gebhart/patrepeval huggingface dataset:
Use of a thiol tether for the site-specific attachment of reporter groups to DNA (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUse of a thiol tether for the site-specific attachment of reporter groups to DNAJacqueline A. Fidanza and Larry W. McLaughlinCite this: J. Org. Chem. 1992, 57, 8, 2340–2346Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/jo00034a028https://doi.org/10.1021/jo00034a028research-articleACS PublicationsRequest reuse permissionsArticle Views335Altmetric-Citations41LEARN 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
High-speed Intravascular Photoacoustic Imaging of Lipid-laden Atherosclerotic Plaque Enabled by a 2-kHz Barium Nitrite Raman Laser (2014)

Lipid deposition inside the arterial wall is a key indicator of plaque vulnerability. An intravascular photoacoustic (IVPA) catheter is considered a promising device for quantifying the amount of lipid inside the arterial wall. Thus far, IVPA systems suffered from slow imaging speed (~50 s per frame) due to the lack of a suitable laser source for high-speed excitation of molecular overtone vibrations. Here, we report an improvement in IVPA imaging speed by two orders of magnitude, to 1.0 s per frame, enabled by a custom-built, 2-kHz master oscillator power amplifier (MOPA)-pumped, barium nitrite [Ba(NO3)2] Raman laser. This advancement narrows the gap in translating the IVPA technology to the clinical setting.
Expression of Ia-like antigens defined by monoclonal OKIal antibody of hemopoietic progenitor cells in cord blood: a comparison with human bone marrow (1982)

Expression of Ia antigens on granulocyte/macrophage colony-forming cells (CFU-GM) in human cord blood was compared with that in bone marrow with the use of monoclonal OKIal antibody. Mononuclear cells prepared from cord blood and bone marrow were pretreated with OKIal antibody plus complement, and, thereafter, the ability of cord blood and bone marrow cells to form colonies of CFU-GM was assayed in semisolid agar culture. Consistent reduction in the number of CFU-GM in cord blood to 58.8% +/- 13.0% (mean +/- SD) of controls treated with complement alone was shown after elimination of Ia-antigen-bearing CFU- GM, but was significantly remarkable than that in bone marrow (18.0% +/- 5.6%). Although the reduction of both granulocyte (CFC-G) and macrophage colony (CFC-M) types of cord blood, characterized by the double staining for esterase activity, was shown following treatment with OKIal antibody plus complement, the relative inhibition of CFC-G weas significantly greater than that of CFC-M (p less than 0.02). These results suggest some differences in the characteristics of Ia-antigen- bearing CFU-GM between cord blood and bone marrow cells. Furthermore, it is suggested that Ia-dependent regulatory mechanisms might participate in the differentiation of CFU-GM to CFC-G and CFC-M.
Extensive Crosstalk Between O-GlcNAcylation and Phosphorylation Regulates Cytokinesis (2010)

Like phosphorylation, the addition of O-linked beta-N-acetylglucosamine (O-GlcNAcylation) is a ubiquitous, reversible process that modifies serine and threonine residues on nuclear and cytoplasmic proteins. Overexpression of the enzyme that adds O-GlcNAc to target proteins, O-GlcNAc transferase (OGT), perturbs cytokinesis and promotes polyploidy, but the molecular targets of OGT that are important for its cell cycle functions are unknown. Here, we identify 141 previously unknown O-GlcNAc sites on proteins that function in spindle assembly and cytokinesis. Many of these O-GlcNAcylation sites are either identical to known phosphorylation sites or in close proximity to them. Furthermore, we found that O-GlcNAcylation altered the phosphorylation of key proteins associated with the mitotic spindle and midbody. Forced overexpression of OGT increased the inhibitory phosphorylation of cyclin-dependent kinase 1 (CDK1) and reduced the phosphorylation of CDK1 target proteins. The increased phosphorylation of CDK1 is explained by increased activation of its upstream kinase, MYT1, and by a concomitant reduction in the transcript for the CDK1 phosphatase, CDC25C. OGT overexpression also caused a reduction in both messenger RNA expression and protein abundance of Polo-like kinase 1, which is upstream of both MYT1 and CDC25C. The data not only illustrate the crosstalk between O-GlcNAcylation and phosphorylation of proteins that are regulators of crucial signaling pathways but also uncover a mechanism for the role of O-GlcNAcylation in regulation of cell division.
Cerebral amyloidosis, amyloid angiopathy, and their relationship to stroke and dementia (2001)

Cerebral amyloid angiopathy (CAA) is the common term used to define the deposition of amyloid in the walls of medium- and small-size leptomeningeal and cortical arteries, arterioles and, less frequently, capillaries and veins. CAA is an important cause of cerebral hemorrhages although it may also lead to ischemic infarction and dementia. It is a feature commonly associated with normal aging, Alzheimer disease (AD), Down syndrome (DS), and Sporadic Cerebral Amyloid Angiopathy. Familial conditions in which amyloid is chiefly deposited as CAA include hereditary cerebral hemorrhage with amyloidosis of Icelandic type (HCHWA-I), familial CAA related to Abeta variants, including hereditary cerebral hemorrhage with amyloidosis of Dutch origin (HCHWA-D), the transthyretin-related meningocerebrovascular amyloidosis of Hungarian and Ohio kindreds, the gelsolin-related spinal and cerebral amyloid angiopathy, familial PrP-CAA, and the recently described chromosome 13 familial dementia in British and Danish kindreds. This review focuses on the various molecules and genetic variants that target the cerebral vessel walls producing clinical features related to stroke and/or dementia, and discusses the potential role of amyloid in the mechanism of neurodegeneration.
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms (2011)

Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret.REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.
Multiple fractures, pain, and severe disability in a patient with adult-onset hypophosphatasia (2015)

Hypophosphatasia (HPP) is a rare, inherited metabolic bone disease resulting from mutations in the gene encoding tissue non-specific alkaline phosphatase. The biochemical hallmark and key diagnostic indicator is low alkaline phosphatase activity, which leads to a variety of clinical manifestations across all ages. The diagnosis is easily missed in adults, who frequently present with nonspecific clinical manifestations such as fractures, osteomalacia, and pain. Here, the pathway to diagnosis and disease course is described in an adult patient presenting with pain. Low serum alkaline phosphatase activity went unnoticed for 2 years until osteomalacia was suspected, during which time he experienced multiple fractures and progressing pain. Currently, accumulated morbidity has rendered the patient unable to work, and treatment is focused on pain management. This case highlights the importance of low alkaline phosphatase in the differential diagnosis of patients with musculoskeletal pain.
ROCK-generated contractility regulates breast epithelial cell differentiation in response to the physical properties of a three-dimensional collagen matrix (2003)

Breast epithelial cells differentiate into tubules when cultured in floating three-dimensional (3D) collagen gels, but not when the cells are cultured in the same collagen matrix that is attached to the culture dish. These observations suggest that the biophysical properties of collagenous matrices regulate epithelial differentiation, but the mechanism by which this occurs is unknown. Tubulogenesis required the contraction of floating collagen gels through Rho and ROCK-mediated contractility. ROCK-mediated contractility diminished Rho activity in a floating 3D collagen gel, and corresponded to a loss of FAK phosphorylated at Y397 localized to 3D matrix adhesions. Increasing the density of floating 3D collagen gels also disrupted tubulogenesis, promoted FAK phosphorylation, and sustained high Rho activity. These data demonstrate the novel finding that breast epithelial cells sense the rigidity or density of their environment via ROCK-mediated contractility and a subsequent down-regulation of Rho and FAK function, which is necessary for breast epithelial tubulogenesis to occur.
AGE-RELATED MACULAR DEGENERATION PHENOTYPES ASSOCIATED WITH MUTUALLY EXCLUSIVE HOMOZYGOUS RISK VARIANTS IN CFH AND HTRA1 GENES (2015)

Central but not peripheral drusen location was strongly associated with both [CFH HTRA1] and [CFH HTRA1]. Only [CFH HTRA1] was significantly associated with increased central drusen area.
Enforced Activation of STAT5A Facilitates the Generation of Embryonic Stem–Derived Hematopoietic Stem Cells That Contribute to Hematopoiesis In Vivo (2004)

Little is known about the molecular mechanisms that direct the transition from primitive to definitive hematopoiesis. In this study, we cocultured murine embryonic stem (ES) cells on OP9 stroma to induce hematopoietic differentiation as a model to study factors involved in the generation of adult hematopoietic stem cells (HSCs). Overexpression of the constitutively activated mutant signal transducer and activator of transcription (STAT) 5A(1*6) in ES cells facilitated the generation of cells that expressed the endothelial-hemangioblast marker Flk-1 within 5 days of coculture on OP9. The first CD41+/ CD45+/c-Kit+/(Flk-1)- hematopoietic cells arose in our culture conditions between days 5 and 7. Persistent activation of STAT5A greatly enhanced the generation of hematopoietic progenitors compared with controls, as determined by colony assays in methylcellulose. Moreover, whereas controls generated only a short transient wave of hematopoiesis lasting less than 3 weeks, expression of STAT5A(1*6) resulted in the generation of hematopoietic cobblestone area-forming cells (CAFCs) on OP9 that could be serially passaged onto new OP9, giving rise to second and third CAFCs that generated hematopoietic progenitors for > or = 5 weeks, indicating a role for STAT5A in HSC self-renewal in vitro. Several definitive hematopoietic genes were upregulated by STAT5A (1*6), as well as Runx1/AML1, vascular endothelial growth factor, oncostatin M receptor, HoxB4, Wnt5A, Delta-like-1, and Bmi-1. Furthermore, ES-derived hematopoietic cells expressing STAT5A(1*6) contributed to myeloid-lymphoid hematopoiesis in primary and secondary nonobese diabetic-severe combined immunodeficiency recipients, although no donor-derived cells could be detected after 7 weeks in the secondary recipients. These data indicate that a persistent activation of STAT5A allows the generation of ES-derived HSCs that can, at least for an intermediate period, contribute to hematopoiesis in vivo.
Neonatal Fc receptor (FcRn): a novel target for therapeutic antibodies and antibody engineering (2014)

The biomedical applications of antibodies as prophylactics, therapeutics and diagnostics are developing rapidly. Neonatal Fc receptor (FcRn) is a major IgG Fc receptor capable of facilitating the translocation of IgG. FcRn can protect IgG from intracellular catabolism, thereby increasing its half-life. In recent decade, the interaction between FcRn and the Fc region has been reported with the focuses on either prolonging the plasma half-life of therapeutic IgG or shortening the half-life of pathogenic IgG. The FcRn-IgG interaction can be altered by modifying the Fc region to change their affinity (increase or decrease), and/or by reducing the Fc fragments of IgG to enhance its penetration into tissues or cells. By over expression of FcRn, the exogenous catabolism can be reduced, meanwhile the circulating IgG level could be enhanced. It has been confirmed in different FcRn over-expressed transgenic mice models, substantial humoral responses against antigens with weak immunogenicity can be mounted. In addition, designing inhibitors for FcRn-IgG interaction is another application prospect for treating IgG-mediated autoimmune diseases. Recent research advancements strengthen the understanding that FcRn is a key and promising drugable target in IgG intervention in the field of antibody engineering.
Safety and Tolerability of Topical Ophthalmic Triamcinolone Acetonide-Loaded Liposomes Formulation and Evaluation of Its Biologic Activity in Patients with Diabetic Macular Edema (2021)

Intravitreal injections (IVTs) of corticosteroids as triamcinolone acetonide (TA) are frequently used for the treatment of many vitreous and retinal disorders. However, IVTs are related to severe ocular complications. Lately, a topical ophthalmic TA-loaded liposomes formulation (TALF) was designed to transport TA into the posterior segment of the eye when instilled on the ocular surface. To evaluate the safety, tolerability, and biological activity of TALF, an animal study and a phase I clinical assay were performed. Moreover, four patients with diabetic macular edema (DME) were treated with TALF in order to explore the biological activity of the formulation. No inflammation, lens opacity, swelling, or increase in intraocular pressure were recorded after the instillation of TALF in any of the animal or clinical studies. Mainly, mild and transient adverse events such as dry eye and burning were reported. TALF significantly improves visual acuity and diminishes central foveal thickness in patients with DME. The current data demonstrate the safety, tolerability, and biological activity of TALF. It seems that TALF can be used topically to treat vitreous and retinal diseases that respond to TA such as DME, avoiding the use of corticosteroid IVTs and their associated hazards.
A frameless stereotaxic operating microscope for neurosurgery (1989)

A new system, which we call the frameless stereotaxic operating microscope, is discussed. Its purpose is to display CT or other image data in the operating microscope in the correct scale, orientation, and position without the use of a stereotaxic frame. A nonimaging ultrasonic rangefinder allows the position of the operating microscope and the position of the patient to be determined. Discrete fiducial points on the patient's external anatomy are located in both image space and operating room space, linking the image data and the operating room. Physician-selected image information, e.g., tumor contours or guidance to predetermined targets, is projected through the optics of the operating microscope using a miniature cathode ray tube and a beam splitter. Projected images superpose the surgical field, reconstructed from image data to match the focal plane of the operating microscope. The algorithms on which the system is based are described, and the sources and effects of errors are discussed. The system's performance is simulated, providing an estimate of accuracy. Two phantoms are used to measure accuracy experimentally. Clinical results and observations are given.
Wedge Optics in Flat Panel Displays (2012)

Liquid crystal display (LCD) technology will struggle to display high resolution on screens as big as whiteboards. Yet there is demand also for less power consumption, 3-D images, and that the display should be able to see gestures and feel touch. Most of these features are possible with projection and wedge light guides make projection slim, but picoprojectors are so dim that many will be needed for such a big screen. For now, we use instead a hybrid of technologies: light guides look out from behind an LCD to see where the viewers' hands and eyes are, and a collimated backlight lets us illuminate one view at a time to each eye. This lets us synthesize 3-D with achievable increases in LCD frame rate. We expect that this combination of a multiview 3-D display and a view-dependent rendered image will give us the potential to televise the experience of looking through a window.
MDA-7 regulates cell growth and radiosensitivity in vitro of primary (Non-Established) human glioma cells (2004)

We examined the impact of purified bacterially synthesized GST-MDA-7 (IL-24) and ionizing radiation on the proliferation and survival of nonestablished human glioblastoma multiforme (GBM) cells. Glioma cell types expressing mutated PTEN and p53 molecules, activated ERBB1VIII, overexpressing wild type ERBB1 or without receptor overexpression were selected. In MTT assays, GST-MDA-7 caused a dose-dependent reduction in the proliferation of nonestablished glioma cells; however only at higher concentrations did GST-MDA-7 reduce cell viability. The anti-proliferative and cytotoxic effects of GST-MDA-7 were enhanced by radiation in a greater than additive fashion that correlated with JNK1/2/3 activation. The reduction in cell growth and enhancement in cell killing by the combination of GST-MDA-7 and radiation were blocked by an ROS scavenger, N-acetyl cysteine (NAC), a JNK1/2/3 inhibitor SP600125, a pan-caspase inhibitor (zVAD) and by an inhibitor of caspase 9 (LEHD), but not by an inhibitor of caspase 8 (IETD). Low concentrations of either GST-MDA-7 or radiation reduced clonogenic survival, however colony formation ability was significantly further decreased when the two treatments were combined, which was also blocked by inhibition of caspase 9 function. In general agreement with activation of the intrinsic caspase pathway, cell death correlated with reduced BCL-XL expression and with increased levels of the pro-apoptotic proteins BAD and BAX. Inhibition of caspase 9 after combination treatment blunted neither JNK1/2/3 activation nor the enhanced expression of BAD and BAX, but did block caspase 3 cleavage, reduced expression of BCL-XL and inhibition of ERK1/2 activity. In contrast, incubation with NAC blocked JNK1/2/3 activation and cell killing, but not the increases in BAD and BAX expression. These findings argue that after combination treatment JNK1/2/3 activation is a primary pro-apoptotic event and loss of BCL-XL expression and ERK1/2 activity are secondary caspase-dependent processes. This data also argues that GST- MDA-7 induces two parallel pro-apoptotic pathways via ROS-dependent and -independent mechanisms. Infection of primary human astrocytes with a recombinant adenovirus to express MDA-7, Ad.mda-7, but not infection with either Ad.cmv or Ad.mda-7SP- lacking MDA-7 secretion, resulted in the suppression of GBM cell colony formation in soft agar overlay assays, an effect that was enhanced in a greater than additive fashion by radiation. Collectively, our findings demonstrate that MDA-7 reduces proliferation and enhances the radiosensitivity of nonestablished human GBM cells in vitro, and when grown in 3 dimensions, and that sensitization occurs independently of basal EGFR/ERK1/2/AKT activity or the functions of PTEN and p53.
The initial steps leading to papillomavirus infection occur on the basement membrane prior to cell surface binding (2009)

Using a murine challenge model, we previously determined that human papillomavirus (HPV) pseudovirions initially bind preferentially to the cervicovaginal basement membrane (BM) at sites of trauma. We now report that the capsids undergo a conformational change while bound to the BM that results in L2 cleavage by a proprotein convertase (PC), furin, and/or PC5/6, followed by the exposure of an N-terminal cross-neutralization L2 epitope and transfer of the capsids to the epithelial cell surface. Prevention of this exposure by PC inhibition results in detachment of the pseudovirions from the BM and their eventual loss from the tissue, thereby preventing infection. Pseudovirions whose L2 had been precleaved by furin can bypass the PC inhibition of binding and infectivity. Cleavage of heparan sulfate proteoglycans (HSPG) with heparinase III prevented infection and BM binding by the precleaved pseudovirions, but did not prevent them from binding robustly to cell surfaces. These results indicate that the infectious process has evolved so that the initial steps take place on the BM, in contrast to the typical viral infection that is initiated by binding to the cell surface. The data are consistent with a dynamic model of in vivo HPV infection in which a conformational change and PC cleavage on the BM allows transfer of virions from HSPG attachment factors to an L1-specific receptor on basal keratinocytes migrating into the site of trauma.
Rapid activation by fungal elicitor of genes encoding “pathogenesis-related” proteins in cultured parsley cells (1986)

Administration of a cell-wall preparation from the fungus Phytophthora megasperma f. sp. glycinea, which acts as an elicitor of phytoalexin production in cell suspension cultures of parsley (Petroselinum crispum), also results in a rapid and dramatic increase in the relative amounts of mRNAs coding for a number of small proteins having low isoelectric points. According to various operational criteria, the translation products are classified as "pathogenesis-related" (PR) proteins. Here we report that the cDNA inserts of two pBR322-derived plasmids, pcPR1 and pcPR2, are homologous to mRNAs coding for one (PR1) and three (PR2) of these proteins in hybrid-selected in vitro translation experiments. Nuclear run-off transcription studies show that activation of the corresponding genes is extremely rapid; we observed a 4-fold increase in the transcription rate of the PR1 gene within 5 min and a 3-fold increase for the PR2 gene within 20 min following elicitation. Subsequent increases in the amounts of PR1 and PR2 mRNAs indicate that regulation of PR protein synthesis occurs at the transcriptional level.