gebhart/patrepeval huggingface dataset:
Co-evolution of social and affiliation networks (2009)

In our work, we address the problem of modeling social network generation which explains both link and group formation. Recent studies on social network evolution propose generative models which capture the statistical properties of real-world networks related only to node-to-node link formation. We propose a novel model which captures the co-evolution of social and affiliation networks. We provide surprising insights into group formation based on observations in several real-world networks, showing that users often join groups for reasons other than their friends. Our experiments show that the model is able to capture both the newly observed and previously studied network properties. This work is the first to propose a generative model which captures the statistical properties of these complex networks. The proposed model facilitates controlled experiments which study the effect of actors' behavior on the evolution of affiliation networks, and it allows the generation of realistic synthetic datasets.
Plasma Membrane Proteomics of Human Embryonic Stem Cells and Human Embryonal Carcinoma Cells (2008)

Human embryonic stem cells (hESCs) are of immense interest in regenerative medicine as they can self-renew indefinitely and can give rise to any adult cell type. Human embryonal carcinoma cells (hECCs) are the malignant counterparts of hESCs found in testis tumors. hESCs that have acquired chromosomal abnormalities in culture are essentially indistinguishable from hECC. Direct comparison of karyotypically normal hESCs with hECCs could lead to understanding differences between their mechanisms of growth control and contribute to implementing safe therapeutic use of stem cells without the development of germ cell cancer. While several comparisons of hECCs and hESCs have been reported, their cell surface proteomes are largely unknown, partly because plasma membrane proteomics is still a major challenge. Here, we present a strategy for the identification of plasma membrane proteins that has been optimized for application to the relatively small numbers of stem cells normally available, and that does not require tedious cell fractionation. The method led to the identification of 237 and 219 specific plasma membrane proteins in the hESC line HUES-7 and the hECC line NT2/D1, respectively. In addition to known stemness-associated cell surface markers like ALP, CD9, and CTNNB, a large number of receptors, transporters, signal transducers, and cell-cell adhesion proteins were identified. Our study revealed that several Hedgehog and Wnt pathway members are differentially expressed in hESCs and hECCs including NPC1, FZD2, FZD6, FZD7, LRP6, and SEMA4D, which play a pivotal role in stem cell self-renewal and cancer growth. Various proteins encoded on chromosome 12p, duplicated in testicular cancer, were uniquely identified in hECCs. These included GAPDH, LDHB, YARS2, CLSTN3, CSDA, LRP6, NDUFA9, and NOL1, which are known to be upregulated in testicular cancer. Distinct HLA molecules were revealed on the surface of hESCs and hECCs, despite their low abundance. Results were compared with genomic and proteomic data sets reported previously for mouse ESCs, hECCs, and germ cell tumors. Our data provides a surface signature for HUES-7 and NT2/D1 cells and distinguishes normal hESCs from hECCs, helping explain their 'benign' versus 'malignant' nature.
Treatment of Metastatic Renal Cell Carcinoma With a Combination of Bevacizumab and Erlotinib (2005)

The combination of bevacizumab and erlotinib is an effective and well-tolerated treatment for patients with advanced renal cell carcinoma. The efficacy of these two drugs in combination suggests that targeting of separate pathways critical to tumor growth and dissemination may achieve results superior to either drug as a single agent. Additional development of this and other combinations of targeted agents is warranted.
A role for the acetylcholine receptor-inducing protein ARIA in oligodendrocyte development. (1994)

ARIA acetylcholine receptor-inducing activity protein, is a member of a family of ligands that includes the Neu differentiation factor, heregulin, and glial growth factor. These ligands all act through one or more receptor tyrosine kinases of approximately 185 kDa. In some conditions these ligands promote proliferation, whereas in others they induce differentiation. ARIA was originally isolated from chick brain on the basis of its ability to induce synthesis of nicotinic acetylcholine receptors in skeletal muscle. In this paper we show that ARIA is expressed in the subventricular zone of the rat brain and that it enhances the development of oligodendrocytes from bipotential (O2A) glial progenitor cells. We have also found that ARIA induces tyrosine phosphorylation of a 185-kDa protein in O2A progenitor cells. ARIA does not increase bromodeoxyuridine incorporation by oligodendrocytes but is mitogenic when added to Schwann cells in vitro. Thus, ARIA accelerates the formation of oligodendrocytes in vitro and is expressed where it could exercise the same influence in vivo.
<I>In Vivo</I> Delivery of Atoh1 Gene to Rat Cochlea Using a Dendrimer-Based Nanocarrier (2013)

Gene therapy is a promising clinical solution to hearing loss. However suitable gene carriers for the auditory system are currently unavailable. Given the unique structure of the inner ear, the route of delivery and gene transfer efficiency are still not optimal at present. This study presented a non-viral delivery system of in vivo delivery of Atoh1 gene (a potentially therapeutic gene for hearing loss) to rat cochlea. We treated polyamidoamine (PAMAM) dendrimers by activating and modifying with Na-carboxymethyl-beta-cyclodextrins (CM-beta-CD) in sequence. A novel gene carrier (CM-beta-CD modified activated PAMAM dendrimers, CMAP) was then constructed. CMAP nanoparticles could bind pRK5-Atoh1-EGFP plasmids to form vector-DNA complexes (dendriplexes) with a mean particle size of 132 +/- 20 nm and zeta potential of 31 +/- 3 mV. These dendriplexes were locally applied on the round window membrane and delivered to the inner ear by passive gradient permeation. Results showed that the Atoh1 gene was successfully transferred into the cells as indicated by the green fluorescence detected in the inner ear. A relatively selective gene transfer with high efficiency was achieved in the auditory hair cells but not much in other cell types in the cochlea. Auditory brainstem response was determined seven days after inoculation, indicating good tolerance. This approach may provide a novel tool for inner ear gene therapy and initiate the applications of biomaterials to treat auditory disorders.
Comparative Immunohistochemical Analysis of IMP3, GLUT1, EMA, CD146, and Desmin for Distinguishing Malignant Mesothelioma From Reactive Mesothelial Cells (2013)

The combination of IMP3 and GLUT1 is most appropriate for distinguishing MM from RMC using FFPE sections.
Prognostic and diagnostic implications of estrogen and progesterone receptor assays in cytology (1994)

Scientific evidence suggests that cancer is a consequence of genetic changes that result in uncontrolled cellular growth, tissue invasion, and metastasis. This concept has led to a great deal of excitement in the medical community in the hope that precise identification of genes involved in human cancer could potentially facilitate our understanding of human malignancies. It may also be possible to apply this information directly to different clinical settings. Many technologies are now available which offer opportunities for pathologists to not only expand their diagnostic abilities, but also to assess the prognosis of a given tumor in a specific patient. These include immunocytochemistry, flow cytometry, cell image analysis, and molecular genetic studies. In this review, the role of immunocytochemical hormone receptor assay as an aid in tumor prognosis and in prediction of tumor response to endocrine therapy will be discussed. Emphasis will be placed on the use of hormone receptor assay as an adjunct in diagnostic pathology and in assessment of metastatic tumors of unknown origin. The potential value of assessment of hormone receptors in different cytologic preparations will also be discussed.
mdm2 Is Critical for Inhibition of p53 during Lymphopoiesis and the Response to Ionizing Irradiation (2002)

The function of the p53 tumor suppressor protein must be highly regulated because p53 can cause cell death and prevent tumorigenesis. In cultured cells, the p90MDM2 protein blocks the transcriptional activation domain of p53 and also stimulates the degradation of p53. Here we provide the first conclusive demonstration that p90MDM2 constitutively regulates p53 activity in homeostatic tissues. Mice with a hypomorphic allele of mdm2 revealed a heretofore unknown role for mdm2 in lymphopoiesis and epithelial cell survival. Phenotypic analyses revealed that both the transcriptional activation and apoptotic functions of p53 were increased in these mice. However, the level of p53 protein was not coordinately increased, suggesting that p90MDM2 can inhibit the transcriptional activation and apoptotic functions of p53 in a manner independent of degradation. Cre-mediated deletion of mdm2 caused a greater accumulation of p53, demonstrating that p90MDM2 constitutively regulates both the activity and the level of p53 in homeostatic tissues. The observation that only a subset of tissues with activated p53 underwent apoptosis indicates that factors other than p90(MDM2) determine the physiological consequences of p53 activation. Furthermore, reduction of mdm2 in vivo resulted in radiosensitivity, highlighting the importance of mdm2 as a potential target for adjuvant cancer therapies.
Basis for hormonal management of advanced prostate cancer (1993)

Thus, the control of the relatively small amounts of DHT remaining after castration became a major focus for therapy in metastatic prostate cancer.
Human hepatic lipase. Cloned cDNA sequence, restriction fragment length polymorphisms, chromosomal localization, and evolutionary relationships with lipoprotein lipase and pancreatic lipase. (1988)

Human hepatic lipase is an important enzyme in high density lipoprotein (HDL) metabolism, being implicated in the conversion of HDL2 to HDL3. Three human hepatic lipase cDNA clones were identified in two lambda gt11 libraries from human liver. The cDNA-derived amino acid sequence predicts a protein of 476 amino acid residues, preceded by a 23-residue signal peptide. Four potential N-glycosylation sites are identified, two of which are conserved in rat hepatic lipase. On alignment with human, mouse, and bovine lipoprotein lipase, the same two sites were also conserved in lipoprotein lipase in all three species. Stringent conservation of the cysteine residues was also evident. Comparative analysis of amino acid sequences shows that hepatic lipase evolves at a rapid rate, 2.07 x 10(-9) substitutions/site/year, about four times that in lipoprotein lipase and half that in pancreatic lipase. Further, hepatic lipase and pancreatic lipase appear to be evolutionarily closer to each other than either of them is to lipoprotein lipase. Southern blot analysis revealed high frequency restriction fragment length polymorphisms of the hepatic lipase gene for the enzymes HindIII and MspI. these polymorphisms will be useful for haplotype and linkage analysis of the hepatic lipase gene. Using cloned human hepatic lipase cDNA as a hybridization probe, we performed Southern blot analysis of a panel of 13 human-rodent somatic cell hybrids. Concordance analysis of the various hybrid clones indicates that the hepatic lipase gene is located on the long arm of human chromosome 15. Analysis of hybrids containing different translocations of chromosome 15 localized the gene to the region 15q15----q22.
Systematic evaluation of the miRNA‐ome and its downstream effects on mRNA expression identifies gastric cancer progression (2010)

We investigated the differential expression of Dicer and Drosha, as well as that of microRNA (miRNA), in adjacent normal and tumour samples of patients with gastric cancer. The expression of Dicer and Drosha was studied by immunohistochemistry in 332 gastric cancers and correlated with clinico-pathological patient characteristics. Differential expression of miRNAs was studied using the Invitrogen NCode(™) Multi-Species miRNA Microarray Probe Set containing 857 mammalian probes in a test set of six primary gastric cancers (three with and three without lymph node metastases). Differential expression was validated by RT-PCR on an independent validation set of 20 patients with gastric cancer. Dicer and Drosha were differentially expressed in non-neoplastic and neoplastic gastric tissue. The expression of Drosha correlated with local tumour growth and was a significant independent prognosticator of patient survival. Twenty miRNAs were up- and two down-regulated in gastric carcinoma compared with non-neoplastic tissue. Six of these miRNAs separated node-positive from node-negative gastric cancers, ie miR-103, miR-21, miR-145, miR-106b, miR-146a, and miR-148a. Five miRNAs expressed differentially in node-positive cancers had conserved binding sites for mRNAs differentially expressed in the same set of tumour samples. Gastric cancer shows a complex derangement of the miRNA-ome, including Dicer and Drosha. These changes correlate independently with patient prognosis and probably influence local tumour growth and nodal spread.
PROMISCUITY AND THE RATE OF MOLECULAR EVOLUTION AT PRIMATE IMMUNITY GENES (2010)

Recently, a positive correlation between basal leukocyte counts and mating system across primates suggested that sexual promiscuity could be an important determinant of the evolution of the immune system. Motivated by this idea, we examined the patterns of molecular evolution of 15 immune defense genes in primates in relation to promiscuity and other variables expected to affect disease risk. We obtained maximum likelihood estimates of the rate of protein evolution for terminal branches of the primate phylogeny at these genes. Using phylogenetically independent contrasts, we found that immunity genes evolve faster in more promiscuous species, but only for a subset of genes that interact closely with pathogens. We also observed a significantly greater proportion of branches under positive selection in the more promiscuous species. Analyses of independent contrasts also showed a positive effect of group size. However, this effect was not restricted to genes that interact closely with pathogens, and no differences were observed in the proportion of branches under positive selection in species with small and large groups. Together, these results suggest that mating system has influenced the evolution of some immunity genes in primates, possibly due to increased risk of acquiring sexually transmitted diseases in species with higher levels of promiscuity.
Progressive External Ophthalmoplegia and Vision and Hearing Loss in a Patient With Mutations in POLG2 and OPA1 (2008)

Although we initially focused on the mutation in POLG2, the mutation in OPA1 is more likely to explain the late-onset PEO and multisystem disorder in this patient.
Complement Factor H Variant Y402H Is a Major Risk Determinant for Geographic Atrophy and Choroidal Neovascularization in Smokers and Nonsmokers (2006)

The CFH Y402H variant is strongly associated with both GA and CNV in the U.K. population. This association is similar in smokers and nonsmokers. Heavier smokers with the CC genotype may be at particular risk.
Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection in 26 Patients (2011)

FMT through colonoscopy was simple, safe, and 92% effective in preventing further diarrhea or CDI relapse in this group of 26 patients with recurrent CDI.
Computational Drug Repositioning: From Data to Therapeutics (2013)

Traditionally, most drugs have been discovered using phenotypic or target-based screens. Subsequently, their indications are often expanded on the basis of clinical observations, providing additional benefit to patients. This review highlights computational techniques for systematic analysis of transcriptomics (Connectivity Map, CMap), side effects, and genetics (genome-wide association study, GWAS) data to generate new hypotheses for additional indications. We also discuss data domains such as electronic health records (EHRs) and phenotypic screening that we consider promising for novel computational repositioning methods.
A Soft Lithographic Approach To Fabricate Patterned Microfluidic Channels (2004)

The control of surface properties and spatial presentation of functional molecules within a microfluidic channel is important for the development of diagnostic assays and microreactors and for performing fundamental studies of cell biology and fluid mechanics. Here, we present a simple technique, applicable to many soft lithographic methods, to fabricate robust microchannels with precise control over the spatial properties of the substrate. In this approach, the patterned regions were protected from oxygen plasma by controlling the dimensions of the poly(dimethylsiloxane) (PDMS) stamp and by leaving the stamp in place during the plasma treatment process. The PDMS stamp was then removed, and the microfluidic mold was irreversibly bonded to the substrate. The approach was used to pattern a nonbiofouling poly(ethylene glycol)-based copolymer or the polysaccharide hyaluronic acid within microfluidic channels. These nonbiofouling patterns were then used to fabricate arrays of fibronectin and bovine serum albumin as well as mammalian cells. In addition, further control over the deposition of multiple proteins onto multiple or individual patterns was achieved using laminar flow. Also, cells that were patterned within channels remained viable and capable of performing intracellular reactions and could be potentially lysed for analysis.
Image Stabilization Based on Fusing the Visual Information in Differently Exposed Images (2007)

The objective of image stabilization is to prevent or remove the motion blur degradation from images. We introduce a new approach to image stabilization based on combining information available in two differently exposed images of the same scene. In addition to the image normally captured by the system, with an exposure time determined by the illumination conditions, a very shortly exposed image is also acquired. The difference between the exposure times of the two images determines differences in their degradations which are exploited in order to recover the original image of the scene. We formulate the problem as a maximum a posteriori (MAP) estimation based on the degradation models of the two observed images, as well as by imposing an edge-preserving image prior. The proposed method is demonstrated through a series of simulation experiments, and visual examples on natural images.
Oncoprotein EWS-FLI1 Activity Is Enhanced by RNA Helicase A (2006)

RNA helicase A (RHA), a member of the DEXH box helicase family of proteins, is an integral component of protein complexes that regulate transcription and splicing. The EWS-FLI1 oncoprotein is expressed as a result of the chromosomal translocation t(11;22) that occurs in patients with the Ewing's sarcoma family of tumors (ESFT). Using phage display library screening, we identified an EWS-FLI1 binding peptide containing homology to RHA. ESFT cell lines and patient tumors highly expressed RHA. GST pull-down and ELISA assays showed that EWS-FLI1 specifically bound RHA fragment amino acids 630 to 1020, which contains the peptide region discovered by phage display. Endogenous RHA was identified in a protein complex with EWS-FLI1 in ESFT cell lines. Chromatin immunoprecipitation experiments showed both EWS-FLI1 and RHA bound to EWS-FLI1 target gene promoters. RHA stimulated the transcriptional activity of EWS-FLI1 regulated promoters, including Id2, in ESFT cells. In addition, RHA expression in mouse embryonic fibroblast cells stably transfected with EWS-FLI1 enhanced the anchorage-independent phenotype above that with EWS-FLI1 alone. These results suggest that RHA interacts with EWS-FLI1 as a transcriptional cofactor to enhance its function.
Online Creation of Panoramic Augmented Reality Annotations on Mobile Phones (2010)

A novel application lets users create panoramic images in real time on a mobile phone and annotate the physical environment using an augmented-reality interface. Annotations can be accurately mapped to the correct objects, despite varying user positions.
Free radical metabolites of L-cysteine oxidation. (1984)

The oxidation of L-cysteine by horseradish peroxidase in the presence of oxygen forms a thiyl free radical as demonstrated with the spin-trapping ESR technique. Reactions of this thiyl free radical result in oxygen consumption, which is inhibited by the spin trap 5,5'-dimethyl-1-pyrroline-N-oxide. Cysteine sulfinic acid, a cysteine metabolite, is a poorer substrate for horseradish peroxidase than cysteine and is oxidized to form both sulfur-centered and carbon-centered free radicals.
Protein tyrosine phosphorylations as an indicator of 2,3,7,8-tetrachloro-p-dioxin exposure in vivo and in vitro (1992)

A dose-dependent increase in tyrosine phosphorylation of five hepatic intracellular proteins with approximate molecular weights of 17, 21, 27, 29, and 34 kDa was seen 24 h after administration of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) to C57BL/6J female mice. The ED50 values for tyrosylphosphorylation of these five proteins, respectively, were 0.26, 0.21, 0.26, 0.31, and 0.38 micrograms TCDD/Kg. TCDD induction of 7-ethoxyresorufin O-deethylase activity (EROD) was characterized by an ED50 of 2.5 micrograms/Kg. An eighteen h exposure of a human lymphoblastoma cell line (X3) to TCDD increased tyrosylphosphorylation status of ten proteins with approximate molecular weights of 16, 17, 24, 26, 27, 32, 33, 34, 35, and 36 kDa in a dose-dependent manner. The EC50 values for these TCDD-dependent tyrosylphosphorylation ranged from 0.01 to 0.07 nM TCDD. EROD induction by TCDD in X3 cells exhibited an EC50 of 0.14 nM. These data indicate that TCDD alters intracellular protein tyrosine phosphorylation and these changes are more sensitive biological indicators of TCDD exposure than induction of EROD.
Reactivity Modes of an Iron Bis(alkoxide) Complex with Aryl Azides: Catalytic Nitrene Coupling vs Formation of Iron(III) Imido Dimers (2015)

The iron bis(alkoxide) complex Fe(OR)2(THF)2 (R = CtBu2Ph), 1, was found to have strikingly different reactivity with various aryl azides, ArN3. Azides with methyl or ethyl groups in the ortho positions of the phenyl ring react catalytically via nitrene coupling to give azoarenes, ArNNAr. Catalyst loading as low as 1 mol % yields clean, quantitative conversion of aryl azides to azoarenes at room temperature in as little as 4 h. A combination of two different aryl azides leads to the catalytic formation of all three possible azoarenes, including the asymmetric one. In contrast, reactions with aryl azides lacking ortho substituents yield stable dimeric iron imido complexes of the form (RO)(THF)Fe(μ-NAr)2Fe(THF)(OR) (Ar = 4-(trifluoromethyl)phenyl, 5; Ar = phenyl, 6; Ar = 3,5-dimethylphenyl, 7), which do not undergo catalytic nitrene coupling. The isocyanide adduct Fe(OR)2(CNR)2 (4, R = 2,6-dimethylphenyl) was obtained from the reaction of Fe(OR)2(THF)2 with two equivalents of isocyanide. No C–N bond formation was observed in the reaction of compound 4 with azides or in the reaction of compounds 5–7 with isocyanides.