gebhart/patrepeval huggingface dataset:
Accuracy and perceptions of virtual microscopy compared with glass slide microscopy in cervical cytology (2010)

Diagnostic accuracy of virtual microscopy can equal that of glass slide microscopy. However, without good computer network connections, wide focal range and software that permits effortless navigation across virtual slides, cytologists are unlikely to be convinced of the utility of this technology for cytology screening and diagnosis.
Identification of Rodent Homologs of Hepatitis C Virus and Pegiviruses (2013)

The genetic and biological characterization of animal homologs of human viruses provides insights into the origins of human infections and enhances our ability to study their pathogenesis and explore preventive and therapeutic interventions. Horses are the only reported host of nonprimate homologs of hepatitis C virus (HCV). Here, we report the discovery of HCV-like viruses in wild rodents. The majority of HCV-like viruses were found in deer mice (Peromyscus maniculatus), a small rodent used in laboratories to study viruses, including hantaviruses. We also identified pegiviruses in rodents that are distinct from the pegiviruses found in primates, bats, and horses. These novel viruses may enable the development of small-animal models for HCV, the most common infectious cause of liver failure and hepatocellular carcinoma after hepatitis B virus, and help to explore the health relevance of the highly prevalent human pegiviruses.
CCR7 Expression and Memory T Cell Diversity in Humans (2001)

CCR7, along with L-selectin and LFA-1, mediates homing of T cells to secondary lymphoid organs via high endothelial venules (HEV). CCR7 has also been implicated in microenvironmental positioning of lymphocytes within secondary lymphoid organs and in return of lymphocytes and dendritic cells to the lymph after passage through nonlymphoid tissues. We have generated mAbs to human CCR7, whose specificities correlate with functional migration of lymphocyte subsets to known CCR7 ligands. We find that CCR7 is expressed on the vast majority of peripheral blood T cells, including most cells that express adhesion molecules (cutaneous lymphocyte Ag alpha(4)beta(7) integrin) required for homing to nonlymphoid tissues. A subset of CD27(neg) memory CD4 T cells from human peripheral blood is greatly enriched in the CCR7(neg) population, as well as L-selectin(neg) cells, suggesting that these cells are incapable of homing to secondary lymphoid organs. Accordingly, CD27(neg) T cells are rare within tonsil, a representative secondary lymphoid organ. All resting T cells within secondary lymphoid organs express high levels of CCR7, but many activated cells lack CCR7. CCR7 loss in activated CD4 cells accompanies CXC chemokine receptor (CXCR)5 gain, suggesting that the reciprocal expression of these two receptors may contribute to differential positioning of resting vs activated cells within the organ. Lymphocytes isolated from nonlymphoid tissues (such as skin, lung, or intestine) contain many CD27(neg) cells lacking CCR7. The ratio of CD27(neg)/CCR7(neg) cells to CD27(pos)/CCR7(pos) cells varies from tissue to tissue, and may correlate with the number of cells actively engaged in Ag recognition within a given tissue.
Lumican Regulates Corneal Inflammatory Responses by Modulating Fas-Fas Ligand Signaling (2004)

The data suggest that lumican binds FasL and facilitates induction of Fas. Poor signaling through Fas-FasL in lumican deficiency leads to impaired induction of inflammatory cytokines and corneal healing.
Ultrasonic Cholangiography (1976)

Gray-scale B-scanning permits evaluation of major portions of the bile ducts, especially those with significant dilatation. Injection of contrast material containing microscopic air bubbles through a T-tube with simultaneous ultrasonography detected multiple echoes filling in the previously echo-free area which represented the common bile duct, outlining both the duct and portions of the major tributaries. Reflections could be obtained from stones within the duct. Follow-up examinations after surgery could be used to demonstrate shrinkage of the duct. Jaundice due to extra- or intrahepatic obstruction was successfully differentiated noninvasively.
Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease (2014)

Next-generation sequencing of the hypervariable V3 region of the 16s rRNA gene isolated from serial stool specimens collected from 31 patients receiving allogeneic stem cell transplantation (SCT) was performed to elucidate variations in the composition of the intestinal microbiome in the course of allogeneic SCT. Metagenomic analysis was complemented by strain-specific enterococcal PCR and indirect assessment of bacterial load by liquid chromatography-tandem mass spectrometry of urinary indoxyl sulfate. At the time of admission, patients showed a predominance of commensal bacteria. After transplantation, a relative shift toward enterococci was observed, which was more pronounced under antibiotic prophylaxis and treatment of neutropenic infections. The shift was particularly prominent in patients that developed subsequently or suffered from active gastrointestinal (GI) graft-versus-host disease (GVHD). The mean proportion of enterococci in post-transplant stool specimens was 21% in patients who did not develop GI GVHD as compared with 46% in those that subsequently developed GI GVHD and 74% at the time of active GVHD. Enterococcal PCR confirmed predominance of Enterococcus faecium or both E. faecium and Enterococcus faecalis in these specimens. As a consequence of the loss of bacterial diversity, mean urinary indoxyl sulfate levels dropped from 42.5 ± 11 μmol/L to 11.8 ± 2.8 μmol/L in all post-transplant samples and to 3.5 ± 3 μmol/L in samples from patients with active GVHD. Our study reveals major microbiome shifts in the course of allogeneic SCT that occur in the period of antibiotic treatment but are more prominent in association with GI GVHD. Our data indicate early microbiome shifts and a loss of diversity of the intestinal microbiome that may affect intestinal inflammation in the setting of allogeneic SCT.
[Screening and identification for cDNA of differentially expressed genes in human primary hepatocellular carcinoma]. (2003)

The subtracted cDNA library constructed by SSH technique contains differentially expressed genes of HCC. Three novel cDNA sequences might be differentially expressed genes of HCC. Further screening the library and gaining the whole gene sequence may lay a foundation for identifying differentially expressed genes in HCC.
The T-Cell Response to HIV (2012)

HIV is a disease in which the original clinical observations of severe opportunistic infections gave the first clues regarding the underlying pathology, namely that HIV is essentially an infection of the immune system. HIV infects and deletes CD4(+) T cells that normally coordinate the adaptive T- and B-cell response to defend against intracellular pathogens. The immune defect is immediate and profound: At the time of acute infection with an AIDS virus, typically more than half of the gut-associated CD4(+) T cells are depleted, leaving a damaged immune system to contend with a life-long infection.
Purine N-oxides. LXII. 2,4-Dioxopyrido[2,3-d]pyrimidine N-oxides (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurine N-oxides. LXII. 2,4-Dioxopyrido[2,3-d]pyrimidine N-oxidesTzoong-Chyh Lee and Gad SalemnickCite this: J. Org. Chem. 1975, 40, 24, 3608–3610Publication Date (Print):November 1, 1975Publication History Published online1 May 2002Published inissue 1 November 1975https://doi.org/10.1021/jo00912a035RIGHTS & PERMISSIONSArticle Views146Altmetric-Citations14LEARN 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 InReddit PDF (478 KB) Get e-Alerts Get e-Alerts
Establishment and characterization of a human leukemic cell line with megakaryocytic features: dependency on granulocyte-macrophage colony-stimulating factor, interleukin 3, or erythropoietin for growth and survival. (1991)

A new human leukemia cell line with megakaryocytic features, designated UT-7, was established from the bone marrow of a patient with acute megakaryoblastic leukemia. Surface marker analysis revealed that the majority of the cells reacted with monoclonal antibodies against platelet glycoprotein Ib (CD42b), glycoprotein IIb/IIIa (CD41a), MY 7 (CD13), MY 9 (CD33), and glycophorin A antigens. Cytogenetic analysis showed a human male near-tetraploid karyotype with a modal chromosome number of 92-96. Flow cytometry-derived DNA histograms demonstrated that the majority of the cells spontaneously contained 4 N DNA ploidy levels. Ultrastructural study showed that platelet peroxidase activity was weakly positive but myeloperoxidase activity was negative. Ferritin and theta-granule, which have been used as ultrastructural markers for the erythroid lineage, could not be detected. In response to phorbol myristate acetate, platelet factor 4 and beta-thromboglobulin, which were specifically synthesized in the process of megakaryocyte maturation, dramatically increased in UT-7 cells. This was accompanied by an increase in cell size, ploidy level, platelet peroxidase activity, and the surface density of glycoprotein IIb/IIIa antigen. These findings suggest that UT-7 is a new leukemic cell line with megakaryocytic features and with the potential to differentiate into cells with more mature megakaryocytic properties in response to phorbol myristate acetate. This cell line showed strict dependency on interleukin 3 (IL-3), granulocyte-macrophage colony-stimulating factor, or erythropoietin. The maximal effective doses of IL-3, granulocyte-macrophage colony-stimulating factor, and erythropoietin for proliferation in liquid culture were 10 units/ml, 1 ng/ml, and 1 unit/ml, respectively. These concentrations were comparable to the doses that maximally stimulate the clonal growth of normal hemopoietic cells. IL-6 could stimulate the proliferation of UT-7 cells but not maintain the line in long-term culture. UT-7 cells may be a useful model for (a) the analysis of gene regulation of megakaryocytic maturation-associated proteins expressed in the process of megakaryocytic differentiation and (b) the study of signal transduction of hemopoietic factors associated with megakaryocytopoiesis.
The Long-term Clinical Results of a Platelet Glycoprotein IIb/IIIa Receptor Blocker Abciximab: ReoProR Coated Stent in Patients with Coronary Artery Disease (2004)

A ReoPro-coated stent is safe, and may be effective in the prevention of coronary restenosis.
Multiplex allele-specific target amplification based on PCR suppression (2001)

We have developed a strategy for multiplex PCR based on PCR suppression. PCR suppression allows DNA target amplification with only one sequence-specific primer per target and a second primer that is common for all targets. Therefore, an n-plex PCR would require only n + 1 primers. We have demonstrated uniform, efficient amplification of targeted sequences in 14-plex PCR. The high specificity of suppression PCR also provides multiplexed amplification with allele specificity. Multiplexed PCR was used to develop assays for genotyping DNA samples from cystic fibrosis-affected individuals. The new approach greatly simplifies primer design, significantly increases the PCR multiplexing level, and decreases the overall primer cost. In addition, this assay is more readily amenable to automation and is therefore suitable for high-throughput genetic diagnostics.
Monomeric Cobalt Oxazoline Palladacycles (COP). Useful Catalysts for Catalytic Asymmetric Rearrangement of Allylic Trichloroacetimidates (2004)

Cobalt oxazoline palladacycles (COP) containing acetylacetonate and hexafluoroacetylacetonate ligands were prepared as catalysts for the asymmetric rearrangement of allylic trichloroacetimidates. These monomeric catalysts are more soluble than the previously described chloride-bridged dimer COP-Cl (1). COP-hfacac (2) provides rearranged allylic trichloroacetamides with high enantiomeric purities (91-98% ee) in solvents of widely varying polarities: cyclohexane, toluene, 1,2-dichloroethane, ethyl acetate, acetone, acetonitrile, and THF. The first single-crystal X-ray structure of a COP catalyst is also reported.
An ortho-Substituted BIPHEP Ligand and Its Applications in Rh-Catalyzed Hydrogenation of Cyclic Enamides (2002)

[reaction: see text] An ortho-substituted BIPHEP ligand, o-Ph-hexaMeO-BIPHEP (1), is designed and synthesized. Compared with chiral biaryl phosphines without ortho substituents such as BINAP and MeO-BIPHEP, o-Ph-hexaMeO-BIPHEP shows higher enantioselectivities in Rh-catalyzed hydrogenation of cyclic enamides.
Nucleosides. XII. Synthesis of 3',4'-unsaturated pyrimidine nucleosides (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleosides. XII. Synthesis of 3',4'-unsaturated pyrimidine nucleosidesJiri Zemlicka, Robert Gasser, and Jerome P. HorwitzCite this: J. Am. Chem. Soc. 1970, 92, 15, 4744–4745Publication Date (Print):July 1, 1970Publication History Published online1 May 2002Published inissue 1 July 1970https://pubs.acs.org/doi/10.1021/ja00718a051https://doi.org/10.1021/ja00718a051research-articleACS PublicationsRequest reuse permissionsArticle Views91Altmetric-Citations12LEARN 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
Preparation of Oxime HI-6 (Dichloride and Dimethanesulphonate) - Antidote against Nerve Agents (2008)

Because of the threat of misuse of nerve agents as terroristic weapons by the terrorists, animmediate need is felt for the preparation of antidotes on large-scale basis.  HI-6 (dichloride anddimethanesulphonate) salt are the most promising acetylcholinesterase reactivators used ascausal antidotes in nerve agents intoxication. In this study, rapid and large-scale preparationof oxime HI-6, the most promising reactivator has been described.
Herding as a Learning System with Edge-of-Chaos Dynamics (2016)

Herding defines a deterministic dynamical system at the edge of chaos.It generates a sequence of model states and parameters by alternating parameter perturbations with state maximizations, where the sequence of states can be interpreted as "samples" from an associated MRF model.Herding differs from maximum likelihood estimation in that the sequence of parameters does not converge to a fixed point and differs from an MCMC posterior sampling approach in that the sequence of states is generated deterministically.Herding may be interpreted as a"perturb and map" method where the parameter perturbations are generated using a deterministic nonlinear dynamical system rather than randomly from a Gumbel distribution.This chapter studies the distinct statistical characteristics of the herding algorithm and shows that the fast convergence rate of the controlled moments may be attributed to edge of chaos dynamics.The herding algorithm can also be generalized to models with latent variables and to a discriminative learning setting.The perceptron cycling theorem ensures that the fast moment matching property is preserved in the more general framework.
Cross‐linking of scleral collagen in the rabbit using riboflavin and UVA (2005)

Our new method of scleral collagen cross-linking proved very effective in increasing the scleral mechanical strength; the new treatment may represent an option for strengthening scleral tissue in progressive myopia. However, serious side-effects were observed in the outer retina. In future studies these side-effects could be avoided by reducing the irradiation dose below the cytotoxic level of the retina. Before its clinical application, the new method should be tested in a myopia animal model.
Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics (2005)

Measurements of mass spectral peak intensities and spectral counts are promising methods for quantifying protein abundance changes in shotgun proteomic analyses. We describe Serac, software developed to evaluate the ability of each method to quantify relative changes in protein abundance. Dynamic range and linearity using a three-dimensional ion trap were tested using standard proteins spiked into a complex sample. Linearity and good agreement between observed versus expected protein ratios were obtained after normalization and background subtraction of peak area intensity measurements and correction of spectral counts to eliminate discontinuity in ratio estimates. Peak intensity values useful for protein quantitation ranged from 10(7) to 10(11) counts with no obvious saturation effect, and proteins in replicate samples showed variations of less than 2-fold within the 95% range (+/-2sigma) when >or=3 peptides/protein were shared between samples. Protein ratios were determined with high confidence from spectral counts when maximum spectral counts were >or=4 spectra/protein, and replicates showed equivalent measurements well within 95% confidence limits. In further tests, complex samples were separated by gel exclusion chromatography, quantifying changes in protein abundance between different fractions. Linear behavior of peak area intensity measurements was obtained for peptides from proteins in different fractions. Protein ratios determined by spectral counting agreed well with those determined from peak area intensity measurements, and both agreed with independent measurements based on gel staining intensities. Overall spectral counting proved to be a more sensitive method for detecting proteins that undergo changes in abundance, whereas peak area intensity measurements yielded more accurate estimates of protein ratios. Finally these methods were used to analyze differential changes in protein expression in human erythroleukemia K562 cells stimulated under conditions that promote cell differentiation by mitogen-activated protein kinase pathway activation. Protein changes identified with p<0.1 showed good correlations with parallel measurements of changes in mRNA expression.
Shape effects in plasmon resonance of individual colloidal silver nanoparticles (2002)

We present a systematic study of the effect of size and shape on the spectral response of individual silver nanoparticles. An experimental method has been developed that begins with the detection and characterization of isolated nanoparticles in the optical far field. The plasmon resonance optical spectrum of many individual nanoparticles are then correlated to their size and shape using high-resolution transmission electron microscopy. We find that specific geometrical shapes give distinct spectral responses. In addition, inducing subtle changes in the particles’ morphology by heating causes a shift in the individual particle spectrum and provides a simple means of tuning the spectral response to a desired optical wavelength. Improved colloidal preparation methods could potentially lead to homogeneous populations of identical particle shapes and colors. These multicolor colloids could be used as biological labels, surface enhanced Raman scattering substrates, or near field optical microscopy sources covering the full range of wavelengths in the visible spectrum.
Tetrabenazine for the treatment of chorea and other hyperkinetic movement disorders (2011)

Tetrabenazine (TBZ; Xenazine) is a potent, selective, reversible depletor of monoamines from nerve terminals. TBZ inhibits the vesicular monoamine transporter type 2 which, in humans, is expressed nearly exclusively in the brain. TBZ is rapidly metabolized in the liver by carbonyl reductase to stereoisomers of hydrotetrabenazine, some of which are potent inhibitors of vesicular monoamine transporter type 2. Initially developed in the 1950s for schizophrenia, since the 1970s several publications have reported on the efficacy of TBZ in the treatment of various hyperkinetic movement disorders. Although quite effective in controlling the involuntary movements, there were considerable inter-individual differences in the optimal dose, defined as the dose judged by the investigator to provide the greatest efficacy with minimal or tolerable adverse events. This variability is in part owing to differences in severity and mechanism of the target symptoms and to variable activity of the enzyme carbonyl reductase that metabolizes TBZ to its active metabolites. Dose-limiting adverse events, consisting mainly of sedation, parkinsonism, akathisia and depression, are usually rapidly reversible upon dosage reduction. In addition to its established antichorea efficacy in Huntington's disease, the drug has been reported to also be effective in a variety of other hyperkinetic movement disorders, including tardive dyskinesia and tics associated with Tourette's syndrome.
Local expression of B7-H1 promotes organ-specific autoimmunity and transplant rejection (2004)

Nonstandard abbreviations used: cyclosporine A (CSA); membrane ovalbumin (mOVA); phycoerythrin (PE); rat insulin promoter (RIP); streptozocin (STZ); T cell receptor (TCR).
IgBLAST: an immunoglobulin variable domain sequence analysis tool (2013)

The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes, including the variable (V) gene, the diversity (D) gene and the joining (J) gene. Analysis of IG sequences typically requires identification of each gene, as well as a comparison of sequence variations in the context of defined regions. General purpose tools, such as the BLAST program, have only limited use for such tasks, as the rearranged nature of an IG sequence and the variable length of each gene requires multiple rounds of BLAST searches for a single IG sequence. Additionally, manual assembly of different genes is difficult and error-prone. To address these issues and to facilitate other common tasks in analysing IG sequences, we have developed the sequence analysis tool IgBLAST (http://www.ncbi.nlm.nih.gov/igblast/). With this tool, users can view the matches to the germline V, D and J genes, details at rearrangement junctions, the delineation of IG V domain framework regions and complementarity determining regions. IgBLAST has the capability to analyse nucleotide and protein sequences and can process sequences in batches. Furthermore, IgBLAST allows searches against the germline gene databases and other sequence databases simultaneously to minimize the chance of missing possibly the best matching germline V gene.