gebhart/patrepeval huggingface dataset:
Cloning of a complementary DNA encoding a new mouse B lymphocyte differentiation antigen, homologous to the human B1 (CD20) antigen, and localization of the gene to chromosome 19. (1988)

The human B1 (CD20) molecule is a differentiation Ag found only on the surface of B lymphocytes. This structurally unique phosphoprotein plays a role in the regulation of human B cell proliferation and differentiation. In order to determine whether this structure is also expressed by murine B cells, cDNA clones that encode the mouse equivalent of the B1 molecule were isolated. The longest murine cDNA clone isolated, pmB1-1, contained a 1.4-kb insert with an 873 base pair open reading frame that encodes a protein of 32 kDa. The predicted mouse B1 protein contains three hydrophobic domains that may span the membrane four times and shares a 73% amino acid sequence homology with the human B1 protein. The pmB1-1 cDNA probe was used to examine mB1 mRNA expression. Northern blot analysis indicated that pmB1-1 hybridized with two mRNA species of 2.3 and 3.0 kb that were expressed only in murine spleen lymphocytes, in B lineage cell lines representing mature B cells, and were weakly expressed in one of two plasmacytoma cell lines. pmB1-1 failed to hybridize with RNA isolated from murine T cell lines, thymus, and nonlymphoid tissues. Southern blot analysis indicated that mB1 was encoded by a single copy gene. In situ hybridization localized the mB1 gene to chromosome 19 band B, a region that also contains the genes that encode the Ly-1, Ly-10, and Ly-12 Ag. These results suggest that only B cells express this heretofore undescribed murine cell-surface protein that is structurally homologous with the membrane-embedded human B1 Ag.
Piezoelectric-based tunable microstrip shunt resonator (2006)

In this work; a simple and efficient tuning method of a microstrip shunt-resonator is presented. A gap coupling capacitance can be tuned by utilizing PZT cantilever which is used to raise one of the gap-electrodes metallization patterns. When employing in shunt microstrip resonator, its resonant frequency tuned from 40.08 GHz to 41.25 GHz with high loaded quality factor. The whole size of the device is 2 x 1 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
rad -Dependent Response of the chk1 -Encoded Protein Kinase at the DNA Damage Checkpoint (1996)

Exposure of eukaryotic cells to agents that generate DNA damage results in transient arrest of progression through the cell cycle. In fission yeast, the DNA damage checkpoint associated with cell cycle arrest before mitosis requires the protein kinase p56chk1. DNA damage induced by ultraviolet light, gamma radiation, or a DNA-alkylating agent has now been shown to result in phosphorylation of p56chk1. This phosphorylation decreased the mobility of p56chk1 on SDS-polyacrylamide gel electrophoresis and was abolished by a mutation in the p56chk1 catalytic domain, suggesting that it might represent autophosphorylation. Phosphorylation of p56chk1 did not occur when other checkpoint genes were inactive. Thus, p56chk1 appears to function downstream of several of the known Schizosaccharomyces pombe checkpoint gene products, including that encoded by rad3+, a gene with sequence similarity to the ATM gene mutated in patients with ataxia telangiectasia. The phosphorylation of p56chk1 provides an assayable biochemical response to activation of the DNA damage checkpoint in the G2 phase of the cell cycle.
Changes in distribution, cell associations, and protein expression levels of NG2, neurocan, phosphacan, brevican, versican V2, and tenascin‐C during acute to chronic maturation of spinal cord scar tissue (2002)

Previous studies have correlated the failure of axon regeneration after spinal cord injury with axons contacting scar tissue rich in chondroitin sulfate proteoglycans (CSPGs; Davies et al., 1999). In the present study, we have conducted immunohistochemical and quantitative Western blot analysis of five axon-growth-inhibitory CSPGs and tenascin-C within stab injuries of adult rat spinal cord at time points ranging from 24 hr to 6 months post injury. Quantitative Western blot analysis showed robust increases in neurocan, tenascin-C, and NG2 levels by 24 hr, suggesting that these molecules play a role in preventing axon regeneration across acutely forming scar tissue. Peak levels of 245/130 kD neurocan, NG2, and 250/200 kD tenascin-C were reached at 8 days, with maximum levels of phosphacan and 140/80 kD brevican attained later, at 1 month post injury. Versican V2 protein levels, however, displayed an opposite trend, dropping below unlesioned spinal cord values at all time points studied. Confocal microscopy at 8 days post injury revealed heightened immunoreactivity for phosphacan, NG2, and tenascin-C, particularly within fibronectin(+) scar tissue at lesion centers. In contrast, neurocan was displayed within lesion margins on the processes of stellate NG2(+) cells and, to a much lesser extent, by astrocytes. At 6 months post injury, 130 kD neurocan, brevican, and NG2 levels within chronic scar tissue remained significantly above control. Our results show novel expression patterns and cell associations of inhibitory CSPGs and tenascin-C that have important implications for axon regeneration across acute and chronic spinal cord scar tissue.
2-Phenylquinoline-Carbohydrate Hybrids: Molecular Design, Chemical Synthesis, and Evaluation of a New Family of Light-Activatable DNA-Cleaving Agents (1999)

Artificial intercalator-carbohydrate hybrids such as that shown in the scheme cleave DNA at the site of guanine on irradiation with UV light with a long wavelength. The hybrids also exhibit strong cytotoxicity when irradiated. The hybrid system is very important for DNA cleavage, and the cytotoxic activity correlates with the DNA-cleaving capacity
Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis (2017)

Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP. Differentially expressed genes (DEGs) were identified by DESeq2. Weighted gene co-expression network analysis (WGCNA) package in R was applied for WGCNA.Data of 275 solid tumor tissues and 19 adjacent tumor tissues of colon cancer were obtained. A total of 1828 DMCs, including 1390 hypermethylated and 438 hypomethylated CpG sites, were identified between tumor and normal groups. A total of 789 DEGs, containing 435 upregulated genes and 354 downregulated genes were observed. It revealed that 8 DMRs-DEGs and 95 DMCs-DEGs pairs were significantly correlated. Furthermore, genes of yellow and brown modules from WGCNA were significantly correlated with tumor/normal status, and significantly enriched in peroxisome proliferator activated receptor signaling pathway, glutamatergic synapse, and neuroactive ligand-receptor interaction. Genes in the above 2 modules were also significantly enriched in DMCs or DMRs-associated genes. Specifically, ADHFE1, HAND2, and GNAO1 were hypermethylated and downregulated in colon cancer, suggesting that the low expression levels of these genes may be regulated by DNA hypermethylation. In addition, the 3 genes were involved in brown module of WGCNA, indicating their important roles in colon cancer.The investigation of the relationship between DNA methylation and gene expression may help to understand the effect of DNA methylation alteration on genes expression, especially gene co-expression network in the development of colon cancer. Genes such as ADHFE1, HAND2, and GNAO1 may be served as potential candidates for diagnosis and therapy targets in colon cancer.
Immersive Virtual Reality Therapy with Myoelectric Control for Treatment-resistant Phantom Limb Pain: Case Report. (2017)

<b>Objective:</b> Phantom limb pain is a condition frequently experienced after amputation. One treatment for phantom limb pain is traditional mirror therapy, yet some patients do not respond to this intervention, and immersive virtual reality mirror therapy offers some potential advantages. We report the case of a patient with severe phantom limb pain following an upper limb amputation and successful treatment with therapy in a custom virtual reality environment. <b>Methods:</b> An interactive 3-D kitchen environment was developed based on the principles of mirror therapy to allow for control of virtual hands while wearing a motion-tracked, head-mounted virtual reality display. The patient used myoelectric control of a virtual hand as well as motion-tracking control in this setting for five therapy sessions. Pain scale measurements and subjective feedback was elicited at each session. <b>Results:</b> Analysis of the measured pain scales showed statistically significant decreases per session [Visual Analog Scale, Short Form McGill Pain Questionnaire, and Wong-Baker FACES pain scores decreased by 55 percent (p=0.0143), 60 percent (p=0.023), and 90 percent (p=0.0024), respectively]. Significant subjective pain relief persisting between sessions was also reported, as well as marked immersion within the virtual environments. On followup at six weeks, the patient noted continued decrease in phantom limb pain symptoms. <b>Conclusions:</b> Currently available immersive virtual reality technology with myolectric and motion tracking control may represent a possible therapy option for treatment-resistant phantom limb pain.
Verification of Controlled Grafting of Styrene from Cellulose via Radiation-Induced RAFT Polymerization (2007)

Reversible addition−fragmentation chain transfer (RAFT) polymerization was applied to radiation-induced graft polymerization of styrene from cellulose. The grafting of styrene from cellulose substrates using the chain transfer agent cumyl phenyldithioacetate was confirmed by Raman and X-ray photoelectron spectroscopy, differential scanning calorimetery, thermogravimetric analysis, scanning electron microscopy, and contact angle analysis. Grafted polystyrene chains were cleaved from the cellulose surface by acidic hydrolysis of the cellulose. The number-average molecular weight and polydispersity index of the grafted and the free (nongrafted) polystyrenes obtained under identical conditions were determined by size exclusion chromatography. Grafted and nongrafted polystyrenes have almost the same (near theoretical) molecular weight and narrow polydispersity, thus proving for the first time the control of the grafting process mediated via RAFT without any prior functionalization of the surface.
Abstract 4963: ERG expression levels reflect functional status of androgen receptor in prostate cancer (2010)

Abstract Background: Expression of the ERG proto-oncogene, is activated in 50-70% of prostate tumors by androgen receptor (AR) mediated signals due to the fusion of AR regulated promoters (primarily TMPRSS2 and to a lesser extent SLC45A3 and NDRG1) to the ERG protein coding sequence. Our previous studies of quantitative expression levels of ERG or TMPRSS2-ERG fusion transcripts have noted that relatively low or no ERG expression in prostate tumors significantly associated with progressive disease. Here, we have tested the hypothesis that ERG expression levels in prostate tumor cells reflect AR transcriptional regulatory function in a given biological context of the tumor progression. Therefore, tumors with lower ERG may represent a subset with attenuated AR signaling. Experimental procedures: Expression of ERG and other AR regulated genes were evaluated in a GeneChip dataset obtained from a panel of laser capture micro-dissected well/moderately differentiated (WD) or poorly differentiated (PD) tumor cells derived from primary tumors of patients, who had no prior androgen ablation treatment. Results: ERG expression pattern was similar to that of other AR regulated genes. Low frequency of ERG expression was noted in PD tumor cells (30%) in comparison to WD tumor cells (80%), suggesting for subdued AR function in a significant fraction of tumors with genomic alterations of ERG. Conclusions: We developed a cumulative AR Function Index (ARFI) by integrating ERG into a panel of defined AR target genes, may have future potential in stratifying patients for targeted therapy on the basis of overall AR functional status in primary tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4963.
CAMERA CALIBRATION FOR FISH-EYE LENSES IN ENDOSCOPYWITH AN APPLICATION TO 3D RECONSTRUCTION (2007)

Image analysis tasks such as 3D reconstruction from endoscopic images require compensation of geometric distortions introduced by the lens system. Appropriate camera calibration is thus necessary. Commonly used calibration algorithms rely on the well-known pinhole camera model, extended by parametric terms for radial distortions. In this paper, we demonstrate that these models are not appropriate if very strong distortions occur as is the case for endoscopic fish-eye lenses. As an alternative, we analyze a generic calibration algorithm published recently by Kannala and Brandt, which is based on more general projection equations. We show qualitatively and quantitatively that this algorithm is well suited to deal with significant distortions especially in the image's rim regions. Furthermore, we demonstrate how images of a colon phantom that were corrected in such a manner can be used to obtain a 3D reconstruction
The Rb/E2F pathway and cancer (2001)

Over the past decade, studies focusing on the mechanisms controlling cellular proliferation have converged with equally intensive efforts directed at the analysis of oncogenic pathways associated with human cancer. These convergent studies have revealed the central role played by the pathway that controls the activity of the retinoblastoma tumor suppressor protein (Rb), which in turn regulates the E2F transcription factor. In particular, it is now clear that the Rb/E2F pathway is critical in regulating the initiation of DNA replication. It is also clear that the control of the pathway is disrupted in virtually all human cancers. Questions remain, however, as to the specific role played by individual activities within the pathway in the control of cell growth and their participation in the development of cancer.
Heparin and cancer revisited: Mechanistic connections involving platelets, P-selectin, carcinoma mucins, and tumor metastasis (2001)

Independent studies indicate that expression of sialylated fucosylated mucins by human carcinomas portends a poor prognosis because of enhanced metastatic spread of tumor cells, that carcinoma metastasis in mice is facilitated by formation of tumor cell complexes with blood platelets, and that metastasis can be attenuated by a background of P-selectin deficiency or by treatment with heparin. The effects of heparin are not primarily due to its anticoagulant action. Other explanations have been suggested but not proven. Here, we bring together all these unexplained and seemingly disparate observations, showing that heparin treatment attenuates tumor metastasis in mice by inhibiting P-selectin-mediated interactions of platelets with carcinoma cell-surface mucin ligands. Selective removal of tumor mucin P-selectin ligands, a single heparin dose, or a background of P-selectin deficiency each reduces tumor cell-platelet interactions in vitro and in vivo. Although each of these maneuvers reduced the in vivo interactions for only a few hours, all markedly reduce long-term organ colonization by tumor cells. Three-dimensional reconstructions by using volume-rendering software show that each situation interferes with formation of the platelet "cloak" around tumor cells while permitting an increased interaction of monocytes (macrophage precursors) with the malignant cells. Finally, we show that human P-selectin is even more sensitive to heparin than mouse P-selectin, giving significant inhibition at concentrations that are in the clinically acceptable range. We suggest that heparin therapy for metastasis prevention in humans be revisited, with these mechanistic paradigms in mind.
Temporal Analysis of Active and Passive Transport in Living Cells (2008)

The cellular cytoskeleton is a fascinating active network, in which Brownian motion is intercepted by distinct phases of active transport. We present a time-resolved statistical analysis dissecting phases of directed motion out of otherwise diffusive motion of tracer particles in living cells. The distribution of active lifetimes is found to decay exponentially with a characteristic time tauA = 0.65 s. The velocity distribution of active events exhibits several peaks, in agreement with a discrete number of motor proteins acting collectively.
Expression of the common acute lymphoblastic leukemia antigen (CALLA) on the surface of individual cells of human lymphoblastoid lines. (1986)

Expression of the common acute lymphoblastic leukemia antigen (CALLA) on the surface of individual cells of the human lymphoblastoid lines CW678, Namalwa, and Nalm-6, and the distribution of the antigen epitopes within the cell populations have been determined quantitatively with the murine monoclonal anti-CALLA antibody J5. The distribution of CALLA epitopes in the cell populations was analyzed by indirect immunofluorescence measured by using flow cytometry. The average number of CALLA epitopes per cell were measured by two assays: in a direct assay by binding 125I-labeled antibody J5 to cells, and indirectly by binding 125I-labeled protein A from Staphylococcus aureus to J5-coated cells. On average, CW678, Namalwa, and Nalm-6 cells bore about 1 X 10(4), 6 X 10(4), and 8 X 10(4) CALLA epitopes per cell respectively. Histograms of the absolute number of CALLA epitopes expressed by individual cells in the populations of CW678, Namalwa, and Nalm-6 cultures were generated by a combined analysis of all the binding data. This is the first example of histograms showing quantitative distribution of antigen epitopes. Previously, the expression of antigens by individual cells as obtained by flow cytometry was only presented in terms of relative fluorescence intensity of individual cells in cell populations.
Growth of the Maize Primary Root at Low Water Potentials (1991)

Seedlings of maize (Zea mays L. cv WF9 x Mo 17) growing at low water potentials in vermiculite contained greatly increased proline concentrations in the primary root growth zone. Proline levels were particularly high toward the apex, where elongation rates have been shown to be completely maintained over a wide range of water potentials. Proline concentration increased even in quite mild treatments and reached 120 millimolal in the apical millimeter of roots growing at a water potential of -1.6 megapascal. This accounted for almost half of the osmotic adjustment in this region. Increases in concentration of other amino acids and glycinebetaine were comparatively small. We have assessed the relative contributions of increased rates of proline deposition and decreased tissue volume expansion to the increases in proline concentration. Proline content profiles were combined with published growth velocity distributions to calculate net proline deposition rate profiles using the continuity equation. At low water potential, proline deposition per unit length increased by up to 10-fold in the apical region of the growth zone compared to roots at high water potential. This response accounted for most of the increase in proline concentration in this region. The results suggest that osmotic adjustment due to increased proline deposition plays an important role in the maintenance of root elongation at low water potentials.
Surface-Enhanced Infrared Absorption: Pushing the Frontier for On-Chip Gas Sensing (2017)

Surface-enhanced infrared absorption (SEIRA) is capable of identifying molecular fingerprints by resonant detection of infrared vibrational modes through the coupling with plasmonic modes of metallic nanostructures. However, SEIRA for on-chip gas sensing is still not very successful due to the intrinsically weak light-matter interaction between photons and gas molecules and the technical challenges in accumulating sufficient gas species in the vicinity of the spatially localized enhanced electric field, namely, the "hot-spots", generated through plasmonics. In this paper, we present a suspended silicon nitride (Si<sub>3</sub>N<sub>4</sub>) nanomembrane device by integrating plasmonic nanopatch gold antennas with metal-organic framework (MOF), which can largely adsorb carbon dioxide (CO<sub>2</sub>) through its nanoporous structure. Unlike conventional SEIRA sensing relying on highly localized hot-spots of plasmonic nanoantennas or nanoparticles, the device reported in this paper engineered the coupled surface plasmon polaritons in the metal-Si<sub>3</sub>N<sub>4</sub> and metal-MOF interfaces to achieve strong optical field enhancement across the entire MOF film. We successfully demonstrated on-chip gas sensing of CO<sub>2</sub> with more than 1800× enhancement factors by combining the concentration effect from the 2.7 μm MOF thin film and the optical field enhancement of the plasmonic nanopatch antennas.
Oral pharmacokinetics of omeprazole and lansoprazole after single and repeated doses as intact capsules or as suspensions in sodium bicarbonate (2000)

Simplified omeprazole suspension 20 mg does not supply adequate omeprazole for systemic absorption. Lansoprazole absorption from simplified lansoprazole suspension is maintained.
Expression of the tumor-associated gene MN: a potential biomarker for human renal cell carcinoma. (1997)

MN is a novel cell surface antigen originally detected in human HeLa cells. Although it is also expressed in normal gastric mucosa, this antigen was previously found to be expressed in cells with a malignant phenotype in certain tissues of the female genital tract (cervix and ovary). Using an oligonucleotide primer set specific for MN-complimentary DNA, we performed reverse transcription-PCR assays on RNAs extracted from human cell lines and tissues to evaluate whether this marker might be expressed at other sites. RNA libraries extracted from normal human heart, lung, kidney, prostate, peripheral blood, brain, placenta, and muscle were negative for MN expression. RNAs extracted from liver and pancreatic tissue were positive for MN expression. Three of six renal cancer cell lines tested revealed MN expression. In addition, 12 of 17 samples of human renal cell carcinoma tissue tested positive for MN, all 12 of which were clear cell adenocarcinomas. This survey identified a unique association of MN expression with renal cell cancers, especially those of the clear cell variety, suggesting that MN is a potential marker for the diagnosis, staging, and therapeutic monitoring of renal cell carcinoma in humans.