gebhart/patrepeval huggingface dataset:
Characterization of the tumorigenic and metastatic properties of a human pancreatic tumor cell line (AsPC-1) implanted orthotopically into nude mice. (1985)

An orthotopic xenograft of the human pancreatic tumor was established by inoculating human pancreatic tumor AsPC-1 cells into the duodenal lobe of the pancreas of the athymic nude mouse. Microscopically, the xenograft was formed by a heterogeneous population of tumor cells, displaying moderately to poorly differentiated adenocarcinomas with the latter capable of invading the adjacent pancreatic islets or non-endocrine elements. At 4 weeks post-transplantation, the tumor was detectable as a focal implant at the site of inoculation and thereafter grew progressively leading to extensive visceral invasion and metastasis. In contrast to the subcutaneous xenograft, all the mice (9/9) bearing orthotopically transplanted tumor developed secondary foci in the gut and at the peritoneum, with 7, 6, and 4 animals showing additional kidney, mesenteric lymphnodal, and diaphragm metastases, respectively. Distant metastases in the lungs were found in 3 mice and malignant ascites developed in two. Human pancreas cancer associated antigen was detected in the tumor, serum, and ascitic fluid of the mice at 63 +/- 24 micrograms/gm, 15 +/- 6 micrograms/ml, and 5 micrograms/ml, respectively. The finding of these regional and distant metastases was quite different from that in the animal bearing subcutaneously xenografted tumor where no metastases to internal organs was observed. The results suggest the potential use of this experimental system in tumor biology and antigen expression of human pancreatic cancer in vivo.
Quantitative Volumetric Perfusion Mapping of the Microvasculature Using Contrast Ultrasound (2010)

Three-dimensional perfusion imaging allows a significant reduction in the error caused by transducer positioning, and significantly improves the reliability of quantitative perfusion time estimates in a rat kidney model. When performing perfusion imaging, it is important to use appropriate and consistent contrast agent infusion rates to avoid bias.
Generation of a Functional Monomolecular Protein Lattice Consisting of an S-Layer Fusion Protein Comprising the Variable Domain of a Camel Heavy Chain Antibody (2003)

Crystalline bacterial cell surface layer (S-layer) proteins are composed of a single protein or glycoprotein species. Isolated S-layer subunits frequently recrystallize into monomolecular protein lattices on various types of solid supports. For generating a functional protein lattice, a chimeric protein was constructed, which comprised the secondary cell wall polymer-binding region and the self-assembly domain of the S-layer protein SbpA from Bacillus sphaericus CCM 2177, and a single variable region of a heavy chain camel antibody (cAb-Lys3) recognizing lysozyme as antigen. For construction of the S-layer fusion protein, the 3'-end of the sequence encoding the C-terminally truncated form rSbpA(31)(-)(1068) was fused via a short linker to the 5'-end of the sequence encoding cAb-Lys3. The functionality of the fused cAb-Lys3 in the S-layer fusion protein was proved by surface plasmon resonance measurements. Dot blot assays revealed that the accessibility of the fused functional sequence for the antigen was independent of the use of soluble or assembled S-layer fusion protein. Recrystallization of the S-layer fusion protein into the square lattice structure was observed on peptidoglycan-containing sacculi of B. sphaericus CCM 2177, on polystyrene or on gold chips precoated with thiolated secondary cell wall polymer, which is the natural anchoring molecule for the S-layer protein in the bacterial cell wall. Thereby, the fused cAb-Lys3 remained located on the outer S-layer surface and accessible for lysozyme binding. Together with solid supports precoated with secondary cell wall polymers, S-layer fusion proteins comprising rSbpA(31)(-)(1068) and cAbs directed against various antigens shall be exploited for building up monomolecular functional protein lattices as required for applications in nanobiotechnology.
Specificity of Staphylococcal Superantigen-Like Protein 10 toward the Human IgG1 Fc Domain (2010)

Staphylococcal superantigen-like protein 10 (SSL10) is a highly conserved member of the SSL family secreted by Staphylococcus aureus that displays structural but not functional similarity to superantigens. SSL10 bound to fibrinogen and fibronectin from plasma and in addition displayed striking specificity toward the gamma-1 subclass of human Igs. SSL10 also bound strongly to primate IgG but not to any other species tested, including rabbit, pig, guinea pig, cow, sheep, or mouse. A soluble form of the 12-kDa beta-grasp C-terminal domain of SSL10 (SSL10(95-197)) retained fibrinogen and fibronectin binding but lost the ability to bind IgG1, indicating that SSL10 bound to IgG1 primarily through its N-terminal oligonucleotide binding fold domain. SSL10 blocked the binding of IgG1 to FcgammaRs on monocytes and neutrophil phagocytosis of IgG1-opsonized bacteria. Mutagenesis of human IgG1 at key sites significantly reduced SSL10 binding including Lys(322) that is important for C1q binding, a combination of Leu(234) and Leu(235) that are important for FcgammaR binding, and a combination of Lys(274) and Asp(276) that together are unique to IgG1. These mutations suggest that the most likely site bound by SSL10 is the outer face of the Cgamma2 domain in close proximity to both the FcgammaR and C1q binding sites. SSL10 is a potential virulence factor for S. aureus targeting IgG1-mediated immunity.
Similarity Searching in Files of Three-Dimensional Chemical Structures:  Flexible Field-Based Searching of Molecular Electrostatic Potentials (1996)

Similarity measures based on the molecular electrostatic potential (MEP) have been used to quantify the degree of resemblance between pairs of rigid three-dimensional (3-D) molecules. This paper discusses the effect of including molecular flexibility on the similarities that are calculated using such measures in searches of large 3-D databases. Experiments with a graph-theoretic approach to MEP-based similarity searching demonstrate the limitations of using multiple conformations to represent the variations in an MEP that arise from torsional flexibility. Better results have been obtained with a genetic algorithm (GA) that has been developed for calculating the similarity between the MEPs of pairs of molecules, one or both of which is flexible. Experiments with two small files of flexible 3-D structures show that this GA identifies significantly better alignments than does a comparable GA for searching rigid 3-D molecules.
Expression and self-assembly of recombinant capsid protein from the antigenically distinct Hawaii human calicivirus (1997)

The Norwalk and Hawaii viruses are antigenically distinct members of the family Caliciviridae and are considered to be important etiologic agents of epidemic gastroenteritis, with most studies focusing on the role of Norwalk virus. To further investigate the importance of Hawaii virus, Hawaii virus-like particles (VLPs) were produced by expression of its capsid protein in the baculovirus system and these VLPs were used as the antigen in an enzyme-linked immunosorbent assay that was efficient in the detection of a serologic response to Hawaii virus. The ready availability of Hawaii VLPs should enable larger-scale epidemiological studies to further elucidate the importance of this agent.
Studies of Catalysis by β-Glucuronidase (1972)

Abstract The relative rates of hydrolysis of monosubstituted phenyl-β-d-glucopyranosiduronic acids (phenyl-β-glucuronides) catalyzed by β-glucuronidase correlate with Hammett values, yielding a biphasic curve with the curve being concave up and with the change-over occurring at the unsubstituted compound. A similar type of plot has not previously been obtained with other enzymes. The relative rates of hydrolysis of p-methoxyphenyl, p-chlorophenyl, and p-nitrophenyl-β-d-glucopyranosiduronic acids, and of the most commonly used substrate, phenolphthalein-β-d-glucopyranosiduronic acid, were compared in D2O and H2O, and it was observed that the pH optimum in D2O shifted towards higher values, with the rate of hydrolysis in D2O decreasing by a factor of 1.7 to 2.0 as compared to that in H2O. These results suggest the involvement of a rate-determining proton transfer in the catalytic steps of the enzymatic reaction. A possible explanation for the change in slope in the Hammett plot is that there is a shift in the relative electronic importance of the general acid-nucleophile portions of the push-pull mechanism.
Persistent p21 Expression after Nutlin-3a Removal Is Associated with Senescence-like Arrest in 4N Cells (2010)

Nutlin-3a is a preclinical drug that stabilizes p53 by blocking the interaction between p53 and MDM2. In our previous study, Nutlin-3a promoted a tetraploid G(1) arrest in two p53 wild-type cell lines (HCT116 and U2OS), and both cell lines underwent endoreduplication after Nutlin-3a removal. Endoreduplication gave rise to stable tetraploid clones resistant to therapy-induced apoptosis. Prior knowledge of whether cells are susceptible to Nutlin-induced endoreduplication and therapy resistance could help direct Nutlin-3a-based therapies. In the present study, Nutlin-3a promoted a tetraploid G(1) arrest in multiple p53 wild-type cell lines. However, some cell lines underwent endoreduplication to relatively high extents after Nutlin-3a removal whereas other cell lines did not. The resistance to endoreduplication observed in some cell lines was associated with a prolonged 4N arrest after Nutlin-3a removal. Knockdown of either p53 or p21 immediately after Nutlin-3a removal could drive endoreduplication in otherwise resistant 4N cells. Finally, 4N-arrested cells retained persistent p21 expression; expressed senescence-associated beta-galactosidase; displayed an enlarged, flattened phenotype; and underwent a proliferation block that lasted at least 2 weeks after Nutlin-3a removal. These findings demonstrate that transient Nutlin-3a treatment can promote an apparently permanent proliferative block in 4N cells of certain cell lines associated with persistent p21 expression and resistance to endoreduplication.
Differentiation Therapy Exerts Antitumor Effects on Stem-like Glioma Cells (2010)

Altogether, these results highlight the potential of differentiation treatment to target the stem-like cell population in glioblastoma.
Role of the Mitogen-Activated Protein Kinase Signaling Pathway in the Regulation of Human Melanocytic Antigen Expression (2006)

Heterogeneous expression of melanocytic antigens occurs frequently in melanomas and represents a potent barrier to immunotherapy. We previously showed that coordinated losses of several melanocytic antigens are generally attributable to down-regulation of antigen gene expression rather than irreversible mutation. Treatment of melanoma cells with mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase (MEK) inhibitors blocks ERK activation and increases steady-state levels of mRNAs and corresponding protein expression for the melanocytic antigens Melan-A/MART-1, gp100, and tyrosinase. Although the degree of MEK inhibitor enhancement of antigen expression varied among different cell lines irrespective of their antigen expression status, all showed detectable responses. Notably, the antigen-enhancing effects of the MEK inhibitors could not be attributed to the master melanocytic regulator MITF-M. Because MAPK pathway activation via constitutively active mutant forms of BRAF is common in melanomas, correlation between BRAF function and antigen expression was investigated. No simple correlation of endogenous BRAF mutational status and antigen levels was observed, but transient overexpression of V600E BRAF increased ERK activation and reduced Melan-A/MART-1 levels in antigen-positive cell lines. These data indicate that whereas multiple factors may regulate antigen expression in melanomas, enhancement of MAPK signaling can act as a negative influence. Blocking such signaling with MEK inhibitors accordingly augments antigen levels, thereby enhancing Melan-A/MART-1-specific cytotoxic T-cell responses to antigen-negative cells following MEK inhibition treatment. Consequently, MAPK inhibition may assist targeting of melanomas for immunotherapy.
ZitB (YbgR), a Member of the Cation Diffusion Facilitator Family, Is an Additional Zinc Transporter in Escherichia coli (2001)

The Escherichia coli zitB gene encodes a Zn(II) transporter belonging to the cation diffusion facilitator family. ZitB is specifically induced by zinc. ZitB expression on a plasmid rendered zntA-disrupted E. coli cells more resistant to zinc, and the cells exhibited reduced accumulation of (65)Zn, suggesting ZitB-mediated efflux of zinc.
Correction of diabetic alterations by glucokinase. (1996)

Hyperglycemia is a common feature of diabetes mellitus. It results from a decrease in glucose utilization by the liver and peripheral tissues and an increase in hepatic glucose production. Glucose phosphorylation by glucokinase is an initial event in glucose metabolism by the liver. However, glucokinase gene expression is very low in diabetic animals. Transgenic mice expressing the P-enolpyruvate carboxykinase/glucokinase chimeric gene were generated to study whether the return of the expression of glucokinase in the liver of diabetic mice might prevent metabolic alterations. In contrast to nontransgenic mice treated with streptozotocin, mice with the transgene previously treated with streptozotocin showed high levels of both glucokinase mRNA and its enzyme activity in the liver, which were associated with an increase in intracellular levels of glucose 6-phosphate and glycogen. The liver of these mice also showed an increase in pyruvate kinase activity and lactate production. Furthermore, normalization of both the expression of genes involved in gluconeogenesis and ketogenesis in the liver and the production of glucose and ketone body by hepatocytes in primary culture were observed in streptozotocin-treated transgenic mice. Thus, glycolysis was induced while gluconeogenesis and ketogenesis were blocked in the liver of diabetic mice expressing glucokinase. This was associated with normalization of blood glucose, ketone bodies, triglycerides, and free fatty acids even in the absence of insulin. These results suggest that the expression of glucokinase during diabetes might be a new approach to the normalization of hyperglycemia.
Considering Therapeutic Antibodies (2006)

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Galactolipase and chilling sensitivity of plants. (1997)

Galactolipase is a lipid acyl hydrolase (EC 3.1.1.26) acting predominantly on galactolipids which constitute up to 80% of total acyl lipids in chloroplast membrane. Evidence is presented on the involvement of this enzyme in plant response to chilling via degradation of membrane lipids and the increase of free fatty acids, associated with reduced oxygen evolution in the Hill reaction. The occurrence of two pools of fatty acids has been hypothesized. Analysis of numerous plant species showed higher galactolipase activity in the chilling-sensitive than in the chilling-resistant plants. Differences in the pH-dependence curve and in the response to detergents of galactolipases from these two groups of plants suggest heterogeneity of the enzyme. Referring to the hypothesis concerning the role of high melting-point fatty acids of phosphatidylglicerol molecular species in chilling sensitivity the data are presented against generalization of this hypothesis.
Clinical and immune responses in advanced colorectal cancer patients treated with anti-idiotype monoclonal antibody vaccine that mimics the carcinoembryonic antigen. (1997)

Carcinoembryonic antigen (CEA) is expressed in a wide variety of adenocarcinomas, and it is well recognized that cancer patients are immunologically "tolerant" to CEA. The purpose of this study was to determine whether we could break immune tolerance to CEA by vaccinating patients with a monoclonal anti-idiotype antibody that is the internal image of CEA and to determine what impact this might have on patient survival. Twenty-four patients with advanced CEA-positive colorectal cancer who failed standard therapies except for two were entered into this Phase Ib trial. One patient was considered not assessable, because on the day of entering into the study, she was diagnosed with acute myelogenous leukemia. Patients were treated with 1, 2, or 4 mg of aluminum hydroxide-precipitated 3H1 anti-idiotype antibody every other week for four injections and then monthly until tumor progression was observed. Immunological monitoring included humoral and cellular idiotypic and CEA responses, and all patients were evaluated for toxicity, response, and survival. Hyperimmune sera from 17 of 23 patients demonstrated an anti-anti-idiotypic Ab3 response, and 13 of these responses were demonstrated to be true anti-CEA responses (Ab1'). The antibody response was polyclonal, and 11 mediated antibody-dependent cellular cytotoxicity. Ten patients had idiotypic T-cell responses, and five had specific T-cell responses to CEA. None of the patients had objective clinical responses, but overall median survival for the 23 evaluable patients was 11.3 months, with 44% 1-year survival (95% confidence interval, 23-64%). Toxicity was limited to local swelling and minimal pain. Anti-idiotype monoclonal antibody 3H1 that mimics CEA was able to break immune tolerance in the majority of treated patients. Overall survival of 11.3 months was comparable to other phase II data with advanced colorectal cancer patients treated with a variety of chemotherapy agents, including irinotecan, with considerably less toxicity. Although it is not clear that the vaccine itself had an impact on survival, this should be determined in a Phase III randomized trial.
A Perceptually-Based Interactive and Immersive Story Environment (1999)

The KidsRoom is a perceptually-based, interactive, narrative playspace for children. Images, music, narration, light, and sound effects are used to transform a normal child's bedroom into a fantasy land where children are guided through a reactive adventure story. The fully automated system was designed with the following goals: (1) to keep the focus of user action and interaction in the physical and not virtual space; (2) to permit multiple, collaborating people to simultaneously engage in an interactive expe- rience combining both real and virtual objects; (3) to use computer-vision algorithms to identify activity in the space without requiring the participants to wear any special clothing or devices; (4) to use narrative to constrain the perceptual recognition, and to use perceptual recognition to allow participants to drive the narrative; and (5) to cre- ate a truly immersive and interactive room environment. We believe the KidsRoom is the first multi-person, fully-automated, interactive, narrative environment ever constructed using non-encumbering sensors. This paper describes the KidsRoom, the technology that makes it work, and the issues that were raised during the system's development. 1
An object oriented approach to multidimensional database conceptual modeling (OOMD) (1998)

Article Free Access Share on An object oriented approach to multidimensional database conceptual modeling (OOMD) Authors: J. Trujillo Grupo de Programación Lógica y Sistemas de Información, Dpto. Economia Financiera, Universidad de Alicante, E-03071, Alicante, Spain Grupo de Programación Lógica y Sistemas de Información, Dpto. Economia Financiera, Universidad de Alicante, E-03071, Alicante, SpainView Profile , M. Palomar Grupo de Programación Lógica y Sistemas de Información, Dpto. Lenguajes y Sistemas Informáticos, Universidad de Alicante, E-03071, Alicante, Spain Grupo de Programación Lógica y Sistemas de Información, Dpto. Lenguajes y Sistemas Informáticos, Universidad de Alicante, E-03071, Alicante, SpainView Profile Authors Info & Claims DOLAP '98: Proceedings of the 1st ACM international workshop on Data warehousing and OLAPNovember 1998 Pages 16–21https://doi.org/10.1145/294260.294266Published:01 November 1998Publication History 25citation861DownloadsMetricsTotal Citations25Total Downloads861Last 12 Months46Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
THE PROTEIN TOLERANCE OF VERY LOW BIRTH WEIGHT INFANTS FED HUMAN MILK PROTEIN ENRICHED MOTHER'S MILK (1982)

Pooled breast milk was ultra-filtrated and freeze-dried to give a product with a protein content of 60 g/100 g powder. More than half of the secretory IgA activity against E. coli O antigen was preserved. This concentrated protein was added to the mother's fresh milk providing a protein supply of 3.0-3.5 g/kg/24 hours in four VLBW infants, at a calorie supply of 110 kcal/kg/24 hours. Growth followed the intrauterine rate. Free amino acid levels, acid-base balance and urea concentrations of peripheral whole blood indicated tolerance of the increased supply of human milk protein.
PREPARATION OF SUSTAINED-RELEASE MATRIX TABLETS OF ASPIRIN WITH ETHYLCELLULOSE, EUDRAGIT RS100 AND EUDRAGIT S100 AND STUDYING THE RELEASE PROFILES AND THEIR SENSITIVITY TO TABLET HARDNESS (2003)

A sustained-release tablet formulation should ideally have a proper release profile insensitive to moderate changes in tablet hardness that is usually encountered in manufacturing. In this study, matrix aspirin (acetylsalicylic acid) tablets with ethylcellulose (EC), Eudragit RS100 (RS), and Eudragit S100 (S) were prepared by direct compression. The release behaviors were then studied in two counterpart series of tablets with hardness difference of three Kp units, and compared by non-linear regression analysis. The release pattern for both the S-containing and RS-containing formulations fitted best in Higuchi model, and the proper equations were suggested. In the EC-containing formulation, Higuchi and also zero-order models were probable models for the release, and a combination equation for the release was suggested. In the Scontaining formulation, the release profile was completely sensitive to the hardness change. In RS-containing series, the slope of the release graph did not change due to the hardness decrease, but the y-intercept or the lag time in release was decreased. In EC-containing matrix tablets, both the slopes and the y-intercepts did not change by the decrease in hardness. In conclusion, EC with an amount as little as 10 percent in formulation could make sustained-release aspirin tablets in which the release profile is not sensitive to moderate changes in hardness.
Achieving Controlled Biomolecule–Biomaterial Conjugation (2018)

The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.