gebhart/patrepeval huggingface dataset:
Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. (1991)

We have developed a strategy for the rapid enrichment and identification of cDNAs encoded by large genomic regions. The basis of this "direct selection" scheme is the hybridization of an entire library of cDNAs to an immobilized genomic clone. Nonspecific hybrids are eliminated and selected cDNAs are eluted. These molecules are then amplified and are either cloned or subjected to further selection/amplification cycles. This scheme was tested using a 550-kilobase yeast artificial chromosome clone that contains the EPO gene. Using this clone and a fetal kidney cDNA library, we have achieved a 1000-fold enrichment of EPO cDNAs in one cycle of enrichment. More significantly, we have further investigated one of the "anonymous" cDNAs that was selectively enriched. We confirmed that this cDNA was encoded by the yeast artificial chromosome. Its frequency in the starting library was 1 in 1 x 10(5) cDNAs and after selection comprised 2% of the selected library. DNA sequence analysis of this cDNA and of the yeast artificial chromosome clone revealed that this gene encodes the beta 2 subunit of the human guanine nucleotide-binding regulatory proteins. Restriction mapping and hybridization data position this gene (GNB2) to within 30-70 kilobases of the EPO gene. The selective isolation and mapping of GNB2 confirms the feasibility of this direct selection strategy and suggests that it will be useful for the rapid isolation of cDNAs, including disease-related genes, across extensive portions of the human genome.
Heterozygosity for Lmna deficiency eliminates the progeria-like phenotypes in Zmpste24 -deficient mice (2004)

Zmpste24 is a metalloproteinase required for the processing of prelamin A to lamin A, a structural component of the nuclear lamina. Zmpste24 deficiency results in the accumulation of prelamin A within cells, a complete loss of mature lamin A, and misshapen nuclear envelopes. Zmpste24-deficient (Zmpste24(-/-)) mice exhibit retarded growth, alopecia, micrognathia, dental abnormalities, osteolytic lesions in bones, and osteoporosis, which are phenotypes shared with Hutchinson-Gilford progeria syndrome, a human disease caused by the synthesis of a mutant prelamin A that cannot undergo processing to lamin A. Zmpste24(-/-) mice also develop muscle weakness. We hypothesized that prelamin A might be toxic and that its accumulation in Zmpste24(-/-) mice is responsible for all of the disease phenotypes. We further hypothesized that Zmpste24(-/-) mice with half-normal levels of prelamin A (Zmpste24(-/-) mice with one Lmna knockout allele) would be subjected to less toxicity and be protected from disease. Thus, we bred and analyzed Zmpste24(-/-)Lmna(+/-) mice. As expected, prelamin A levels in Zmpste24(-/-)Lmna(+/-) cells were significantly reduced. Zmpste24(-/-)Lmna(+/-) mice were entirely normal, lacking all disease phenotypes, and misshapen nuclei were less frequent in Zmpste24(-/-)Lmna(+/-) cells than in Zmpste24(-/-) cells. These data suggest that prelamin A is toxic and that reducing its levels by as little as 50% provides striking protection from disease.
Influence of genetic background and age on the expression of the obese hyperglycaemic syndrome in Aston ob/ob mice. (1982)

Expression of the obese hyperglycaemic (bo/ob) syndrome in mice is modified by the background genome. The Aston colony carries the ob gene on a mixed background which produces a unique combination of different features shown by ob/ob mice on other backgrounds. The maximum body weight of Aston ob/ob mice exceeded that of other colonies, possibly reflecting a trait for higher growth rate in the background genome. The hyperphagia, marked hyperinsulinaemia and moderate hyperglycaemia observed during the development of the syndrome receded in old mice. Plasma glucagon concentrations in the fed state were similar to +/+ mice and did nor Vary throughout life. Hyperplasia of the B-cells increased inordinately during the development of the syndrome, but declined in older mice coincident with progressive intercellular vacuolation and the appearance of acinar-like cells within the islets. A-cell hyperplasia was greater in young mice, and A-cells became relocated throughout the islets of older mice. The distinct pattern of age-related changes in ob/ob mice indicates that experiments using this gene type should define clearly their age as well as genetic background.
Advances in optical fiber Bragg grating sensor technologies (2012)

The authors review their recent advances in the development of optical fiber Bragg grating (FBG) sensor technologies. After a brief review of the fiber grating sensors, several newly developed FBG sensors are described. With the continuous development of fiber materials, microstructures and post-processing technologies, FBG sensors are still creative after the first demonstration of permanent gratings thirty years ago.
Retrovirally Delivered Random Cyclic Peptide Libraries Yield Inhibitors of Interleukin-4 Signaling in Human B Cells (2002)

Inteins are polypeptide sequences found in a small set of primarily bacterial proteins that promote the splicing of flanking pre-protein sequences to generate mature protein products. Inteins can be engineered in a "split and inverted" configuration such that the protein splicing product is a cyclic polypeptide consisting of the sequence linking two intein subdomains. We have engineered a split intein into a retroviral expression system to enable the intracellular delivery of a library of random cyclic peptides in human cells. Cyclization of peptides could be detected in cell lysates using mass spectrometry. A functional genetic screen to identify 5-amino acid-long cyclic peptides that block interleukin-4 mediated IgE class switching in B cells yielded 13 peptides that selectively inhibited germ line epsilon transcription. These results demonstrate the generation of cyclic peptide libraries in human cells and the power of functional screening to rapidly identify biologically active peptides.
Word Polysemy: A Cognitive Perspective (2010)

Word polysemy is a pervasive phenomenon in all languages. The phenomenon of word polysemy reveals the economy of human language. What are the principles that relate the meanings of polysemous word? How can people understand word polysemy? This paper aims at the investigation of the mechanism of polysemy, so as to build up a new system for the network of meanings based on category prototype, metonymy and metaphor and try to explain how the same word acquires different senses, which in turn can provide an efficient way of English word study and English teaching.
Condensed Phase Relations in the Systems ZrO 2 ‐WO 2 ‐WO 3 and HfO 2 ‐WO 2 ‐WO 3 (1967)

Phase relations for the systems ZrO 2 –WO 2 –WO 3 and HfO 2 –WO 2 –WO 3 from 1000° to 1700° C were determined by the quenching technique using sealed sample containers. In the system ZrO 2 –WO 3 , 1:2 compound, ZrW 2 O 8 forms, having a cubic structure with a = 9.159 A. The ZrW 2 O 8 melts incongruently at 1257°± 3°C to ZrO 2 and liquid and has a lower limit of stability at 1105°C, below which ZrO 2 and WO 3 coexist in equilibrium. One eutectic and one peritectic were established: at 1231°± 3°C and 74 mole % WO 3 , and at 1257°± 3°C and 71 mole % WO 3 , respectively. Along the join ZrO 2 –WO 2 , no compound formed. Two invariant points were determined: ZrO 2 , WO 2 , W, and liquid are in equilibrium at 1430°± 5°C and 76 mole % WO 2 , whereas WO 2 , W 18 O 49 , W, and liquid coexist at 1530°± 5°C and 89 mole % WO 2 ‐ Equilibrium relations in the system ZrO 2 –WO 2 –WO 3 were investigated at four temperatures. At 1200°C, a cubic phase with composition near W 20 O 58 was found; it exists in equilibrium with ZrO 2 , W 18 O 49 , W 20 O 58 , and WO 3 . As the temperature increases, the liquid formed along the ZrO 2 –WO 3 join extends into the ternary system, crosses the join ZrO 2 –W 20 O 58 at 1300°C, and crosses the join ZrO 2 –W 18 O 49 at 1400°C. The cubic phase can take more zirconium into its solid solution at 1300° than at 1200°C. At 1500°C, the system can no longer be treated as a simple ternary oxide system because of the presence of metallic tungsten, and equilibrium relations are presented on the basis of the system ZrO 2 –W–WO 3 . Phase equilibrium relations in the systems HfO 2 –WO 3 , HfO 2 –WO 2 , and HfO 2 –WO 2 –WO 3 in the temperature ranges studied are much like those in the corresponding zirconium system.
Molecular characterization of a mouse prostaglandin D receptor and functional expression of the cloned gene. (1994)

Prostanoid receptors belong to the family of G protein-coupled receptors with seven transmembrane domains. By taking advantage of nucleotide sequence homology among the prostanoid receptors, we have isolated and identified a cDNA fragment and its gene encoding a mouse prostaglandin (PG) D receptor by reverse transcription polymerase chain reaction and gene cloning. This gene codes for a polypeptide of 357 amino acids, with a calculated molecular weight of 40,012. The deduced amino acid sequence has a high degree of similarity with the mouse PGI receptor and the EP2 subtype of the PGE receptor, which together form a subgroup of the prostanoid receptors. Chinese hamster ovary cells stably expressing the gene showed a single class of binding sites for [#H]PGD2 with a Kd of 40 nM. This binding was displaced by unlabeled ligands in the following order: PGD2 > BW 245C (a PGD agonist) > BW A868C (a PGD antagonist) > STA2 (a thromboxane A2 agonist). PGE2, PGF2 alpha, and iloprost showed little displacement activity at concentrations up to 10 microM. PGD2 and BW 245C also increased cAMP levels in Chinese hamster ovary cells expressing the receptor, in a concentration-dependent manner. BW A868C showed a partial agonist activity in the cAMP assay. Northern blotting analysis with mouse poly(A)+ RNA identified a major mRNA species of 3.5 kb that was most abundantly expressed in the ileum, followed by lung, stomach, and uterus.
IL4Rα+ Myeloid-Derived Suppressor Cell Expansion in Cancer Patients (2009)

Myeloid-derived suppressor cells (MDSC) contribute to immune dysfunctions induced by tumors both in experimental models and patients. In mice, MDSC are phenotypically heterogeneous cells that vary in their surface markers, likely depending on soluble factors produced by different tumors. We recently described a subset of inflammatory monocytes with immunosuppressive properties that can be found within the tumor mass, blood, and lymphoid organs of tumor-bearing mice. These cells expressed the alpha-chain of the receptor for IL-4 (IL4Ralpha) that was critical for their negative activity on CD8(+) T cells. In cancer patients, the nature of MDSC is still poorly defined because evidence exists for both monocytic and granulocytic features. We show in this study that myeloid cells with immunosuppressive properties accumulate both in mononuclear and polymorphonuclear fractions of circulating blood leukocytes of patients with colon cancer and melanoma, thus unveiling a generalized alteration in the homeostasis of the myeloid compartment. Similarly to mouse MDSC, IL4Ralpha is up-regulated in both myeloid populations but its presence correlates with an immunosuppressive phenotype only when mononuclear cells, but not granulocytes, of tumor-bearing patients are considered.
Carbohydrate residues modulate the activation of coagulation factor X. (1993)

Factor X is a plasma protein involved in both the intrinsic and extrinsic pathways of blood coagulation. Post-translational modifications of the protein involve gamma-carboxylation of specific glutamic acid residues, beta-hydroxylation of one aspartic acid residue, and N- and O-linked glycosylation. Even though it is known that gamma-carboxylation is instrumental in regulating biological activity, the role of glycosylation in the function and properties of factor X has not been previously investigated. We utilized lectin binding and glycosidase treatment to investigate the functional role of carbohydrates on the activation peptide of factor X. Sambucus nigra agglutinin, a lectin that binds to sialic acid terminally linked alpha(2-6) to galactose or N-acetyl-galactosamine inhibits activation of human factor X in a dose-dependent manner. Inhibition of activation was observed for both intrinsic (factor IXa/VIIIa) and extrinsic (factor VIIa/tissue factor) pathway complexes. In accordance with this, selective removal of sialic acid residues on the activation peptide of factor X by neuraminidase also results in a drastic reduction of activation of the zymogen by these complexes. Corresponding reduction of activity in classical clotting assays (activated partial thromboplastin time and prothrombin time) also agrees with this observation. These results suggest a possible role of N-linked carbohydrates in the activation of factor X.
Photonic crystal laser sources for chemical detection (2003)

We have realized photonic crystal lasers that permit the introduction of analyte within the peak of the optical field of the lasing mode. We have explored the design compromises for developing such sensitive low-threshold spectroscopy sources, and demonstrate the operation of photonic crystal lasers in different ambient organic solutions. We show that nanocavity lasers can be used to perform spectroscopic tests on femtoliter volumes of analyte, and propose to use these lasers for high-resolution spectroscopy with single-molecule sensitivity.
patient tracking for video/EEG monitoring based on change detection in DCT domain (2005)

Video/EEG monitoring is an important application for diagnosis of epilepsy patient. During the recording, the camera needs to be manually controlled to cover the patient. As the recording procedure is usually extensive in time, automatic tracking of the patient is a practical need. In this paper, we present a tracking method based on change detection techniques. Movements of the subject are detected and utilized to determine the subject's location. The proposed change detection algorithm is carried out in DCT domain to handle video in a compressed format. Promising results have been obtained from simulation experiments.
Poly(ethylene glycol) Hydrogel System Supports Preadipocyte Viability, Adhesion, and Proliferation (2005)

The ultimate goal of this research is to develop an injectable cell-scaffold system capable of permitting adipogenesis to abrogate soft tissue deficiencies resulting from trauma, tumor resection, and congenital abnormalities. The present work compares the efficacy of photopolymerizable poly(ethylene glycol) and specific derivatives as a scaffold for preadipocyte (adipocyte precursor cell) viability, adhesion, and proliferation. Four variations of a poly(ethylene glycol) scaffold are prepared and examined. The first scaffold consists of poly(ethylene glycol) diacrylate, which is not susceptible to hydrolysis or enzymatic degradation. Preadipocyte death is observed over 1 week in this hydrogel configuration. Adhesion sites, specifically the laminin-binding peptide sequence YIGSR, were incorporated into the second scaffold to promote cellular adhesion as a prerequisite for preadipocyte proliferation. Preadipocytes remain viable in this scaffold system, but do not proliferate in this nondegradable hydrogel. The third scaffold system studied consists of poly(ethylene glycol) modified with the peptide sequence LGPA to permit polymer degradation by cell-secreted collagenase. No adhesion peptide is incorporated into this scaffold system. Cellular proliferation is initially observed, followed by cell death. The previous three scaffold configurations do not permit preadipocyte adhesion and proliferation. In contrast, the fourth system studied, poly(ethylene glycol) modified to incorporate both LGPA and YIGSR, permits preadipocyte adherence and proliferation subsequent to polymer degradation. Our results indicate that a scaffold system containing specific degradation sites and cell adhesion ligands permits cells to adhere and proliferate, thus providing a potential cell-scaffold system for adipogenesis.
Solvent and pH resistance of surface crosslinked chitosan/poly(acrylonitrile) composite nanofiltration membranes (2000)

The resistance of novel surface crosslinked Chitosan/poly(acrylonitrile) (PAN) composite nanofiltration (NF) membranes to pH and organic solvents was studied with respect to the effects of crosslinking parameters, namely, glutaraldehyde concentration and crosslinking time. The pH resistance was determined by permeation of aqueous acidic (pH 2.5) and basic (pH 11) solutions as well as swelling studies in the pH range of 2.5–11. The solvent resistance was determined by swelling, immersion, and permeation studies with several industrially important organic solvents, namely methanol, ethanol, iso-propanol, methyl ethyl ketone, ethyl acetate and hexane. It was observed that the crosslinked composite membranes maintain the permeate fluxes for test solvents for 2 h of continuous operation without any significant change in flux. SEM studies on membrane samples after immersion as well as permeation with the above-mentioned solvents indicated that the membrane morphology was maintained. The results are explained in terms of solvent–membrane polar and hydrophobic interactions, using solubility parameters of membrane and solvents and dielectric constants of solvents. Pure water flux and polyethylene glycol transmission data indicated that at pH 2.5 and 11, the membrane stability increased with increasing glutaraldehyde concentration and was much better at pH 11 than at pH 2.5. All surface crosslinked membranes showed reduced swelling between pH 4–10. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 1782–1793, 2000
Anti-PD-1 antibodies for the treatment of B-cell lymphoma (2014)

Monoclonal antibodies specific for programmed cell death 1 (PDCD1, best known as PD-1) have been shown to mediate antineoplastic effects in follicular lymphoma patients. However, the relative proportion of intratumoral PD-1<sup>+</sup> T-cell subsets, in particular follicular helper T cells (which exert pro-tumor functions) and effector T cells (which have anticancer activity), may impact clinical outcome, and should therefore be carefully considered for patient selection in this setting.
Line Probe Assay for Detection of Human Immunodeficiency Virus Type 1 Mutations Conferring Resistance to Nucleoside Inhibitors of Reverse Transcriptase: Comparison with Sequence Analysis (1998)

We compared the line probe assay (LiPA) to sequence analysis for the detection of mutations conferring resistance to nucleoside inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Plasma samples from 40 patients who had received zidovudine, dideoxyinosine, and dideoxycytosine, alone or in combination, and who were enrolled in the ALTIS 2 clinical trial (lamivudine [3TC] plus stavudine) were tested at enrollment and at week 24. RT PCR products from plasma were used for LiPA, and DNA was used for sequence analysis. LiPA gave uninterpretable results for 8.5% of the analyzed codons corresponding to 63 samples, mainly for codons 41, 69, and 70. Several minor discrepancies between the two methods occurred, mainly due to the ability of LiPA to detect mixed populations while sequence analyses detect a single homogeneous population. LiPA is suitable for detecting mixed populations and easy to implement in clinical laboratories and might be useful for epidemiological surveys of primary HIV-1 resistance.
Mutational analysis of vaccinia virus topoisomerase identifies residues involved in DNA binding (1997)

Vaccinia DNA topoisomerase catalyzes the cleavage and re-joining of DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate formed at a specific target sequence, 5'-(C/T)CCTT downward arrow. The 314 aa protein consists of three protease-resistant structural domains demarcated by protease-sensitive interdomain segments referred to as the bridge and the hinge. The bridge is defined by trypsin-accessible sites at Arg80, Lys83 and Arg84. Photocrosslinking and proteolytic footprinting experiments suggest that residues near the interdomain bridge interact with DNA. To assess the contributions of specific amino acids to DNA binding and transesterification chemistry, we introduced alanine substitutions at 16 positions within a 24 aa segment from residues 63 to 86(DSKGRRQYFYGKMHVQNRNAKRDR). Assays of the rates of DNA relaxation under conditions optimal for the wild-type topoisomerase revealed significant mutational effects at six positions; Arg67, Tyr70, Tyr72, Arg80, Arg84 and Asp85. The mutated proteins displayed normal or near-normal rates of single-turnover transesterification to DNA. The effects of amino acid substitutions on DNA binding were evinced by inhibition of covalent adduct formation in the presence of salt and magnesium. The mutant enzymes also displayed diminished affinity for a subset of cleavage sites in pUC19 DNA. Tyr70 and Tyr72 were subjected to further analysis by replacement with Phe, His, Gln and Arg. At both positions, the aromatic moiety was important for DNA binding.
Rapid Preparation of Fluorinated Aromatic Heterocycles (2009)

Nucleophilic aromatic substitution (SNAr) reactions are typically used for fluoride introduction into heterocyclic aromatic compounds, but substitution occurs sluggishly with unactivated substrates. This chapter discusses new reagents and methods for fluorination of key heterocyclic pharmacophores. Purines, pyrimidines, pyridines, and even imidazoles are fluorinated readily with anhydrous tetralkylammonium fluorides in DMSO. Though the tetraalkylammonium fluoride reagents themselves are prone to decomposition, the presence of substrate protects these fragile reagents and permits rapid fluorination of relatively reluctant substrates at high temperature. Use of anhydrous fluorinating reagents in radiochemistry is facilitated by a fluoride-relay process that quickly converts hydrated potassium fluoride into anhydrous, exceptionally nucleophilic tetraalkylammonium fluorides.
Complementation of the ionizing radiation sensitivity, DNA end binding, and V(D)J recombination defects of double-strand break repair mutants by the p86 Ku autoantigen. (1995)

Two ionizing radiation-sensitive (IRs) and DNA double-strand break (DSB) mutants, sxi-3 and sxi-2, were shown to be severely deficient in a DNA end binding activity, similar to a previously described activity of the Ku autoantigen, correlating with the xrs (XRCC5) mutations. Cell fusions with xrs-6, another IRs, DSB repair-deficient cell line, defined these sxi mutants in the XRCC5 group. sxi-3 cells have low expression levels of the p86Ku mRNA. Introduction of the Ku p86 gene, but not the p70 Ku gene, complemented the IRs, DNA end binding, and variable (diversity) joining [V(D)J] recombination signal and coding junction deficiencies of sxi-3. Thus, the p86 Ku gene product is essential for DSB repair and V(D)J recombination.
Multiple cis Regulatory Elements for Maximal Expression of the Cauliflower Mosaic Virus 35S Promoter in Transgenic Plants (1989)

Rong-Xiang Fang, Ferenc Nagy, Shanthi Sivasubramaniam, Nam-Hai Chua, Multiple cis Regulatory Elements for Maximal Expression of the Cauliflower Mosaic Virus 35S Promoter in Transgenic Plants, The Plant Cell, Vol. 1, No. 1 (Jan., 1989), pp. 141-150