has not been demonstrated that PSGL-1 contributes to the rolling of neutrophils on P-selectin. We developed two IgG mAbs, PL1 and PL2, that appear to recognize protein-dependent epitopes on human PSGL-1. The mAbs bound to PSGL-1 on all leukocytes as well as on heterologous cells transfected with PSGL-1 cDNA. PL1, but not PL2, blocked binding of 125-I-PSGL-1 to immobilized P-selectin, binding of fluid-phase P-selectin to myeloid and lymphoid leukocytes, adhesion of neutrophils to immobilized P-selectin under static conditions, and rolling of neutrophils on P-selectin-expressing CHO cells under a range of shear stresses. PSGL-1 was localized to microvilli on neutrophils, a topography that may facilitate its adhesive function. These data indicate that (a) PSGL-1 accounts for the high affinity binding sites for P-selectin on leukocytes, and (b) PSGL-1 must interact with P-selectin in order for neutrophils to roll on P-selectin at physiological shear stresses.
For Profit, Pleasure, and Power? Cultural Diversity and the Mixed Motives of Foreign Language Education (1998)

This paper is a revised version of a paper which appeared under the same title in the NACFLA Proceedings Journal, Vol. 7, 1997, 132-152.
X-ray Crystal Structure of Escherichia coli Taurine/α-Ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates, (2002)

Taurine/alpha-ketoglutarate dioxygenase (TauD), a non-heme Fe(II) oxygenase, catalyses the conversion of taurine (2-aminoethanesulfonate) to sulfite and aminoacetaldehyde concurrent with the conversion of alpha-ketoglutarate (alphaKG) to succinate and CO(2). The enzyme allows Escherichia coli to use taurine, widely available in the environment, as an alternative sulfur source. Here we describe the X-ray crystal structure of TauD complexed to Fe(II) and both substrates, alphaKG and taurine. The tertiary structure and fold of TauD are similar to those observed in other enzymes from the broad family of Fe(II)/alphaKG-dependent oxygenases, with closest structural similarity to clavaminate synthase. Using the TauD coordinates, a model was determined for the closely related enzyme 2,4-dichlorophenoxyacetate/alphaKG dioxygenase (TfdA), supporting predictions derived from site-directed mutagenesis and other studies of that biodegradative protein. The TauD structure and TfdA model define the metal ligands and the positions of nearby aromatic residues that undergo post-translational modifications involving self-hydroxylation reactions. The substrate binding residues of TauD were identified and those of TfdA predicted. These results, along with sequence alignment information, reveal how TauD selects a tetrahedral substrate anion in preference to the planar carboxylate selected by TfdA, providing insight into the mechanism of enzyme catalysis.
Conditional deletion of the colony stimulating factor-1 receptor (c-fms proto-oncogene) in mice (2006)

Colony stimulating factor-1 (CSF-1) is the primary regulator of the mononuclear phagocytic lineage acting through its transmembrane tyrosine kinase receptor, CSF-1R, that is the product of the c-fms proto-oncogene. Null mutations in either the ligand or the receptor genes result in a severe osteopetrosis as well as a number of other phenotypes, including reproductive defects and perturbations in organ development. The CSF-1R is also expressed in oocytes, myoblast progenitors, decidual, and trophoblastic cells. To distinguish cell type specific phenotypes, we have created a conditional allele of the Csf1r by placing LoxP sites around Exon 5 of the Csf1r gene in mice. Excision of this floxed sequence results in a null allele that in the homozygous state gives a phenotype indistinguishable of the complete Csf1r null mutant mouse. This conditional allele will prove extremely valuable to study the spatial and temporal roles of CSF-1R.
Detection of Live and Antibiotic-Killed Bacteria by Quantitative Real-Time PCR of Specific Fragments of rRNA (2006)

Assessing bacterial viability by molecular markers might help accelerate the measurement of antibiotic-induced killing. This study investigated whether rRNA could be suitable for this purpose. Cultures of penicillin-susceptible and penicillin-tolerant (Tol1 mutant) Streptococcus gordonii were exposed to mechanistically different penicillin and levofloxacin. Bacterial survival was assessed by viable counts and compared to quantitative real-time PCR amplification of either the 16S rRNA genes or the 16S rRNA, following reverse transcription. Penicillin-susceptible S. gordonii lost > or =4 log(10) CFU/ml of viability over 48 h of penicillin treatment. In comparison, the Tol1 mutant lost < or =1 log(10) CFU/ml. Amplification of a 427-bp fragment of 16S rRNA genes yielded amplicons that increased proportionally to viable counts during bacterial growth but did not decrease during drug-induced killing. In contrast, the same 427-bp fragment amplified from 16S rRNA paralleled both bacterial growth and drug-induced killing. It also differentiated between penicillin-induced killing of the parent and the Tol1 mutant (> or =4 log(10) CFU/ml and < or =1 log(10) CFU/ml, respectively) and detected killing by mechanistically unrelated levofloxacin. Since large fragments of polynucleotides might be degraded faster than smaller fragments, the experiments were repeated by amplifying a 119-bp region internal to the original 427-bp fragment. The amount of 119-bp amplicons increased proportionally to viability during growth but remained stable during drug treatment. Thus, 16S rRNA was a marker of antibiotic-induced killing, but the size of the amplified fragment was critical for differentiation between live and dead bacteria.
Therapeutic Effects of Selective Atrioventricular Node Vagal Stimulation in Atrial Fibrillation and Heart Failure (2012)

AVN-VS achieved consistent rate slowing, which was associated with improved ventricular function in a canine AF and HF model. Thus, AVN-VS may be a novel, effective therapeutic option in the combined condition of AF and HF.
MHC class I–associated peptides derive from selective regions of the human genome (2016)

MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.
Telomere shortening associated with disease evolution patterns in myelodysplastic syndromes. (1994)

We identified the telomere length at different hematological phases in 16 patients with myelodysplastic syndromes (MDS), showing disease evolution with a conventional Southern blot hybridization using the (TTAGGG)4 probe. The MDS patients studied were classified into three groups according to the pattern of telomere length reduction. The first group had telomere shortening at the time of disease diagnosis. In four of the six MDS patients in this group, the disease progressed within 6 months postdiagnosis and each of them survived for less than 1 year. Moreover, in this group four patients showed a 5q anomaly with or without additional changes, and 50% of patients in this group had complex chromosome abnormalities. The patients in the second group showed reductions in telomere length after disease progression; two of these three patients showed gradual disease progression and had one or two chromosome abnormalities. The third group comprised the remaining seven MDS patients; they showed no telomere reduction by disease evolution. Two patients in this group experienced rapid disease progression. These results may indicate that telomere reduction is linked to disease evolution in some MDS patients, perhaps as a result of genomic instability because patients with complex chromosome abnormalities were clustered in the first group. However, because some MDS patients show disease progression without telomere reduction, genetic changes, including point mutations of certain gene(s), may also contribute to disease progression. We further noted that telomere shortening at the time of MDS diagnosis might indicate a poor MDS prognosis.