gebhart/patrepeval huggingface dataset:
Involvement of T44 molecules in an antigen-independent pathway of T cell activation. Analysis of the correlations to the T cell antigen-receptor complex. (1985)

Prior studies indicate that the 9.3 monoclonal antibody (mAb) which defines a 44 kD T lineage-specific glycoprotein (T44) enhances the proliferative response of peripheral blood T lymphocytes to phytohemagglutinin (PHA) or allogeneic cells. The T44 molecule was expressed in both resting and activated T lymphocytes and in a subset of thymocytes, as assessed by indirect immunofluorescence and flow cytofluorometry. In view of the potential importance of T44 in T cell activation, we investigated the ability of the 9.3 (anti-T44) antibody to stimulate peripheral blood T lymphocytes under culture conditions giving optimal proliferative responses to anti-T3 mAb. Like UCHT1 (anti-T3) mAb, the 9.3 (anti-T44 mAb) promoted strong proliferative responses of purified T cells, provided that adherent cells were added to the culture. Maximal proliferation in response to 9.3 antibody was consistently detected at day 5 (at day 3 with anti-T3 or PHA). Moreover, triggering of T lymphocytes with 9.3 antibody (in the presence of adherent cells) resulted in strong IL-2 production that peaked at 48 h. Analysis of the physical and functional relationship between the T44 molecule and other molecules involved in T cell activation, including the clonotypically restricted Ti and the monomorphic T3 or T11 molecules, was carried out on a mutagenized jurkat T leukemia cell line. This mutant, termed JA3 (surface phenotype: T11+, T3+, 3A1+, T4-, T8-, DR-, Tac-, 4F2+, T44+) produced large amounts of IL-2 upon stimulation with PHA, anti-T3, or anticlonotypic mAb in conjunction with phorbol myristate acetate (or adherent cells). The molecules precipitated by anti-T44 mAb from 125I-labeled JA3 cells appeared as a diffuse band of Mr 40-45,000 under reducing conditions; under nonreducing conditions, a prominent band of Mr 80-85,000 was observed, while the Mr 40-45,000 band was greatly reduced. Thus, T44 molecules in both reducing and nonreducing conditions had relative molecular weights similar to that of molecules carrying clonotypic (Ti) determinants. In addition, like anti-Ti or anti-T3 mAb, anti-T44 antibody induced JA3 cells to produce large amounts of IL-2 in the presence of phorbol myristate acetate. Other similarities between T44 and molecules carrying clonotypic structures included the susceptibility to antibody-induced modulation and the late reexpression (72 h) at the cell surface after modulation. Taken together, these experiments suggest that anti-T44 mAb might recognize a monomorphic determinant of the T cell receptor molecule or be physically or functionally linked to the T3-Ti complex.(ABSTRACT TRUNCATED AT 400 WORDS)
Abstract 1853: Single-cell multiplexed profiling of protein-level changes induced by EGFR inhibitor gefitinib (2016)

Abstract Single-cell molecular analysis has become increasingly important in biomedical research, especially in the field of cancer research, where cell heterogeneity is a characteristic feature. We developed a multiplexed single-cell protein detection assay for the C1™ system that can isolate and process 96 individual cells in parallel. The assay uses oligonucleotide-conjugated antibodies, which produce a detectable DNA amplicon only when they bind to the target protein. The resulting DNA amplicons are quantified by qPCR on the Biomark™ HD system. Data are analyzed using the Singular™ Analysis Toolset. A total of 50 antibody binders were developed for this assay to target proteins related to apoptosis, cell cycle, cell proliferation, tumor suppressors, biomarkers, stem cells, growth factors and proteins associated with specific cancers, such as breast and prostate cancers. The assay can be performed in a 48-plex format, which yields over 4,600 datapoints in two days. Assay sensitivity and specificity were assessed using recombinant proteins and various cell lysates. To demonstrate the usefulness of this assay, we used it to profile the protein level changes in A431 cells treated with epidermal growth factor receptor (EGFR) inhibitor gefitinib. EGFR is a member of ErbB family of type I tyrosine kinases, whose overexpression and mutations are involved in a variety of cancers. While much effort has been made to investigate the consequences of EGFR activation or inhibition, hardly any information is available regarding how EGFR regulation changes protein expression in single cells. Using a multiplexed protein assay, we discovered some interesting co-expression patterns of proteins in single cells. We also demonstrated that TNFRSF10B was upregulated, while MET, GATA3, BRCA1, CCNB1, Ki-67 and CCNA2 were downregulated by gefitinib treatment. Notably, the reduction of the cell cycle-related proteins CCNB1 and CCNA2 and the cell proliferation marker Ki-67 was consistent with the inhibited cell growth by gefitinib. In addition, we measured mRNA expression to investigate the association between protein and mRNA levels in single cells. Single-cell analysis—determining protein changes and analyzing the correlation between different proteins at the single-cell level—yields valuable information that is not achievable using bulk-cell analysis. Citation Format: Ilona Holcomb, Gajalakshmi Dakshinamoorthy, Benjamin Liu, Marc Unger, Ramesh Ramakrishnan, Haibiao Gong. Single-cell multiplexed profiling of protein-level changes induced by EGFR inhibitor gefitinib. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1853.
Regioselectivity Control in Diels−Alder Reactions of Surfactant 1,3-Dienes with Surfactant Dienophiles (2000)

The ability of surfactant aggregate−H2O interfaces to control the regioselectivity of Diels−Alder reactions has been investigated. Cycloadditions of surfactant 1,3-dienes 2-[[3-(dimethyldodecylsilyl)-1,3-butadien-2-yl]thio]-N,N,N-trimethyl-1-ethanaminium iodide (1a) and 6-[[3-(dimethyloctylsilyl)-1,3-butadien-2-yl]thio]-N,N,N-trimethyl-1-hexanaminium iodide (1b) with surfactant dienophiles (E)-2-[[[2-(dodecoxycarbonyl)ethenyl]carbonyl]oxy]-N,N,N-trimethyl-1-ethanaminium iodide (2a) and (E)-6-[[[2-(octoxycarbonyl)ethenyl]carbonyl]oxy]-N,N,N-trimethyl-1-hexanaminium bromide (2b) within their aqueous mixed micelles have been performed at 25(35) °C. The cycloaddition of 1a and 2a gave a 30:1 ratio of trans-1-[(2-trimethylammonio)ethylthio]-2-(dimethyldodecylsilyl)-4-(dodecoxycarbonyl)-5-[(2-trimethylammonio)ethoxycarbonyl]-1-cyclohexene dihalide (15a) and trans-1-[(2-trimethylammonio)ethylthio]-2-(dimethyldodecylsilyl)-4-[(2-trimethylammonio)ethoxycarbonyl]-5-(dodecoxycarbonyl)-1-cyclohexene dihalide (16a), respectively, and that of 1b and 2b a 6.6:1 ratio of trans-1-[(6-trimethylammonio)hexylthio]-2-(dimethyloctylsilyl)-4-(octoxycarbonyl)-5-[6-(trimethylammonio)hexoxycarbonyl]-1-cyclohexene dihalide (15b) and trans-1-[(6-trimethylammonio)hexylthio]-2-(dimethyloctylsilyl)-4-[6-(trimethylammonio)hexoxycarbonyl]-5-(octoxycarbonyl)-1-cyclohexene dihalide (16b), respectively. The excess of 15 over 16 is consistent with the reaction of 1 and 2 within mixed aggregates in their preferred orientations at the aggregate−H2O interface. The greater regioselectivity obtained in the reaction of 1a and 2a is ascribed to the shorter tether between their reactive functional groups and quaternary ammonium headgroups. A monolayer study of 15a and 16a was also performed.
Femtosecond Laser-Assisted Corneal Flap Cuts: Morphology, Accuracy, and Histopathology (2006)

LASIK flap cuts were easily performed without any complications. The accuracy and morphology were very precise and consistent. Histopathology revealed a smooth cut with hinge angulations, as expected.
Optimization of Electrochemical Etching Parameters in Porous Silicon Layer Transfer Process for Thin Film Solar Cell (2011)

Fabrication of porous silicon(PS) double layer by electrochemical etching is the first step in process of ultrathin solar cell using PS layer transfer process. The porosity of the porous silicon layer can be controlled by regulating the formation parameters such as current density and HF concentration. PS layer is fabricated by electrochemical etching in a chemical mixture of HF and ethanol. For electrochemical etching, highly boron doped (100) oriented monocrystalline Si substrates was used. Ths resistivity of silicon is . The solution composition for electrochemical etching was HF (40%) : (99 %) : = 1 : 1 : 2 (by volume). In order to fabricate porous silicon double layer, current density was switched. By switching current density from low to high level, a high-porosity layer was fabricated beneath a low-porosity layer. Etching time affects only the depth of porous silicon layer.
The Prevalence and Etiology of Elevated Aminotransferase Levels in The United States (2003)

Chronic liver disease is a major cause of morbidity and mortality in the United States. Although often used to detect liver disease, the prevalence and etiology of elevated aminotransferases are unknown. We analyzed data on adults ages 17 yr and older (N = 15,676) from the Third National Health and Nutrition Examination Survey (1988-1994). Participants were classified as having elevated aminotransferase levels if either aspartate aminotransferase or alanine aminotransferase was elevated above normal. Aminotransferase elevation was classified as "explained" if there was laboratory evidence of hepatitis B or C infection, iron overload, or if there was a history of alcohol consumption. Analyses were weighted to provide national estimates. The prevalence of aminotransferase elevation in the United States was 7.9%. Aminotransferase elevation was more common in men compared to women (9.3% vs 6.6%, p = 0.002), in Mexican Americans (14.9%) and non-Hispanic blacks (8.1%) compared to non-Hispanic whites (7.1%, p < 0.001). High alcohol consumption, hepatitis B or C infection and high transferrin saturation were found in only 31.0% of cases. Aminotransferase elevation was unexplained in the majority (69.0%). In both men and women, unexplained aminotransferase elevation was significantly associated with higher body mass index, waist circumference, triglycerides, fasting insulin, and lower HDL; and with type 2 diabetes and hypertension in women (all p < 0.05). Aminotransferase elevation was common in the United States, and the majority could not be unexplained by alcohol consumption, viral hepatitis or hemochromatosis. Unexplained aminotransferase elevation was strongly associated with adiposity and other features of the metabolic syndrome, and thus may represent nonalcoholic fatty liver disease.
Mutational analysis of interferon (IFN) regulatory factors 1 and 2. Effects on the induction of IFN-beta gene expression (1994)

Interferon (IFN) regulatory factor 1 (IRF-1) and IRF-2 are structurally similar but functionally distinct transcription factors that bind to the positive regulatory domains I and III (PRDI/III) within the human IFN-beta promoter. To begin structure-function analysis of IRF-1 and IRF-2, the regulatory potential of carboxyl-terminal deletion mutants was analyzed by co-transfection studies in human cells and was correlated with DNA binding capacity. Transcriptional repression by IRF-2 was contained within the first 125 amino-terminal amino acids and correlated directly with IRF-2 DNA binding; deletion to a protein of 100 amino acids resulted in loss of repression and IRF-2 DNA binding. Thus, the carboxyl terminus appears dispensible for trans-repression. Hybrid constructs which fuse the DNA binding domain of IRF-1 and IRF-2 to the trans-activation domain of NF-kappa B p65 were also generated; both IRF-1/p65 and IRF-2/p65 chimeras were strong transcriptional activators. IRF-2-mediated repression was also dominant over trans-activation by these fusion proteins. The trans-activation region of IRF-1 resides in the carboxyl terminus, primarily carboxyl-terminal to amino acid 250. Mutation of three potential casein kinase II phosphorylation sites within the IRF carboxyl terminus failed to identify an essential site that contributes to IRF-1 trans-activation potential.
An object-oriented model for spatio-temporal synchronization of multimedia information (1994)

Proposes an extension to an earlier proposed temporal synchronization model, called OCPN. The new model allows one to specify spatial operations at the time of authoring the multimedia information. The authors present a mechanism to translate the model into an object-oriented environment. For this purpose the temporal operations are selected as objects. This scheme has many advantages over the existing object-oriented model since it requires fewer number of objects as well as do not limit the users to share the actual raw data. A polynomial time algorithm is proposed to translate the new OCPN into an object hierarchy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Superior Epithelial Arcuate Lesions with Soft Contact Lens Wear (2001)

The reported low incidence of SEALs is partly because SEALs are not usually symptomatic. The etiology of SEALs is multifactorial. Our current hypothesis is that SEALs are produced by mechanical chaffing at the peripheral cornea. This chaffing occurs as a result of inward pressure of the upper lid, in an area where the peripheral corneal topography and lens design, rigidity, and surface characteristics combine to create excessive "frictional" pressure and abrasive shear force on the epithelial surface. Patient characteristics such as gender, age, and specific corneal and lid topographies also appear to influence the occurrence of SEALs. Prototype silicone hydrogel lenses are made from higher modulus materials with surfaces that seem to differ subtly in wettability in some patients. The prevalence of SEALs may well increase with the first generations of these lenses.
Predicting oligomerization states of coiled coils (1995)

An algorithm based on the profile method was developed that faithfully distinguishes between the amino acid sequences of dimeric and trimeric coiled coils. Normalized sequence profiles derived from nonhomologous, two- and three-stranded, coiled-coil sequences with unambiguous registers were used to assign dimer and trimer propensities to test sequences. The difference between the dimer and trimer profile scores accurately reflected the preferred oligomerization state. The method relied on two strategies that may be generally applicable to profile calculations--profile values of solvent-exposed residues and of amino acids that were underrepresented in the data-base were given zero weight. Differences between the dimer and trimer profiles revealed sequence patterns that match and extend experimental studies of oligomer specification.
The Effect of Interface States on Single-Walled Carbon Nanotube Transistors (2016)

Different from p-type single-walled carbon nanotubes (SWCNT) thin film transistors (TFTs) with SiO2 dielectrics, air-stable top-gated n-type SWCNT TFTs are reported with amorphous silicon nitride (SiNx) dielectrics exhibiting the strong dependence of deposition methods and conditions, and metal contacts. Amorphous silicon TFTs-like characteristics was observed from semiconducting single-chirality (6,5) SWCNT TFTs with SiNx deposited at 225°C and appropriate NH3/SiH4 feeding ratio of 10 sccm/5.3 sccm using plasma enhanced chemical vapor deposition (PECVD). These results are interpreted as the effect of interface states between (6,5) SWCNT and SiNx gate dielectrics, which provide the avenue to alter the ratio of free electrons and trapped electrons along applied gate potential.
Digital Portable Transceiver Using GMSK Modem and ADM Codec (1984)

Digital mobile radio transmission techniques and integrated circuit devices have been developed for application to a digital portable transceiver utilizing narrow-band GMSK modulation and ADM voice coding. Design and performance of a quadrature type GMSK modulator and a single-chip coherent demodulator as the GMSK modem are described. To overcome slow fading, encountered in portable applications, switching diversity using a jitter detection type sensor is Proposed and shown to be effective. An experimental Portable transceiver, developed to demonstrate hardware feasibility, is also described.
The Acid-catalyzed Decomposition of Diazo Carbonyl Compounds. II. Synthesis of 2- or 5-Heteroatom-substituted Oxazoles (1984)

Abstract The BF3-catalyzed decomposition of m- and p-substituted α-diazoacetophenones in excess of methyl thiocyanate and ethyl thiocyanate gave the corresponding 2-methylthio-, and 2-ethylthio-5-aryloxazoles, respectively in good yields along with s-alkyl-n-aroylmethylthiocarbamates and α-ethoxyacetophenones. However, yields of 2-dimethylamino-5-aryloxazoles by the reaction of dimethylcyanamide with α-diazoacetophenones were poor. 5-Dimethylamino- or 5-alkoxy-4-aryl-2-methyloxazoles were prepared by the reaction of N,N-dimethyl-α-(p-nitrophenyl)diazoacetamide or alkyl aryldiazoacetates with nitriles. When ethyl phenyldiazoacetate or methyl p-chlorophenyldiazoacetate were used, ketazines of alkyl arylglyoxylates were obtained together with oxazoles.
Photoaffinity labeling and its application in structural biology (2007)

This review contains a brief consideration of some theoretical aspects of photoaffinity (photoreactive) labeling (PAL), and the most widely used photoreactive groups, such as arylazide, benzophenone, and 3-(trifluoromethyl)-3-phenyldiazirine, are characterized in comparison. Experimental methodology is described, including modern approaches of mass spectrometry for analysis of cross-linking products between the photoreactive probes and biomolecules. Examples of PAL application in diverse fields of structural biology during the last five-ten years are presented. Potential drug targets, transport processes, stereochemistry of interaction of G-protein-coupled receptors with ligands, as well as structural changes in nicotinic acetylcholine receptor are considered. Applications of photoaffinity ganglioside and phospholipid probes for studying biological membranes and of nucleotide probes in investigations of replicative and transcriptional complexes, as well as photoaffinity glycoconjugates for detecting carbohydrate-binding proteins are covered. In combination with modern techniques of instrumental analysis and computer-aided modeling, PAL remains the most important approach in studies on the organization of biological systems.
A study of proton bombardment induced swelling of GaP single crystals (1985)

On proton bombarded GaP single crystals swelling, strain, and their connection with radiation damage and implanted hydrogen are studied dependent on proton energy (Ep = 0.3 to 1.7 MeV), irradiated fluence (D = 1015 to 1019 cm−2) and annealing temperature (Tan = 300 to 720 K). To characterize these effects step height measurements, X-ray diffraction, Rutherford back-scattering, and channeling technique and particle induced γ-spectroscopy are used. An protonenbestrahlten GaP-Einkristallen wird die Volumenänderung des bestrahlten Gebiets und die Änderung des Netzebenenabstandes untersucht. Dabei wird die wechselseitige Bedingtheit dieser Effekte und ihr Bezug zur Strahlenschädigung und zum implantierten Wasserstoff in Abhängigkeit von der Protonenenergie (Ep = 0,3 bis 1,7 MeV), der implantierten Dosis (D = 1015 bis 1019 cm−2) und Ausheiltemperatur (Tan = 300 bis 720 K) betrachtet. Als Untersuchungsmethoden werden Stufenhöhenmessungen, röntgenographische Verfahren, Rutherford-Rückstreu-Kanalisierungstechnik und teilcheninduzierte γ-Spektroskopie benutzt.
Regulation of apoptosis by low serum in cells of different stages of neoplastic progression: enhanced susceptibility after loss of a senescence gene and decreased susceptibility after loss of a tumor suppressor gene. (1994)

A cell culture model system has been used to study the susceptibility of cells to apoptotic cell death during different stages of neoplastic progression. This system consists of normal diploid Syrian hamster embryo (SHE) cells, two preneoplastic cell lines [tumor suppressor stage I (sup +I) and non-tumor suppressor stage II (sup -II)], and hamster tumor cell lines. Stage I preneoplastic cells are nontumorigenic immortal clones that suppress tumorigenicity when hybridized to tumor cells, whereas stage II cells have lost the ability to suppress tumorigenicity in cell hybrids. We refer to these two types of preneoplastic cells as sup +I and sup -II, respectively. Neoplastic progression is generally associated with cellular alterations in growth factor responsiveness. Therefore, to study the regulation of apoptosis in the system described above, cells were cultured in low serum (0.2%) as a means of withdrawing growth factors. In low serum, normal SHE cells were quiescent (labeling index of 0.2%), with little cell death. The sup +I cells showed a relatively low labeling index (1.6%) but, in contrast to the normal cells, died at a high rate (55% cell loss after 48 h) by apoptosis, as evidenced by morphology, DNA fragmentation, and in situ end-labeling of fragmented DNA. The apoptotic cells did not go through a replicative cycle while in low serum, implying that apoptosis was initiated in the G0/G1 phase of the cell cycle. The sup -II cell line showed a high labeling index (40%) after 48 h, but cell growth was balanced by cell death that occurred at approximately the same rate. The cells died, however, predominantly by necrosis. The tumor cell lines continued to proliferate in low serum, with high labeling indices (ranging from 27% to 43%) and a low level of apoptotic or necrotic cell death. To determine the relative ability of these cells to survive in vivo, normal SHE cells, sup +I cells, and sup -II cells were injected s.c. into nude mice. At 5 or 21 days after injection, the normal SHE cells were readily retrieved from the mice and grew well in culture. In contrast, few sup +I cells were retrieved 5 days after injection and no viable cells were retrieved after 21 days. Sup -II cells were not retrieved at either the 5-day or 21-day harvest, and histological examinations of the sites of injection showed the presence of macrophages, eosinophils, and neutrophils, indicating an inflammatory response associated with necrotic cell death.(ABSTRACT TRUNCATED AT 400 WORDS)