gebhart/patrepeval huggingface dataset:
A New and Easy Synthesis of Silylated Furanoid Glycals in One Step from Nucleosides (1994)

Silylated furanoid glycals are synthesized in high yields by elimination of the nucleobase in thymidine (1a) and 5′-O- (tert-butyldiphenylsilyl)thymidine (1b) on treatment with 1,1,1,3,3,3-hexamethyldisilazane (HMDS) in the presence of ammonium sulfate at reflux temperature for 2 hours.
Two types of mouse helper T cell clone. III. Further differences in lymphokine synthesis between Th1 and Th2 clones revealed by RNA hybridization, functionally monospecific bioassays, and monoclonal antibodies. (1987)

Lymphokine synthesis patterns of a panel of 19 T cell clones have been evaluated, using mRNA hybridization methods to examine 11 different mRNAs induced by Con A. The two types of CD4+ Th cell clone described previously were clearly distinguished by this procedure, and the differences between the two types have now been extended to six induced products. With minor exceptions, only Th1 clones synthesized mRNA for IL-2, IFN-gamma, and lymphotoxin, and only Th2 clones synthesized mRNA for IL-4, IL-5, and another induced gene, P600. Four more induced products were expressed preferentially but not uniquely by one or another type of clone: mRNAs for GM-CSF, TNF, and another induced, secreted product (TY5) were produced in larger amounts by Th1 clones, whereas preproenkephalin was preferentially expressed by Th2 clones. IL-3 was produced in similar amounts by both types of clone. mAbs were used to establish three bioassays that were functionally monospecific for IL-2, IL-3, and IL-4, and a new anti-IFN gamma mAb, XMG1.2, was used to establish an ELISA for IFN-gamma. These four assays were used to show that secreted protein and mRNA levels correlated well for all cell lines. The implications of these findings for normal T cells are discussed.
Rapid and simple single nanogram detection of glycoproteins in polyacrylamide gels and on electroblots (2001)

The fluorescent hydrazide, Pro-Q Emerald 300 dye, may be conjugated to glycoproteins by a periodic acid Schiff’s (PAS) mechanism. The glycols present in glycoproteins are initially oxidized to aldehydes using periodic acid. The dye then reacts with the aldehydes to generate a highly fluorescent conjugate. Reduction with sodium metabisulfite or sodium borohydride is not required to stabilize the conjugate. Though glycoprotein detection may be performed on transfer membranes, direct detection in gels avoids electroblotting and glycoproteins may be visualized within 2–4 h of electrophoresis. This is substantially more rapid than PAS labeling with digoxigenin hydrazide followed by detection with an antidigoxigenin antibody conjugate of alkaline phosphatase, or PAS labeling with biotin hydrazide followed by detection with horseradish peroxidase or alkaline phosphatase conjugates of streptavidin, which require more than eight hours to complete. Pro-Q Emerald 300 dye-labeled gels and blots may be post-stained with SYPRO Ruby dye, allowing sequential two-color detection of glycosylated and nonglycosylated proteins. Both fluorophores are excited with mid-range UV illumination. Pro-Q Emerald 300 dye maximally emits at 530 nm (green) while SYPRO Ruby dye maximally emits at 610 nm (red). As little as 300 pg of α1-acid glycoprotein (40% carbohydrate) and 1 ng of glucose oxidase (12% carbohydrate) or avidin (7% carbohydrate) are detectable in gels after staining with Pro-Q Emerald 300 dye. Besides glycoproteins, as little as 2–4 ng of lipopolysaccharide is detectable in gels using Pro-Q Emerald 300 dye while 250–1000 ng is required for detection with conventional silver staining. Detection of glycoproteins may be achieved in sodium dodecyl sulfate-polyacrylamide gels, two-dimensional gels and on polyvinylidene difluoride membranes.
Loss of heterozygosity on chromosome 11 q in breast cancer. (1995)

The frequency of allelic loss at the DS11S29 locus is high. The significance of novel alleles at NCAM and their relation to allelic loss at D11S29 are unclear. The results presented here do not permit fine mapping of a region of allelic loss, but suggest that the region of greatest loss lies distal to DRD2. The results provide further evidence for the importance of gene(s) near 11q23 in the pathogenesis of breast cancer, and of tumours in general.
Technology evaluation: BLP-25, Biomira Inc. (2001)

Biomira is developing the MUC-1 peptide-based vaccine BLP-25 for the potential treatment of cancer. It is in phase II trials for non-small cell lung cancer (NSCLC) [335997], [353448], [384703]. The MUC-1 mucin secreted by cancer cells has been shown to decrease the activity of certain immune response cells, including killer T-cells, and can inhibit the immune T-cell response by > 70%. BLP-25 is designed to target an immune response to the MUC-1 mucin that is shown by > 90% of common solid tumors. The introduction of IL-2 reverses the T-cell suppression caused by MUC-1 mucin, and enhances the cellular immune response > 100-fold. Biomira has been incorporating IL-2 into a liposomal delivery system for BLP-25 [274576]. In late 1998, Biomira entered into a research collaboration with Axis Genetics. The collaboration will assess the further potential of therapeutic cancer vaccines against MUC-1. Each company has developed a vaccine targeting the MUC-1 peptide and Biomira will be evaluating Axis's vaccine in preclinical trials [313395]. In December 1996, Biomira signed a licensing agreement whereby it was granted the rights to use Dana-Farber Cancer Institute's two US patents relating to MUC-1 (based on pioneering work at the Institute on the identification of cell-surface molecules that are characteristic of cancer cells) for peptide-based cancer vaccines [228101].
Tumor malignancy defined by aberrant glycosylation and sphingo(glyco)lipid metabolism. (1996)

Aberrant glycosylation expressed in glycosphingolipids and glycoproteins in tumor cells has been implicated as an essential mechanism in defining stage, direction, and fate of tumor progression. This general concept is supported by results from three lines of study: (a) Numerous clinicopathological studies have shown a clear correlation between aberrant glycosylation status of primary tumor and invasive/metastatic potential of human cancer as reflected by 5- or 10-year survival rates of patients. (b) Carbohydrates expressed in tumor cells are either adhesion molecules per se or modulate adhesion receptor function. Some are directly involved in cell adhesion. They are recognized by selectins or other carbohydrate-binding proteins or by complementary carbohydrates (through carbohydrate-carbohydrate interaction). N- or O-glycosylation of functionally important membrane components may alter tumor cell adhesion or motility in a direction that either promotes or inhibits invasion and metastasis. Examples of such receptors are E-cadherin, integrins, immunoglobulin family receptors (e.g., CD44), and lysosome-associated membrane protein. (c) Gangliosides and sphingolipids modulate transmembrane signaling essential for tumor cell growth, invasion, and metastasis. The transducer molecules susceptible to gangliosides and sphingolipids include integrin receptors, tyrosine kinase-linked growth factor receptors, protein kinase C, and G-protein-linked receptor affecting protein kinase A. Some glycosphingolipids (e.g., Gb3Cer, Le(y), ceramide, and sphingosine induce tumor cell differentiation and subsequent apoptosis. Shedded gangliosides may block immunogenicity of tumor cells, providing conditions favorable for "escape" from immunological suppression of tumor growth by the host. Various reagents that block carbohydrate-mediated tumor cell adhesion or block glycosylation processing have been shown to inhibit tumor cell metastasis. This provides the basis for further development of "anti-adhesion therapy." Ganglioside analogues and sphingolipid analogues that inhibit protein kinase C and receptor-associated tyrosine kinase have been applied for inhibition of metastasis. A crucial mechanism for inhibition of metastasis by these reagents may involve blocking of transmembrane signaling for expression of P- and E-selectin. This provides the basis for development of "ortho-signaling therapy."
Application of a Time&ndash;Resolved Fluoroimmunoassay for the Analysis of Normal Prion Protein in Human Blood and Its Components (1999)

The majority of blood PrP(c) is found in the platelet and plasma compartments.
Amino terminus of the interleukin-8 receptor is a major determinant of receptor subtype specificity. (1992)

Interleukin-8 (IL-8) is a key mediator in the migration of neutrophils from the circulation to the site of inflammation in the tissue. IL-8 is secreted by many cell types in response to proinflammatory stimuli such as interleukin 1, tumor necrosis factor, and lipopolysaccharide and is a potent chemoattractant and activator of neutrophils. Neutrophil activating peptide-2 (NAP-2) and melanoma growth-stimulatory activity (MGSA/GRO) are structurally and functionally related to IL-8 and, like IL-8, bind to specific G protein-coupled receptors on neutrophils. In the present study two closely related cloned IL-8 receptor subtypes are characterized by expression of the cDNA clones in monkey kidney cells (COS-7) or chinese hamster ovary cells and analysis of their ligand binding profiles. Both receptor subtypes bind 125I-labeled IL-8 with similar high affinity, however, the F3R receptor binds IL-8 exclusively, while the 4Ab receptor binds both IL-8 and MGSA/GRO with high affinity and NAP-2 with lesser affinity. Furthermore, we demonstrate with the use of intersubtype chimeric receptors that the specificity of ligand binding to both IL-8 receptor subtypes is dictated by the heterogeneous NH2-terminal domain. The F3R receptor is representative of a restricted IL-8 receptor subtype, and 4Ab represents a nonrestricted receptor subtype. It is proposed that these subtypes be named IL-8 receptors alpha and beta, respectively.
Pump-Probe Imaging Differentiates Melanoma from Melanocytic Nevi (2011)

Melanoma diagnosis is clinically challenging: the accuracy of visual inspection by dermatologists is highly variable and heavily weighted toward false positives. Even the current gold standard of biopsy results in varying diagnoses among pathologists. We have developed a multiphoton technique (based on pump-probe spectroscopy) that directly determines the microscopic distribution of eumelanin and pheomelanin in pigmented lesions of human skin. Our initial results showed a marked difference in the chemical variety of melanin between nonmalignant nevi and melanoma, as well as a number of substantial architectural differences. We examined slices from 42 pigmented lesions and found that melanomas had an increased eumelanin content compared to nonmalignant nevi. When used as a diagnostic criterion, the ratio of eumelanin to pheomelanin captured all investigated melanomas but excluded three-quarters of dysplastic nevi and all benign dermal nevi. Additional evaluation of architectural and cytological features revealed by multiphoton imaging, including the maturation of melanocytes, presence of pigmented melanocytes in the dermis, number and location of melanocytic nests, and confluency of pigmented cells in the epidermis, further increased specificity, allowing rejection of more than half of the remaining false-positive results. We then adapted this multiphoton imaging technique to hematoxylin and eosin (H&E)-stained slides. By adding melanin chemical contrast to H&E-stained slides, pathologists will gain complementary information to increase the ease and accuracy of melanoma diagnosis.
Mechanisms of Bcl-2 family protein function and dysfunction in health and disease. (1996)

The Bcl-2 protein blocks a distal step in an evolutionarily conserved pathway for programmed cell death and apoptosis. The gene encoding this protein was first discovered because of its involvement in the t(14;18) chromosomal translocations commonly found in B-cell lymphomas, where it contributes to neoplastic cell expansion by preventing cell turnover due to programmed cell death. Overexpression of BCL-2 also occurs in many other types of human tumors, including cancers of the prostate, colon, and lung, and has been associated with chemoresistance and radioresistance in some types of malignancy. Conversely, expression of BCL-2 is frequently reduced in the circulating lymphocytes of persons infected with Human Immunodeficiency Virus (HIV), which are prone to apoptotic cell death. Since the discovery of Bcl-2 a decade ago, several other cellular and viral genes encoding homologous proteins have been identified, some of which suppress cell death akin to Bcl-2 (Bcl-XL, Mcl-1, A1/Bfl-1, Nr13, Ced-9, BHRF-1) and others which promote apoptosis (Bax, Bcl-Xs, Bak, Bik, Bad). Several of these Bcl-2 family proteins are capable of physically interacting with each other through a complex network of homo- and heterodimers. The expression of some of these other BCL-2 family genes becomes altered in human cancers, as well as in the setting of ischemia and some other pathological conditions, suggesting a potentially important role for these Bcl-2 homologs in human diseases characterized by either insufficient or excessive cell death. Despite intensive investigation, the mechanisms by which Bcl-2 and its homologs control cell life and death largely remain enigmatic. Knowledge about the specific domains in Bcl-2 family proteins that are required for interactions with other proteins and for function however is beginning to provide insights into the molecular mechanisms through which these proteins regulate the programmed cell death pathway in normalcy and disease.
Parallax photography: creating 3D cinematic effects from stills (2009)

We present an approach to convert a small portion of a light field with extracted depth information into a cinematic effect with simulated, smooth camera motion that exhibits a sense of 3D parallax. We develop a taxonomy of the cinematic conventions of these effects, distilled from observations of documentary film footage and organized by the number of subjects of interest in the scene. We present an automatic, content-aware approach to apply these cinematic conventions to an input light field. A face detector identifies subjects of interest. We then optimize for a camera path that conforms to a cinematic convention, maximizes apparent parallax, and avoids missing information in the input. We describe a GPU-accelerated, temporally coherent rendering algorithm that allows users to create more complex camera moves interactively, while experimenting with effects such as focal length, depth of field, and selective, depth-based desaturation or brightening. We evaluate and demonstrate our approach on a wide variety of scenes and present a user study that compares our 3D cinematic effects to their 2D counterparts.
Oncogenic co-operation in beta-cell tumorigenesis. (2001)

Pancreatic islet neoplasms are rare endocrine tumours. The most common type is of beta-cell origin and is known as insulinoma, which can be either benign or malignant. The majority of insulinomas arise sporadically, but a small proportion develop as part of the hereditary multiple endocrine neoplasia type 1 (MEN1) syndrome. As for many human tumours, the genetic events that occur during the initiation and progression of insulinoma are poorly known. The men1 gene product, menin, is deficient in most hereditary cases, but is not obviously affected in the majority of sporadic tumours. Activation of the proto-oncogenes c-myc and ras has been observed during malignant progression, but their role in tumour initiation remains unproven. To address these questions, transgenic mouse models have been increasingly used to explore molecular and genetic events that might also precipitate human neoplasia. Transgenic mice expressing SV40 large T-antigen (Tag) oncogene in beta-cells develop tumours in a multi-stage progression from hyperplasia, angiogenesis, to solid encapsulated tumours. However, Tag, which inactivates the key tumour suppressors p53 and Rb, is not known to be involved in the pathogenesis of human insulinoma. The proto-oncogene, c-myc is implicated in beta-cell growth in both diabetes and tumorigenesis. Activation of Myc appears to be an early event in progression of human insulinoma. The effect of deregulated Myc expression on adult beta-cells in vivo has recently been investigated by developing transgenic mouse models in which the activity of Myc can be regulated ectopically. Although Myc activation initially promotes both proliferation and apoptosis in pancreatic beta-cells, apoptosis is the predominant outcome, giving rise to islet involution and diabetes. Importantly, inhibiting Myc-induced apoptosis (by co-expression of Bcl-x(L)) leads to significantly enlarged islets, many becoming highly vascularized, hyperplastic and invasive. These results suggest that, in the pancreatic beta-cells, early suppression of apoptosis is essential for the survival of Myc-activated beta-cells and islet neoplasia.
Chromosomal mapping of members of the cdc2 family of protein kinases, cdk3, cdk6, PISSLRE, and PITALRE, and a cdk inhibitor, p27Kip1, to regions involved in human cancer. (1995)

Orderly progression through the cell cycle requires sequential activation and inactivation of cyclin-dependent kinases (cdks). This is achieved in part through the association of cdks with positive regulators called cyclins and inactivation of cyclin-cdk complexes by a rapidly growing number of cyclin-cdk inhibitors. Recently, the role of cell cycle control proteins both as primary effectors and as mediators of tumorigenesis has become a subject of increased interest. Here we report the chromosomal mapping of two cdks, cdk3 and cdk6, two putative cdks, PISSLRE and PITALRE, and one cyclin-dependent kinase inhibitor, p27, to chromosomal regions which may be altered in human tumors and examine their possible involvement in some of these malignancies. In particular, two of the kinases, cdk3 and PISSLRE and PITALRE, the cdc2-related kinases recently cloned by us, map to regions previously shown to exhibit loss of heterozygosity in breast and other tumors.
Molecular cloning of 3-hydroxy-3-methylglutaryl coenzyme a reductase and evidence for regulation of its mRNA. (1982)

A recombinant plasmid containing a 1.2-kilobase cDNA for 3-hydroxy-3-methylglutaryl coenzyme A reductase was isolated from a cDNA library prepared from UT-1 cells, a clone of Chinese hamster ovary cells that has markedly elevated reductase activity. This plasmid, designated pRed-10, was identified by differential colony hybridization and hybrid-selected mRNA translation. The mRNA that hybridized to pRed-10 directed the synthesis in vitro of a 90,000-dalton protein that was immunoprecipitated by an antireductase antibody. The same 90,000-dalton protein was immunoprecipitated when UT-1 cells were pulse labeled with [35S]methionine in vivo and rapidly solubilized with boiling NaDodSO4. By blot hybridization, pRed-10 hybridized to mRNAs of 4.2 and 4.7 kilobases in UT-1 cells. Both mRNAs were reduced to undetectable levels when low density lipoprotein, a suppressor of the reductase, was present in the culture medium. These data indicate that the primary translation product of reductase mRNA is a 90,000-dalton protein and that LDL suppresses the reductase in UT-1 cells by drastically reducing the level of its mRNA.
Current and emerging therapeutic strategies for preventing inflammation and aggrecanase-mediated cartilage destruction in arthritis (2014)

Arthritis is a multifactorial disease for which current therapeutic intervention with high efficacy remains challenging. Arthritis predominately affects articular joints, and cartilage deterioration and inflammation are key characteristics. Current therapeutics targeting inflammatory responses often cause severe side effects in patients because of the systemic inhibition of cytokines or other global immunosuppressive activities. Furthermore, a lack of primary response or failure to sustain a response to treatment through acquired drug resistance is an ongoing concern. Nevertheless, treatments such as disease-modifying anti-rheumatic drugs, biological agents, and corticosteroids have revealed promising outcomes by decreasing pain and inflammation in patients and in some cases reducing radiographic progression of the disease. Emerging and anecdotal therapeutics with anti-inflammatory activity, alongside specific inhibitors of the A Disintegrin-like And Metalloproteinase domain with Thrombospondin-1 repeats (ADAMTS) cartilage-degrading aggrecanases, provide promising additions to current arthritis treatment strategies. Thus, it is paramount that treatment strategies be optimized to increase efficacy, reduce debilitating side effects, and improve the quality of life of patients with arthritis. Here, we review the current strategies that attempt to slow or halt the progression of osteoarthritis and rheumatoid arthritis, providing an up-to-date summary of pharmaceutical treatment strategies and side effects. Importantly, we highlight their potential to indirectly regulate ADAMTS aggrecanase activity through their targeting of inflammatory mediators, thus providing insight into a mechanism by which they might inhibit cartilage destruction to slow or halt radiographic progression of the disease. We also contrast these with anecdotal or experimental administration of statins that could equally regulate ADAMTS aggrecanase activity and are available to arthritis sufferers worldwide. Finally, we review the current literature regarding the development of synthetic inhibitors directed toward the aggrecanases ADAMTS4 and ADAMTS5, a strategy that might directly inhibit cartilage destruction and restore joint function in both rheumatoid arthritis and osteoarthritis.
Nonsurgical modalities to enhance healing and care of soft tissue wounds. (1997)

The rapidly aging population and patients with multiple concomitant pathologies present an increasing population of patients with nonhealing and problem wounds causing an unwelcome challenge for all health care providers. Many of these patients are not surgical candidates, or surgical procedures have failed to close their wounds. These wounds are particularly worrisome when an orthopaedic component is included, since bone and hardware must be covered as quickly as possible to prevent infection and even worse complications. We present a brief overview of several nonsurgical modalities that may be used to heal soft tissue wounds completely or to prepare the wound so a smaller surgical intervention may be done with greater chance for success. We include exogenous application of growth factors, cultured keratinocyte grafts, electrical stimulation, hyperbaric oxygen, and a vacuum-assisted closure system (V.A.C.).